@article {pmid37747555, year = {2023}, author = {Kunnummal, SP and Khan, M}, title = {Diet-gut microbiome interaction and ferulic acid bioavailability: implications on neurodegenerative disorders.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, pmid = {37747555}, issn = {1436-6215}, support = {No.5/7/1741/CH/Adhoc/2021-RBMCH//Indian Council of Medical Research/ ; }, abstract = {PURPOSE OF THE REVIEW: Ferulic acid (FA), which occurs naturally as the feruloylated sugar ester in grains, fruits, and vegetables, is critical for combating oxidative stress and alleviating neurodegenerative diseases resulting from free radical-generated protein aggregates in brain cells. However, FA cannot be absorbed in conjugated form. Therefore, strategies to improve the bioavailability of FA are gaining more importance. Ferulic acid esterases (FAE) of the gut microbiota are critical enzymes that facilitate FA release from feruloylated sugar ester conjugates and influence systemic health. This review provides insight into a nutrition-based approach to preventing neurodegenerative disorders such as Alzheimer's and Parkinson's by altering the diversity of FAE-producing gut microbiota.<br><br>RECENT FINDINGS: The human gut is a niche for a highly dense microbial population. Nutrient components and the quality of food shape the gut microbiota. Microbiota-diet-host interaction primarily involves an array of enzymes that hydrolyse complex polysaccharides and release covalently attached moieties, thereby increasing their bio-accessibility. Moreover, genes encoding polysaccharide degrading enzymes are substrate inducible, giving selective microorganisms a competitive advantage in scavenging nutrients. Nutraceutical therapy using specific food components holds promise as a prophylactic agent and as an adjunctive treatment strategy in neurotherapeutics, as it results in upregulation of polysaccharide utilisation loci containing fae genes in the gut microbiota, thereby increasing the release of FA and other antioxidant molecules and combat neurodegenerative processes.}, }
@article {pmid37747397, year = {2023}, author = {Chen, YJ and Yong, SB}, title = {Inhaled corticosteroid treatment's impact on asthma exacerbations: Influence of human genetics on microbiome composition.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaci.2023.08.022}, pmid = {37747397}, issn = {1097-6825}, }
@article {pmid37747198, year = {2023}, author = {Duan, Z and Fu, J and Zhang, F and Cai, Y and Wu, G and Ma, W and Zhou, H and He, Y}, title = {The association between BMI and serum uric acid is partially mediated by gut microbiota.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0114023}, doi = {10.1128/spectrum.01140-23}, pmid = {37747198}, issn = {2165-0497}, abstract = {Obesity is a risk factor for the development of hyperuricemia, both of which were related to gut microbiota. However, whether alterations in the gut microbiota lie in the pathways mediating obesity's effects on hyperuricemia is less clear. Body mass index (BMI) and serum uric acid (SUA) were separately important indicators of obesity and hyperuricemia. Our study aims to investigate whether BMI-related gut microbiota characteristics would mediate the association between BMI and SUA levels. A total of 6,280 participants from Guangdong Gut Microbiome Project were included in this study. Stool samples were collected for 16S rRNA gene sequencing. The results revealed that BMI was significantly and positively associated with SUA. Meanwhile, BMI was significantly associated with the abundance of 102 gut microbial genera, 16 of which were also significantly associated with SUA. The mediation analysis revealed that the association between BMI and SUA was partially mediated by the abundance of Proteobacteria (proportion mediated: 0.94%, P < 0.05). At the genus level, 25 bacterial genera, including Ralstonia, Oscillospira, Faecalibacterium, etc., could also partially mediate the association of BMI with SUA (the highest proportion is mediated by Ralstonia, proportion mediated: 2.76%, P < 0.05). This study provided evidence for the associations among BMI, gut microbiota, and SUA, and the mediation analysis suggested that the association of BMI with SUA was partially mediated by the gut microbiota. IMPORTANCE Using 16S rRNA sequencing analysis, local interpretable machine learning technique analysis and mediation analysis were used to explore the association between BMI with SUA, and the mediating effects of gut microbial dysbiosis in the association were investigated.}, }
@article {pmid37747192, year = {2023}, author = {Islam, T and Hoque, MN}, title = {Gut and flesh microbiome sequencing of the Bangladesh national fish hilsa (Tenualosa ilisha).}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0044823}, doi = {10.1128/MRA.00448-23}, pmid = {37747192}, issn = {2576-098X}, abstract = {The gut and flesh microbiome of the national fish of Bangladesh, Tenualosa ilisha, were analyzed using 16S rRNA gene sequencing. Our findings revealed a significant microbial disparity between sample categories and the habitat of hilsa fish, which will serve as a valuable foundation for further comprehensive studies on the hilsa microbiome.}, }
@article {pmid37747182, year = {2023}, author = {Wang, H and Feyereisen, GW and Wang, P and Rosen, C and Sadowsky, MJ and Ishii, S}, title = {Impacts of biostimulation and bioaugmentation on woodchip bioreactor microbiomes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0405322}, doi = {10.1128/spectrum.04053-22}, pmid = {37747182}, issn = {2165-0497}, abstract = {Woodchip bioreactors (WBRs) are used to remove nutrients, especially nitrate, from subsurface drainage. The nitrogen removal efficiency of WBRs, however, is limited by low temperatures and the availability of labile carbon. Bioaugmentation and biostimulation are potential approaches to enhance nitrate removal of WBRs under cold conditions, but their effectiveness is still unclear. Here, we clarified the effects of bioaugmentation and biostimulation on the microbiomes and nitrate removal rates of WBRs. As a bioaugmentation treatment, we inoculated WBR-borne cold-adapted denitrifying bacteria Cellulomonas cellasea strain WB94 and Microvirgula aerodenitrificans strain BE2.4 into the WBRs located at Willmar, MN, USA. As a biostimulation treatment, acetate was added to the WBRs to promote denitrification. Woodchip samples were collected from multiple locations in each WBR before and after the treatments and used for the microbiome analysis. The 16S rRNA gene amplicon sequencing showed that the microbiomes changed by the treatments and season. The high-throughput quantitative PCR for nitrogen cycle genes revealed a higher abundance of denitrification genes at locations closer to the WBR inlet, suggesting that denitrifiers are unevenly present in WBRs. In addition, a positive relationship was identified between the abundance of M. aerodenitrificans strain BE2.4 and those of norB and nosZ in the WBRs. Based on generalized linear modeling, the abundance of norB and nosZ was shown to be useful in predicting the nitrate removal rate of WBRs. Taken together, these results suggest that the bioaugmentation and biostimulation treatments can influence denitrifier populations, thereby influencing the nitrate removal of WBRs. IMPORTANCE Nitrate pollution is a serious problem in agricultural areas in the U.S. Midwest and other parts of the world. Woodchip bioreactor is a promising technology that uses microbial denitrification to remove nitrate from agricultural subsurface drainage, although the reactor's nitrate removal performance is limited under cold conditions. This study showed that the inoculation of cold-adapted denitrifiers (i.e., bioaugmentation) and the addition of labile carbon (i.e., biostimulation) can influence the microbial populations and enhance the reactor's performance under cold conditions. This finding will help establish a strategy to mitigate nitrate pollution.}, }
@article {pmid37746961, year = {2023}, author = {McMillan, A and Perez, C and Brooks, AE}, title = {A review of the long-term use of proton pump inhibitors and risk of celiac disease in the context of HLA-DQ2 and HLA-DQ8 genetic predisposition.}, journal = {Medicine}, volume = {102}, number = {38}, pages = {e35351}, pmid = {37746961}, issn = {1536-5964}, mesh = {Humans ; *Proton Pump Inhibitors/adverse effects ; Genetic Predisposition to Disease ; *Celiac Disease/chemically induced/genetics ; Omeprazole ; }, abstract = {Proton pump inhibitors (PPIs) are among the most prescribed and widely used medications; however, the long-term effects of these medications are only beginning to be investigated. Since the introduction of omeprazole in 1989, PPIs have become the first-choice treatment for esophagitis, peptic ulcer disease, Zoster-Ellison syndrome, dyspepsia, and the prevention of ulcers with non-steroidal anti-inflammatory drugs. Recent studies have specifically examined the rise in celiac disease (CD) in this context. This review explores how PPIs may impact the development of CD and highlights the need for additional research into the environmental and genetic factors that influence the development and progression of the disease. A literature search was performed using the keywords celiac disease, proton pump inhibitors, human leukocyte antigen (HLA)-DQ2, HLA-DQ8. The pathogenesis of CD is multifactorial, and human leukocyte antigens are one factor that may contribute to its development. Additionally, pharmaceuticals, such as PPIs, that cause gut dysbiosis have been linked to the inflammatory response present in CD. Recent studies have suggested that the rise in CD could be attributed to changes in the gut microbiome, highlighting the significant role that gut microbiota is proposed to play in CD pathogenesis. Although PPI therapy is helpful in reducing acid production in gastroesophageal disorders, additional information is needed to determine whether PPIs are still an appropriate treatment option with the possibility of developing CD in the future, particularly in the context of HLA-DQ2 and HLA-DQ8 predispositions. This review emphasizes the importance of personalized medicine for individuals with gastroesophageal disorders that require long-term use of PPIs.}, }
@article {pmid37746695, year = {2023}, author = {Kim, J and Lee, S and Moodley, Y and Yagnik, L and Birnie, D and Dwivedi, G}, title = {The role of the host-microbiome and metabolomics in sarcoidosis.}, journal = {American journal of physiology. Cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpcell.00316.2023}, pmid = {37746695}, issn = {1522-1563}, abstract = {Sarcoidosis is a complex inflammatory fibrotic disease that affects multiple organ systems. It is characterised by the infiltration of lymphocytes and mononuclear phagocytes, which form non-caseating granulomas in affected organs. The lungs and intrathoracic lymph nodes are the most commonly affected organs. The underlying cause of sarcoidosis is unknown, but it is believed to occur in genetically predisposed individuals who are exposed to pathogenic organisms, environmental contaminants, or self and non-self-antigens. Recent research has suggested that the microbiome may play a role in the development of respiratory conditions, including sarcoidosis. Additionally, metabolomic studies have identified potential biomarkers for monitoring sarcoidosis progression. This review will focus on recent microbiome and metabolomic findings in sarcoidosis, with the goal of shedding light on the pathogenesis and possible diagnostic and therapeutic approaches.}, }
@article {pmid37746691, year = {2023}, author = {Mugge, RL and Rakocinski, CF and Woolsey, M and Hamdan, LJ}, title = {Proximity to built structures on the seabed promotes biofilm development and diversity.}, journal = {Biofouling}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/08927014.2023.2255141}, pmid = {37746691}, issn = {1029-2454}, abstract = {The rapidly expanding built environment in the northern Gulf of Mexico includes thousands of human built structures (e.g. platforms, shipwrecks) on the seabed. Primary-colonizing microbial biofilms transform structures into artificial reefs capable of supporting biodiversity, yet little is known about formation and recruitment of biofilms. Short-term seafloor experiments containing steel surfaces were placed near six structures, including historic shipwrecks and modern decommissioned energy platforms. Biofilms were analyzed for changes in phylogenetic composition, richness, and diversity relative to proximity to the structures. The biofilm core microbiome was primarily composed of iron-oxidizing Mariprofundus, sulfur-oxidizing Sulfurimonas, and biofilm-forming Rhodobacteraceae. Alpha diversity and richness significantly declined as a function of distance from structures. This study explores how built structures influence marine biofilms and contributes knowledge on how anthropogenic activity impacts microbiomes on the seabed.}, }
@article {pmid37746426, year = {2023}, author = {Makkena, VK and Jaramillo, AP and Awosusi, BL and Ayyub, J and Dabhi, KN and Gohil, NV and Tanveer, N and Hussein, S and Pingili, S and Khan, S}, title = {Probing the Relationship Between the Human Gut Microbiome and Prospects of Prostate Cancer: A Systematic Review.}, journal = {Cureus}, volume = {15}, number = {8}, pages = {e43892}, pmid = {37746426}, issn = {2168-8184}, abstract = {Prostate neoplasia is one of the most commonly occurring neoplasias in males and has a high mortality rate. Prostate cancer (PCA) risk factors include tall stature, male sex, known family history, obesity, high blood pressure, lack of fitness, higher levels of testosterone for a long time, increasing age, and ethnicity are well known. The association and role of the gut microbiota in different diseases in our body have been highlighted recently. Therefore, finding the influence of gut microbiota on the prostatic cells can be useful for preventing prostatic neoplasia and/or reducing its severity. We aimed to assess its impact on PCA risk. We thoroughly searched databases for the relevant literature for our systematic review. The final research papers analyzed how bacteria played a role in the risk of PCA, either through inflammation or the production of metabolites that increase/decrease the risk of PCA. Based on the studies reviewed, we found that some gut bacteria play a role in the formation of PCA. In contrast, some bacteria can help prevent PCA, but the metabolism of the dietary components is the major factor for PCA.}, }
@article {pmid37746131, year = {2023}, author = {Hoosein, S and Neuenkamp, L and Trivedi, P and Paschke, MW}, title = {AM fungal-bacterial relationships: what can they tell us about ecosystem sustainability and soil functioning?.}, journal = {Frontiers in fungal biology}, volume = {4}, number = {}, pages = {1141963}, pmid = {37746131}, issn = {2673-6128}, abstract = {Considering our growing population and our continuous degradation of soil environments, understanding the fundamental ecology of soil biota and plant microbiomes will be imperative to sustaining soil systems. Arbuscular mycorrhizal (AM) fungi extend their hyphae beyond plant root zones, creating microhabitats with bacterial symbionts for nutrient acquisition through a tripartite symbiotic relationship along with plants. Nonetheless, it is unclear what drives these AM fungal-bacterial relationships and how AM fungal functional traits contribute to these relationships. By delving into the literature, we look at the drivers and complexity behind AM fungal-bacterial relationships, describe the shift needed in AM fungal research towards the inclusion of interdisciplinary tools, and discuss the utilization of bacterial datasets to provide contextual evidence behind these complex relationships, bringing insights and new hypotheses to AM fungal functional traits. From this synthesis, we gather that interdependent microbial relationships are at the foundation of understanding microbiome functionality and deciphering microbial functional traits. We suggest using pattern-based inference tools along with machine learning to elucidate AM fungal-bacterial relationship trends, along with the utilization of synthetic communities, functional gene analyses, and metabolomics to understand how AM fungal and bacterial communities facilitate communication for the survival of host plant communities. These suggestions could result in improving microbial inocula and products, as well as a better understanding of complex relationships in terrestrial ecosystems that contribute to plant-soil feedbacks.}, }
@article {pmid37746004, year = {2023}, author = {Khan, AL}, title = {The phytomicrobiome: solving plant stress tolerance under climate change.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1219366}, pmid = {37746004}, issn = {1664-462X}, abstract = {With extraordinary global climate changes, increased episodes of extreme conditions result in continuous but complex interaction of environmental variables with plant life. Exploring natural phytomicrobiome species can provide a crucial resource of beneficial microbes that can improve plant growth and productivity through nutrient uptake, secondary metabolite production, and resistance against pathogenicity and abiotic stresses. The phytomicrobiome composition, diversity, and function strongly depend on the plant's genotype and climatic conditions. Currently, most studies have focused on elucidating microbial community abundance and diversity in the phytomicrobiome, covering bacterial communities. However, least is known about understanding the holistic phytomicrobiome composition and how they interact and function in stress conditions. This review identifies several gaps and essential questions that could enhance understanding of the complex interaction of microbiome, plant, and climate change. Utilizing eco-friendly approaches of naturally occurring synthetic microbial communities that enhance plant stress tolerance and leave fewer carbon-foot prints has been emphasized. However, understanding the mechanisms involved in stress signaling and responses by phytomicrobiome species under spatial and temporal climate changes is extremely important. Furthermore, the bacterial and fungal biome have been studied extensively, but the holistic interactome with archaea, viruses, oomycetes, protozoa, algae, and nematodes has seldom been studied. The inter-kingdom diversity, function, and potential role in improving environmental stress responses of plants are considerably important. In addition, much remains to be understood across organismal and ecosystem-level responses under dynamic and complex climate change conditions.}, }
@article {pmid37746002, year = {2023}, author = {Marín, C and Bueno, CG and Wang, J and Kokkoris, V}, title = {Editorial: Biodiversity and ecosystem-level function of the rhizosphere.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1278662}, pmid = {37746002}, issn = {1664-462X}, }
@article {pmid37745723, year = {2023}, author = {Lamichhane, S and Sen, P and Dickens, AM and Kråkström, M and Ilonen, J and Lempainen, J and Hyöty, H and Lahesmaa, R and Veijola, R and Toppari, J and Hyötyläinen, T and Knip, M and Orešič, M}, title = {Circulating metabolic signatures of rapid and slow progression to type 1 diabetes in islet autoantibody-positive children.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1211015}, pmid = {37745723}, issn = {1664-2392}, mesh = {Humans ; Child ; *Diabetes Mellitus, Type 1 ; *Islets of Langerhans ; Metabolomics ; Amino Acids ; Autoantibodies ; }, abstract = {AIMS/HYPOTHESIS: Appearance of multiple islet cell autoantibodies in early life is indicative of future progression to overt type 1 diabetes, however, at varying rates. Here, we aimed to study whether distinct metabolic patterns could be identified in rapid progressors (RP, disease manifestation within 18 months after the initial seroconversion to autoantibody positivity) vs. slow progressors (SP, disease manifestation at 60 months or later from the appearance of the first autoantibody).<br><br>METHODS: Longitudinal samples were collected from RP (n=25) and SP (n=41) groups at the ages of 3, 6, 12, 18, 24, or &#x2265; 36 months. We performed a comprehensive metabolomics study, analyzing both polar metabolites and lipids. The sample series included a total of 239 samples for lipidomics and 213 for polar metabolites.<br><br>RESULTS: We observed that metabolites mediated by gut microbiome, such as those involved in tryptophan metabolism, were the main discriminators between RP and SP. The study identified specific circulating molecules and pathways, including amino acid (threonine), sugar derivatives (hexose), and quinic acid that may define rapid vs. slow progression to type 1 diabetes. However, the circulating lipidome did not appear to play a major role in differentiating between RP and SP.<br><br>CONCLUSION/INTERPRETATION: Our study suggests that a distinct metabolic profile is linked with the type 1 diabetes progression. The identification of specific metabolites and pathways that differentiate RP from SP may have implications for early intervention strategies to delay the development of type 1 diabetes.}, }
@article {pmid37745638, year = {2023}, author = {Revel-Muroz, A and Akulinin, M and Shilova, P and Tyakht, A and Klimenko, N}, title = {Stability of human gut microbiome: Comparison of ecological modelling and observational approaches.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {4456-4468}, pmid = {37745638}, issn = {2001-0370}, abstract = {The gut microbiome plays a pivotal role in the human body, and perturbations in its composition have been linked to various disorders. Stability is an essential property of a healthy human gut microbiome, which allows it to maintain its functional richness under the external influences. This property has been explored through two distinct methodologies - mathematical modelling based on ecological principles and statistical analysis drawn from observations in interventional studies. Here we conducted a meta-analysis aimed to compare the two approaches utilising the data from 9 interventional and time series studies encompassing 3512 gut microbiome profiles obtained via 16S rRNA gene sequencing. By employing the previously published compositional Lotka-Volterra method, we modelled the dynamics of the microbial community and evaluated ecological stability measures. These measures were compared to those based on observed microbiome changes. There was a substantial correlation between the outcomes of the two approaches. Particularly, local stability assessed within the ecological paradigm was positively correlated with observational stability measures accounting for the compositional nature of microbiome data. Additionally, we were able to reproduce the previously reported inverse relationship between the community's robustness to microorganism loss and local stability, attributed to the distinct impacts of coefficient characterising the network decomposition on these two stability assessments. Our findings demonstrate harmonisation between the ecological and observational approaches to microbiome analysis, advancing the understanding of healthy gut microbiome concept. This paves the way to develop efficient microbiome-targeting interventions for disease prevention and treatment.}, }
@article {pmid37745509, year = {2023}, author = {Stindt, KR and McClean, MN}, title = {Tuning Interdomain Conjugation Toward in situ Population Modification in Yeast.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.09.12.557379}, pmid = {37745509}, abstract = {The ability to modify and control natural and engineered microbiomes is essential for biotechnology and biomedicine. Fungi are critical members of most microbiomes, yet technology for modifying the fungal members of a microbiome has lagged far behind that for bacteria. Interdomain conjugation (IDC) is a promising approach, as DNA transfer from bacterial cells to yeast enables in situ modification. While such genetic transfers have been known to naturally occur in a wide range of eukaryotes, and are thought to contribute to their evolution, IDC has been understudied as a technique to control fungal or fungal-bacterial consortia. One major obstacle to widespread use of IDC is its limited efficiency. In this work, we utilize interactions between genetically tractable Escherichia coli and Saccharomyces cerevisiae to control the incidence of IDC. We test the landscape of population interactions between the bacterial donors and yeast recipients to find that bacterial commensalism leads to maximized IDC, both in culture and in mixed colonies. We demonstrate the capacity of cell-to-cell binding via mannoproteins to assist both IDC incidence and bacterial commensalism in culture, and model how these tunable controls can predictably yield a range of IDC outcomes. Further, we demonstrate that these lessons can be utilized to lastingly alter a recipient yeast population, by both "rescuing" a poor-growing recipient population and collapsing a stable population via a novel IDC-mediated CRISPR/Cas9 system.}, }
@article {pmid37745460, year = {2023}, author = {Day, AW and Kumamoto, CA}, title = {Selection of Ethanol Tolerant Strains of Candida albicans by Repeated Ethanol Exposure Results in Strains with Reduced Susceptibility to Fluconazole.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.09.13.557677}, pmid = {37745460}, abstract = {UNLABELLED: Candida albicans is a commensal yeast that has important impacts on host metabolism and immune function, and can establish life-threatening infections in immunocompromised individuals. Previously, C. albicans colonization has been shown to contribute to the progression and severity of alcoholic liver disease. However, relatively little is known about how C. albicans responds to changing environmental conditions in the GI tract of individuals with alcohol use disorder, namely repeated exposure to ethanol. In this study, we repeatedly exposed C. albicans to high concentrations (10% vol/vol) of ethanol-a concentration that can be observed in the upper GI tract of humans following consumption of alcohol. Following this repeated exposure protocol, ethanol small colony (Esc) variants of C. albicans isolated from these populations exhibited increased ethanol tolerance, altered transcriptional responses to ethanol, and cross-resistance/tolerance to the frontline antifungal fluconazole. These Esc strains exhibited chromosomal copy number variations and carried polymorphisms in genes previously associated with the acquisition of fluconazole resistance during human infection. This study identifies a selective pressure that can result in evolution of fluconazole tolerance and resistance without previous exposure to the drug.<br><br>AUTHOR SUMMARY: Previous work has shown that Candida albicans , a common fungal component of the gastrointestinal (GI) microbiome, is found in high abundance in the alcoholic GI tract. However, it was unknown how repeated ethanol exposure, similar to what C. albicans would be exposed to in the upper GI tract of individuals with alcohol use disorder, would affect the yeast. In this work, we show that repeated ethanol exposure selects for C. albicans strains with altered transcriptional responses to ethanol, increased ethanol tolerance, and cross-resistance/tolerance to the common frontline antifungal fluconazole. This work shows that ethanol exposure can promote evolution of C. albicans to antifungal resistance without previous exposure to the antifungal drug. These findings could be relevant to C. albicans in the upper GI tract in individuals with alcohol use disorder and further studies could reveal optimized antifungal regimens for C. albicans infections in these patients.}, }
@article {pmid37746232, year = {2022}, author = {Flores, GAM and Lopez, RP and Cerrudo, CS and Consolo, VF and Berón, CM}, title = {Culex quinquefasciatus Holobiont: A Fungal Metagenomic Approach.}, journal = {Frontiers in fungal biology}, volume = {3}, number = {}, pages = {918052}, pmid = {37746232}, issn = {2673-6128}, abstract = {Microorganisms associated with mosquitoes have fundamental roles, not only in their nutrition, but also in physiological and immunological processes, and in their adaptation to the environment as well. Studies on mosquito hologenomes have increased significantly during the last years, achieving important advances in the characterization of the "core bacteriome" of some species of health importance. However, the fungal mycobiome has not been exhaustively researched, especially throughout the life cycle of some hematophagous mosquito species. In this work, the diversity and composition of fungal communities in different developmental stages, sexes, and adult nutrition of Culex quinquefasciatus reared on laboratory conditions were characterized, using internal transcribed spacer high throughput amplicon sequencing. Larvae presented a higher fungal richness, while sucrose-fed males and females showed a similar diversity between them. Blood-fed females presented few operational taxonomic units with an even distribution. Results are consistent with the reduction of larval microbiota after molting, observed for the bacterial microbiome in other mosquito species. The filamentous Ascomycota Penicillium polonicum and Cladosporium sp. were present in all stages of the mosquitoes; in addition, the presence of yeasts in the insects or their subsequent colonization associated with their diet is also discussed. These results suggest that some species of fungi could be essential for the nutrition and development of mosquitoes throughout their life cycle.}, }
@article {pmid37745448, year = {2023}, author = {Robertson, EB and Willett, JLE}, title = {Streptococcus mutans inhibits the growth of Enterococcus via the non-ribosomal cyclic peptide mutanobactin.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.09.12.557362}, pmid = {37745448}, abstract = {UNLABELLED: Enterococcus faecalis is a Gram-positive commensal bacterium in the gastrointestinal tract and an opportunistic pathogen. Enterococci are a leading cause of nosocomial infections, treatment of which is complicated by intrinsic and acquired antibiotic resistance mechanisms. Additionally, E. faecalis has been associated with various oral diseases, and it is frequently implicated in the failure of endodontic treatment. For establishment and persistence in a microbial community, E. faecalis must successfully compete against other bacteria. Streptococcal species play an important role in the establishment of the oral microbiome and co-exist with Enterococcus in the small intestine, yet the nature of interactions between E. faecalis and oral streptococci remains unclear. Here, we describe a mechanism by which Streptococcus mutans inhibits the growth of E. faecalis and other Gram-positive pathogens through the production of mutanobactin, a cyclic lipopeptide. Mutanobactin is produced by a polyketide synthase-nonribosomal peptide synthetase hybrid system encoded by the mub locus. Mutanobactin-producing S. mutans inhibits planktonic and biofilm growth of E. faecalis and is also active against other Enterococcus species and Staphylococcus aureus . Mutanobactin damages the cell envelope of E. faecalis , similar to other lipopeptide antibiotics like daptomycin. E. faecalis resistance to mutanobactin is mediated by the virulence factor gelatinase, a secreted metalloprotease. Our results highlight the anti-biofilm potential of the microbial natural product mutanobactin, provide insight into how E. faecalis interacts with other organisms in the human microbiome, and demonstrate the importance of studying E. faecalis dynamics within polymicrobial communities.<br><br>SIGNIFICANCE: Entercoccus faecalis is a leading cause of hospital-acquired infections, treatment of which is complicated by virulence factors, biofilm formation, and antibiotic resistance. Here, we demonstrate the antibiotic and anti-biofilm activity of mutanobactin, a cyclic lipopeptide produced by Streptococcus mutans , against Enterococcus and Staphylococcus spp., including vancomycin-resistant Enterococci (VRE). Similar to other lipopeptides, mutanobactin damages the bacterial cell envelope. E. faecalis may overcome antagonism from mutanobactin through production of gelatinase, a secreted protease and prevalent virulence factor. Our results demonstrate the antibiotic and anti-biofilm potential of mutanobactin and highlight the role of bacterial proteases in resistance to bacteria- and host-derived antimicrobial compounds.}, }
@article {pmid37745080, year = {2023}, author = {Zhang, B and Liu, J and Li, H and Huang, B and Zhang, B and Song, B and Bao, C and Liu, Y and Wang, Z}, title = {Integrated multi-omics identified the novel intratumor microbiome-derived subtypes and signature to predict the outcome, tumor microenvironment heterogeneity, and immunotherapy response for pancreatic cancer patients.}, journal = {Frontiers in pharmacology}, volume = {14}, number = {}, pages = {1244752}, pmid = {37745080}, issn = {1663-9812}, abstract = {Background: The extremely malignant tumour known as pancreatic cancer (PC) lacks efficient prognostic markers and treatment strategies. The microbiome is crucial to how cancer develops and responds to treatment. Our study was conducted in order to better understand how PC patients' microbiomes influence their outcome, tumour microenvironment, and responsiveness to immunotherapy. Methods: We integrated transcriptome and microbiome data of PC and used univariable Cox regression and Kaplan-Meier method for screening the prognostic microbes. Then intratumor microbiome-derived subtypes were identified using consensus clustering. We utilized LASSO and Cox regression to build the microbe-related model for predicting the prognosis of PC, and utilized eight algorithms to assess the immune microenvironment feature. The OncoPredict package was utilized to predict drug treatment response. We utilized qRT-PCR to verify gene expression and single-cell analysis to reveal the composition of PC tumour microenvironment. Results: We obtained a total of 26 prognostic genera in PC. And PC samples were divided into two microbiome-related subtypes: Mcluster A and B. Compared with Mcluster A, patients in Mcluster B had a worse prognosis and higher TNM stage and pathological grade. Immune analysis revealed that neutrophils, regulatory T cell, CD8[+] T cell, macrophages M1 and M2, cancer associated fibroblasts, myeloid dendritic cell, and activated mast cell had remarkably higher infiltrated levels within the tumour microenvironment of Mcluster B. Patients in Mcluster A were more likely to benefit from CTLA-4 blockers and were highly sensitive to 5-fluorouracil, cisplatin, gemcitabine, irinotecan, oxaliplatin, and epirubicin. Moreover, we built a microbe-derived model to assess the outcome. The ROC curves showed that the microbe-related model has good predictive performance. The expression of LAMA3 and LIPH was markedly increased within pancreatic tumour tissues and was linked to advanced stage and poor prognosis. Single-cell analysis indicated that besides cancer cells, the tumour microenvironment of PC was also rich in monocytes/macrophages, endothelial cells, and fibroblasts. LIPH and LAMA3 exhibited relatively higher expression in cancer cells and neutrophils. Conclusion: The intratumor microbiome-derived subtypes and signature in PC were first established, and our study provided novel perspectives on PC prognostic indicators and treatment options.}, }
@article {pmid37744933, year = {2023}, author = {Chhimwal, J and Anand, P and Mehta, P and Swarnkar, MK and Patial, V and Pandey, R and Padwad, Y}, title = {Metagenomic signatures reveal the key role of phloretin in amelioration of gut dysbiosis attributed to metabolic dysfunction-associated fatty liver disease by time-dependent modulation of gut microbiome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1210517}, pmid = {37744933}, issn = {1664-302X}, abstract = {The importance of gut-liver axis in the pathophysiology of metabolic dysfunction-associated fatty liver disease (MAFLD) is being investigated more closely in recent times. However, the inevitable changes in gut microbiota during progression of the disease merits closer look. The present work intends to assess the time-dependent gut dysbiosis in MAFLD, its implications in disease progression and role of plant-derived prebiotics in its attenuation. Male C57BL/6J mice were given western diet (WD) for up to 16 weeks and phloretin was administered orally. The fecal samples of mice were collected every fourth week for 16 weeks. The animals were sacrificed at the end of the study and biochemical and histological analyses were performed. Further, 16S rRNA amplicon sequencing analysis was performed to investigate longitudinal modification of gut microbiome at different time points. Findings of our study corroborate that phloretin alleviated the metabolic changes and mitigated circulating inflammatory cytokines levels. Phloretin treatment resists WD induced changes in microbial diversity of mice and decreased endotoxin content. Prolonged exposure of WD changed dynamics of gut microbiota abundance and distribution. Increased abundance of pathogenic taxa like Desulfovibrionaceae, Peptostreptococcus, Clostridium, and Terrisporobacter was noted. Phloretin treatment not only reversed this dysbiosis but also modulated taxonomic signatures of beneficial microbes like Ruminococcus, Lactobacillus, and Alloprevotella. Therefore, the potential of phloretin to restore gut eubiosis could be utilized as an intervention strategy for the prevention of MAFLD and related metabolic disorders.}, }
@article {pmid37744908, year = {2023}, author = {Arishi, RA and Lai, CT and Geddes, DT and Stinson, LF}, title = {Impact of breastfeeding and other early-life factors on the development of the oral microbiome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1236601}, pmid = {37744908}, issn = {1664-302X}, abstract = {The oral cavity is home to the second most diverse microbiome in the human body. This community contributes to both oral and systemic health. Acquisition and development of the oral microbiome is a dynamic process that occurs over early life; however, data regarding longitudinal assembly of the infant oral microbiome is scarce. While numerous factors have been associated with the composition of the infant oral microbiome, early feeding practices (breastfeeding and the introduction of solids) appear to be the strongest determinants of the infant oral microbiome. In the present review, we draw together data on the maternal, infant, and environmental factors linked to the composition of the infant oral microbiome, with a focus on early nutrition. Given evidence that breastfeeding powerfully shapes the infant oral microbiome, the review explores potential mechanisms through which human milk components, including microbes, metabolites, oligosaccharides, and antimicrobial proteins, may interact with and shape the infant oral microbiome. Infancy is a unique period for the oral microbiome. By enhancing our understanding of oral microbiome assembly in early life, we may better support both oral and systemic health throughout the lifespan.}, }
@article {pmid37744901, year = {2023}, author = {Zhao, C and Wang, L and Zhang, K and Zhu, X and Li, D and Ji, J and Luo, J and Cui, J}, title = {Variation of Helicoverpa armigera symbionts across developmental stages and geographic locations.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1251627}, pmid = {37744901}, issn = {1664-302X}, abstract = {Cotton bollworm (Helicoverpa armigera) poses a global problem, causing substantial economic and ecological losses. Endosymbionts in insects play crucial roles in multiple insect biological processes. However, the interactions between H. armigera and its symbionts have not been well characterized to date. We investigated the symbionts of H. armigera in the whole life cycle from different geographical locations. In the whole life cycle of H. armigera, Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were the dominant bacteria at the phylum level, while Enterococcus, Enterobacter, Glutamicibacter, and Bacillus were the four dominant bacteria at the genus level. Furthermore, high similarity in symbiotic bacterial community was observed in different stages of H. armigera, which were dominated by Enterococcus and Enterobacter. In fields, the dominant bacteria were Proteobacteria and Bacteroidetes, whereas, in the laboratory, the dominant bacteria were Proteobacteria. At the genus level, the dominant bacteria in cotton bollworm eggs of wild populations were Enterobacter, Morganella, Lactococcus, Asaia, Apibacter, and Enterococcus, and the subdominant bacteria were Bartonella, Pseudomonas, and Orbus. Moreover, the symbionts varied with geographical locations, and the closer the geographical distance, the more similar the microbial composition. Taken together, our study identifies and compares the symbiont variation along with geographical gradients and host development dynamic and reveals the high flexibility of microbiome communities in H. armigera, which probably benefits for the successful survival in a complicated changing environment.}, }
@article {pmid37744900, year = {2023}, author = {Bose, T and Wasimuddin,  and Acharya, V and Pinna, NK and Kaur, H and Ranjan, M and SaiKrishna, J and Nagabandi, T and Varma, B and Tallapaka, KB and Sowpati, DT and Haque, MM and Dutta, A and Siva, AB and Mande, SS}, title = {A cross-sectional study on the nasopharyngeal microbiota of individuals with SARS-CoV-2 infection across three COVID-19 waves in India.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1238829}, pmid = {37744900}, issn = {1664-302X}, abstract = {BACKGROUND: Multiple variants of the SARS-CoV-2 virus have plagued the world through successive waves of infection over the past three years. Independent research groups across geographies have shown that the microbiome composition in COVID-19 positive patients (CP) differs from that of COVID-19 negative individuals (CN). However, these observations were based on limited-sized sample-sets collected primarily from the early days of the pandemic. Here, we study the nasopharyngeal microbiota in COVID-19 patients, wherein the samples have been collected across the three COVID-19 waves witnessed in India, which were driven by different variants of concern.<br><br>METHODS: The nasopharyngeal swabs were collected from 589 subjects providing samples for diagnostics purposes at the Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India and subjected to 16s rRNA gene amplicon - based sequencing.<br><br>FINDINGS: We found variations in the microbiota of symptomatic vs. asymptomatic COVID-19 patients. CP showed a marked shift in the microbial diversity and composition compared to CN, in a wave-dependent manner. Rickettsiaceae was the only family that was noted to be consistently depleted in CP samples across the waves. The genera Staphylococcus, Anhydrobacter, Thermus, and Aerococcus were observed to be highly abundant in the symptomatic CP patients when compared to the asymptomatic group. In general, we observed a decrease in the burden of opportunistic pathogens in the host microbiota during the later waves of infection.<br><br>INTERPRETATION: To our knowledge, this is the first analytical cross-sectional study of this scale, which was designed to understand the relation between the evolving nature of the virus and the changes in the human nasopharyngeal microbiota. Although no clear signatures were observed, this study shall pave the way for a better understanding of the disease pathophysiology and help gather preliminary evidence on whether interventions to the host microbiota can help in better protection or faster recovery.}, }
@article {pmid37744507, year = {2023}, author = {Zeigler, MK and Vander Wyst, KB}, title = {Microbial associations and transfers across the One Health Triad effects on human and animal adiposity and temperament: a protocol for an observational pilot study.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1225188}, pmid = {37744507}, issn = {2296-2565}, abstract = {INTRODUCTION: It is known that humans and pet dogs harbor microbial communities that are important regulators of health and disease. Pet dogs have been shown to promote microbial exchange between members of a household, a process that may have lasting health implications. Infancy marks a unique period of development as environmental exploration and introduction to complementary foods occur. This may lead to greater opportunities for microbial transfer between pet dogs and human infants due to a more confined shared environment, similar means of mobility, greater physical contact, and increased frequency of shared foods. This human-animal bond has led to extensive research in the areas of childhood allergies and behavioral health; however, there is a paucity in the available literature that has evaluated how this unique ecological relationship may impact both human and animal health.<br><br>METHODS: Infants who reside in a household with a pet dog will be recruited from the greater Phoenix metropolitan area for this longitudinal, observational pilot study and followed through the complementary feeding period. Infant and pet dog fecal, salivary, and skin samples, as well as environmental samples from feeding areas/surfaces and main indoor play areas from both infants and pet dogs will be collected through in-home visits before (~5 mos), during (~9 mos), and after (~12 mos) the complementary feeding (CF) period. Anthropometrics, temperament, and dietary habits of both infants and pet dogs along with assessment of the home condition will also be collected. Microbial comparisons between infant and pet dog samples and evaluation of microbial changes during the CF period will be evaluated. Further, we will assess relationships between microbial composition and adiposity and temperament of both infants and pet dogs.<br><br>DISCUSSION: The proposed observational pilot study will advance the available science by exploring how microbial communities are associated and change between infants and pet dogs before, during, and after the CF period, a unique period of human growth and development. Findings from this study will provide insights into the impact these ecological relationships have on each other and how transfer across the One Health Triad impacts human and animal health.}, }
@article {pmid37744347, year = {2023}, author = {Corbett, AJ and Ussher, JE and Hinks, TSC}, title = {Editorial: MAIT cells come of age.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1281881}, pmid = {37744347}, issn = {1664-3224}, }
@article {pmid37744040, year = {2023}, author = {Galià-Camps, C and Baños, E and Pascual, M and Carreras, C and Turon, X}, title = {Multidimensional variability of the microbiome of an invasive ascidian species.}, journal = {iScience}, volume = {26}, number = {10}, pages = {107812}, pmid = {37744040}, issn = {2589-0042}, abstract = {Animals, including invasive species, are complex entities consisting of a host and its associated symbionts (holobiont). The interaction between the holobiont components is crucial for the host's survival. However, our understanding of how microbiomes of invasive species change across different tissues, localities, and ontogenetic stages, is limited. In the introduced ascidian Styela plicata, we found that its microbiome is highly distinct and specialized among compartments (tunic, gill, and gut). Smaller but significant differences were also found across harbors, suggesting local adaptation, and between juveniles and adults. Furthermore, we found a correlation between the microbiome and environmental trace element concentrations, especially in adults. Functional analyses showed that adult microbiomes possess specific metabolic pathways that may enhance fitness during the introduction process. These findings highlight the importance of integrated approaches in studying the interplay between animals and microbiomes, as a first step toward understanding how it can affect the species' invasive success.}, }
@article {pmid37744031, year = {2023}, author = {Zhao, ZS and Yang, LY and Li, FX and Cun, W and Wang, XY and Cao, CQ and Zhang, QL}, title = {Gut flora alterations among aquatic firefly Aquatica leii inhabiting various dissolved oxygen in fresh water.}, journal = {iScience}, volume = {26}, number = {10}, pages = {107809}, pmid = {37744031}, issn = {2589-0042}, abstract = {Knowledge about the impact of different dissolved oxygen (DO) on the composition and function of gut bacteria of aquatic insects is largely unknown. Herein, we constructed freshwater environments with different DOs (hypoxia: 2.50 ± 0.50, normoxia: 7.00 ± 0.50, and hyperoxia: 13.00 ± 0.50 mg/L) where aquatic firefly Aquatica leii larvae lived for three months. Their gut flora was analyzed using the combination of 16S rRNA amplicon sequencing and metagenomics. The results showed no difference in alpha diversity of the gut flora between A. leii inhabiting various DOs. However, the relative abundance of several bacterial lineages presented significant changes, such as Pseudomonas. In addition, bacterial genes with an altered relative abundance in response to various DOs were primarily related to metabolism. The alteration of these functions correlated with the DO change. This is the first to uncover structure of gut flora under various DOs in aquatic insect larvae.}, }
@article {pmid37743884, year = {2023}, author = {Tran, DM and Nguyen, TH}, title = {Rice (Oryza sativa L.) cultivated in the Central Highlands of Vietnam: Dataset on the endophytic microbiome.}, journal = {Data in brief}, volume = {50}, number = {}, pages = {109551}, pmid = {37743884}, issn = {2352-3409}, abstract = {Rice (Oryza sativa L.) is the main annual crop cultivated in the Central Highlands region of Vietnam. Understanding the endophytic bacterial community of this plant, a new technique for sustainable production can be developed. In this work, a representative sample was obtained by combining rice (RVT variety) root samples collected from five different fields in Dray Sap Commune, Krong Ana District, Dak Lak Province, the Central Highlands of Vietnam. Using the Illumina MiSeq technology, the 16S rRNA metagenomics was applied to the sequencing amplicons library. The QIIME2 matched with the SILVA SSURef reference database was employed to analyze the taxonomic profile, and the PICRUSt2 and MetaCyc databases were used to predict the functional profile of rice endophytic prokaryotes. Results revealed that Enterobacterales was the most predominant class (57.7%) in the bacterial community, and biosynthesis was the primary function of the rice endophytic microbiome (75.95%). Raw sequences obtained in this work are available from the National Center for Biotechnology Information (NCBI) (Bioproject ID: PRJNA994482) and Mendeley Data [1]. Data in this work provide insight into the endophytic microbiome of rice (RVT variety) cultivated in the Central Highlands of Vietnam. These data are valuable for developing a new method for producing locally sustainable rice employing endophytic bacteria. This is the first report on the endophytic microbiome of rice cultivated in this region.}, }
@article {pmid37743871, year = {2023}, author = {Liu, Y and Chan, MTV and Chan, FKL and Wu, WKK and Ng, SC and Zhang, L}, title = {Lower gut abundance of Eubacterium rectale is linked to COVID-19 mortality.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1249069}, pmid = {37743871}, issn = {2235-2988}, abstract = {INTRODUCTION: Emerging preclinical and clinical studies suggest that altered gut microbiome composition and functions are associated with coronavirus 2019 (COVID- 19) severity and its long-term complications. We hypothesize that COVID-19 outcome is associated with gut microbiome status in population-based settings.<br><br>METHODS: Gut metagenomic data of the adult population consisting of 2871 subjects from 16 countries were obtained from ExperimentHub through R, while the dynamic death data of COVID-19 patients between January 22, 2020 and December 8, 2020 in each country was acquired from Johns Hopkins Coronavirus Resource Center. An adjusted stable mortality rate (SMR) was used to represent these countries' mortality and correlated with the mean relative abundance (mRA) of healthy adult gut microbiome species.<br><br>RESULTS: After excluding bacterial species with low prevalence (prevalence <0.2 in the included countries), the &#x3b2;-diversity was significantly higher in the countries with high SMR when compared with those with median or low SMR (p <0.001). We then identified the mRA of two butyrate producers, Eubacterium rectale and Roseburia intestinalis, that were negatively correlated with SMR during the study period. And the reduction of these species was associated with severer COVID-19 manifestation.<br><br>CONCLUSION: Population-based microbiome signatures with the stable mortality rate of COVID-19 in different countries suggest that altered gut microbiome composition and functions are associated with mortality of COVID-19.}, }
@article {pmid37743870, year = {2023}, author = {Palanisamy, V and Bosilevac, JM and Barkhouse, DA and Velez, SE and Chitlapilly Dass, S}, title = {Shotgun-metagenomics reveals a highly diverse and communal microbial network present in the drains of three beef-processing plants.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1240138}, pmid = {37743870}, issn = {2235-2988}, abstract = {BACKGROUND: Multi-species biofilms pose a problem in various environments, especially food-processing environments. The diversity of microorganisms in these biofilms plays a critical role in their integrity and protection against external biotic and abiotic factors. Compared to single-species biofilms, mixed-species biofilms are more resistant to various stresses, including antimicrobials like sanitizers. Therefore, understanding the microbiome composition and diversity in biofilms and their metabolic potential is a priority when developing intervention techniques to combat foodborne pathogens in food processing environments.<br><br>METHODS: This study aimed to describe and compare the microbiome profile of 75 drain biofilm samples obtained from five different locations (Hotscale, Hotbox, Cooler, Processing, &amp; Grind room) of three beef-processing plants (Plant A, B &amp; C) taken over two timepoints 2017-18 (T1) and 2021 (T2) by shotgun sequencing.<br><br>RESULTS: Core microbiome analysis found Pseudomonas, Psychrobacter, and Acinetobacter to be the top three prevalent genera among the plants and locations. Alpha diversity analysis demonstrated a high diversity of microbiome present in all the plants and locations across the time points. Functional analysis showed the high metabolic potential of the microbial community with abundance of genes in metabolism, cell-adhesion, motility, and quorum sensing. Moreover, Quaternary Ammonium Compound (QAC) resistance genes were also observed, this is significant as QAC sanitizers are commonly used in many food processing facilities. Multi-functional genes such as transposases, polymerases, permeases, flagellar proteins, and Mobile Genetic Elements (MGEs) were found suggesting these are dynamic microbial communities that work together to protect themselves against environmental stresses through multiple defense mechanisms.<br><br>CONCLUSION: This study provides a framework for understanding the collective microbial network spanning a beef processing system. The results can be used to develop intervention strategies to best control these highly communicative microbial networks.}, }
@article {pmid37743862, year = {2023}, author = {Howe, S and Kegley, B and Powell, J and Chen, S and Zhao, J}, title = {Effect of bovine respiratory disease on the respiratory microbiome: a meta-analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1223090}, pmid = {37743862}, issn = {2235-2988}, abstract = {BACKGROUND: Bovine respiratory disease (BRD) is the most devastating disease affecting beef and dairy cattle producers in North America. An emerging area of interest is the respiratory microbiome's relationship with BRD. However, results regarding the effect of BRD on respiratory microbiome diversity are conflicting.<br><br>RESULTS: To examine the effect of BRD on the alpha diversity of the respiratory microbiome, a meta-analysis analyzing the relationship between the standardized mean difference (SMD) of three alpha diversity metrics (Shannon's Diversity Index (Shannon), Chao1, and Observed features (OTUs, ASVs, species, and reads) and BRD was conducted. Our multi-level model found no difference in Chao1 and Observed features SMDs between calves with BRD and controls. The Shannon SMD was significantly greater in controls compared to that in calves with BRD. Furthermore, we re-analyzed 16S amplicon sequencing data from four previously published datasets to investigate BRD's effect on individual taxa abundances. Additionally, based on Bray Curtis and Jaccard distances, health status, sampling location, and dataset were all significant sources of variation. Using a consensus approach based on RandomForest, DESeq2, and ANCOM-BC2, we identified three differentially abundant amplicon sequence variants (ASVs) within the nasal cavity, ASV5_Mycoplasma, ASV19_Corynebacterium, and ASV37_Ruminococcaceae. However, no ASVs were differentially abundant in the other sampling locations. Moreover, based on SECOM analysis, ASV37_Ruminococcaceae had a negative relationship with ASV1_Mycoplasma_hyorhinis, ASV5_Mycoplasma, and ASV4_Mannheimia. ASV19_Corynebacterium had negative relationships with ASV1_Mycoplasma_hyorhinis, ASV4_Mannheimia, ASV54_Mycoplasma, ASV7_Mycoplasma, and ASV8_Pasteurella.<br><br>CONCLUSIONS: Our results confirm a relationship between bovine respiratory disease and respiratory microbiome diversity and composition, which provide additional insight into microbial community dynamics during BRD development. Furthermore, as sampling location and sample processing (dataset) can also affect results, consideration should be taken when comparing results across studies.}, }
@article {pmid37743857, year = {2023}, author = {Mao, X and Chen, H and Peng, X and Zhao, X and Yu, Z and Xu, D}, title = {Dysbiosis of vaginal and cervical microbiome is associated with uterine fibroids.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1196823}, pmid = {37743857}, issn = {2235-2988}, abstract = {Dysbiosis of the female reproductive tract is closely associated with gynecologic diseases. Here, we aim to explore the association between dysbiosis in the genital tract and uterine fibroids (UFs) to further provide new insights into UF etiology. We present an observational study to profile vaginal and cervical microbiome from 29 women with UFs and 38 healthy women, and 125 samples were obtained and sequenced. By comparing the microbial profiles between different parts of the reproductive tract, there is no significant difference in microbial diversity between healthy subjects and UF patients. However, alpha diversity of UF patients was negatively correlated with the number of fibroids. Increased Firmicutes were observed in both the cervical and vaginal microbiome of UF patients at the phylum level. In differential analysis of relative abundance, some genera were shown to be significantly enriched (e.g., Erysipelatoclostridium, Mucispirillum, and Finegoldia) and depleted (e.g., Erysipelotrichaceae UCG-003 and Sporolactobacillus) in UF patients. Furthermore, the microbial co-occurrence networks of UF patients showed lower connectivity and complexity, suggesting reduced interactions and stability of the cervical and vaginal microbiota in UF patients. In summary, our findings revealed the perturbation of microbiome in the presence of UFs and a distinct pattern of characteristic vaginal and cervical microbiome involved in UFs, offering new options to further improve prevention and management strategies.}, }
@article {pmid37743772, year = {2023}, author = {Wojciech, L and Png, CW and Koh, EY and Kioh, DYQ and Deng, L and Wang, Z and Wu, LZ and Hamidinia, M and Tung, DW and Zhang, W and Pettersson, S and Chan, ECY and Zhang, Y and Tan, KS and Gascoigne, NR}, title = {A tryptophan metabolite made by a gut microbiome eukaryote induces pro-inflammatory T cells.}, journal = {The EMBO journal}, volume = {}, number = {}, pages = {e112963}, doi = {10.15252/embj.2022112963}, pmid = {37743772}, issn = {1460-2075}, support = {//China Scholarship Council (CSC)/ ; NUHSRO/2019/049/T1/SEED-MAR/02//Ministry of Education - Singapore (MOE)/ ; T1-NUHS Joint Grant Call FY17-1st call-03//Ministry of Education - Singapore (MOE)/ ; //National University of Singapore (NUS)/ ; }, abstract = {The large intestine harbors microorganisms playing unique roles in host physiology. The beneficial or detrimental outcome of host-microbiome coexistence depends largely on the balance between regulators and responder intestinal CD4[+] T cells. We found that ulcerative colitis-like changes in the large intestine after infection with the protist Blastocystis ST7 in a mouse model are associated with reduction of anti-inflammatory Treg cells and simultaneous expansion of pro-inflammatory Th17 responders. These alterations in CD4[+] T cells depended on the tryptophan metabolite indole-3-acetaldehyde (I3AA) produced by this single-cell eukaryote. I3AA reduced the Treg subset in vivo and iTreg development in vitro by modifying their sensing of TGFβ, concomitantly affecting recognition of self-flora antigens by conventional CD4[+] T cells. Parasite-derived I3AA also induces over-exuberant TCR signaling, manifested by increased CD69 expression and downregulation of co-inhibitor PD-1. We have thus identified a new mechanism dictating CD4[+] fate decisions. The findings thus shine a new light on the ability of the protist microbiome and tryptophan metabolites, derived from them or other sources, to modulate the adaptive immune compartment, particularly in the context of gut inflammatory disorders.}, }
@article {pmid37743718, year = {2023}, author = {Ma, Y and Cao, Y and Song, X and Xu, W and Luo, Z and Shan, J and Zhou, J}, title = {Integration of semi-empirical MS/MS library with characteristic features for the annotation of novel amino acid-conjugated bile acids.}, journal = {The Analyst}, volume = {}, number = {}, pages = {}, doi = {10.1039/d3an01237a}, pmid = {37743718}, issn = {1364-5528}, abstract = {Recently, amino acids other than glycine and taurine were found to be conjugated with bile acids by the gut microbiome in mouse and human. As potential diagnostic markers for inflammatory bowel disease and farnesoid X receptor agonists, their physiological effects and mechanisms, however, remain to be elucidated. A tool for the rapid and comprehensive annotation of such new metabolites is required. Thus, we developed a semi-empirical MS/MS library for bile acids conjugated with 18 common amino acids, including alanine, arginine, asparagine, aspartate, glutamine, glutamate, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine. To investigate their fragmentation rules, these amino acids were chemically conjugated with lithocholic acid, deoxycholic acid, and cholic acid, and their accurate-mass MS/MS spectra were acquired. The common fragmentation patterns from the amino acid moieties were combined with 10 general bile acid skeletons to generate a semi-empirical MS/MS library of 180 structures. Software named BAFinder 2.0 was developed to combine the semi-empirical library in negative mode and the characteristic fragments in positive mode for automatic unknown identification. As a proof of concept, this workflow was applied to the LC-MS/MS analysis of the feces of human, beagle dogs, and rats. In total, 171 common amino acid-conjugated bile acids were annotated and 105 of them were confirmed with the retention times of synthesized compounds. To explore other potential bile acid conjugates, user-defined small molecules were in-silico conjugated with bile acids and searched in the fecal dataset. Four novel bile acid conjugates were discovered, including D-Ala-D-Ala, Lys(iso)-Gly, L-2-aminobutyric acid, and ornithine.}, }
@article {pmid37743606, year = {2023}, author = {Monteiro, RC and Fernandes, M}, title = {Are antibiotics still relevant in acne? A review of the therapeutic conundrum.}, journal = {International journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/ijd.16854}, pmid = {37743606}, issn = {1365-4632}, abstract = {Antibiotics have constituted the mainstay of acne therapy despite acne being classified as an inflammatory disorder. The indiscriminate usage of antibiotics over the years has thus fueled the issue of antimicrobial resistance. Cutibacterium acnes (C. acnes) can acquire resistance due to chromosomal mutation or genetic acquisition. C. acnes can transfer resistance to other resident flora, complicating the management of skin and soft tissue infections. It can also transfer resistant strains to other body sites and to immunocompromised and elderly patients thus putting them at risk of serious infections. Recent studies have highlighted the physiologic role of C. acnes in maintaining the normal homeostasis of the skin microbiome. The role of Malassezia in causation of acne has piqued interest in recent times. The efficacy of antibiotics in acne is attributed to their para-antibiotic, anti-inflammatory action rather than antimicrobial action. Thus, usage of low-dose antibiotics and alternatives to antibiotics has been advocated. Some alternative therapies showing efficacy in acne are probiotics, oral zinc, precision therapy using succinic acid, bacteriophages, and anti-biofilm therapy like myrtacin, topical azelaic acid, and salicylic acid. Using isotretinoin in early stages of acne can reduce the incidence of scarring and alleviate the need for antibiotics. Thus, a gradual shift from antibiotics to alternative therapies in acne is the need of the hour.}, }
@article {pmid37743497, year = {2023}, author = {Huang, C and Gin, C and Fettweis, J and Foxman, B and Gelaye, B and MacIntyre, DA and Subramaniam, A and Fraser, W and Tabatabaei, N and Callahan, B}, title = {Meta-analysis reveals the vaginal microbiome is a better predictor of earlier than later preterm birth.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {199}, pmid = {37743497}, issn = {1741-7007}, support = {R35GM133745/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: High-throughput sequencing measurements of the vaginal microbiome have yielded intriguing potential relationships between the vaginal microbiome and preterm birth (PTB; live birth prior to 37 weeks of gestation). However, results across studies have been inconsistent.<br><br>RESULTS: Here, we perform an integrated analysis of previously published datasets from 12 cohorts of pregnant women whose vaginal microbiomes were measured by 16S rRNA gene sequencing. Of 2039 women included in our analysis, 586 went on to deliver prematurely. Substantial variation between these datasets existed in their definition of preterm birth, characteristics of the study populations, and sequencing methodology. Nevertheless, a small group of taxa comprised a vast majority of the measured microbiome in all cohorts. We trained machine learning (ML) models to predict PTB from the composition of the vaginal microbiome, finding low to modest predictive accuracy (0.28-0.79). Predictive accuracy was typically lower when ML models trained in one dataset predicted PTB in another dataset. Earlier preterm birth (< 32 weeks, < 34 weeks) was more predictable from the vaginal microbiome than late preterm birth (34-37 weeks), both within and across datasets. Integrated differential abundance analysis revealed a highly significant negative association between L. crispatus and PTB that was consistent across almost all studies. The presence of the majority (18 out of 25) of genera was associated with a higher risk of PTB, with L. iners, Prevotella, and Gardnerella showing particularly consistent and significant associations. Some example discrepancies between studies could be attributed to specific methodological differences but not most study-to-study variations in the relationship between the vaginal microbiome and preterm birth.<br><br>CONCLUSIONS: We believe future studies of the vaginal microbiome and PTB will benefit from a focus on earlier preterm births and improved reporting of specific patient metadata shown to influence the vaginal microbiome and/or birth outcomes.}, }
@article {pmid37742888, year = {2023}, author = {Jiang, D and Li, S and Liang, Y and Xu, R and Qi, Q and Wang, B and Zhang, C}, title = {16S rRNA and transcriptome analysis of the FOS-mediated alleviation of Aeromonas hydrophila-induced intestinal damage in Megalobrama amblycephala.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {127040}, doi = {10.1016/j.ijbiomac.2023.127040}, pmid = {37742888}, issn = {1879-0003}, abstract = {This study was conducted to elucidate the effects of FOS that alleviate Aeromonas hydrophila-induced intestinal damage. The results showed that A. hydrophila disrupted the intestinal structure and increased intestinal permeability, causing abnormalities in mucosal pathology. Additionally, A. hydrophila induced an imbalance in the intestinal flora and disturbed its stability. Dietary FOS ameliorated the injury to the intestinal structure of fish, but also in part improved the condition of the intestinal tight junction complex. Transcriptomic analysis showed that 120 genes were up-regulated and 320 genes were down-regulated. The intestinal immune network for the IgA production signalling pathway was enriched following A. hydrophila infection, and the change in the FOS group was mainly in the Tight junction signalling pathway. Similarly, dietary FOS reduced the disruption of the intestinal microbiota induced by A. hydrophila and improved the intestinal microbiota's stability; FOS was also partially implicated in the upregulation of Tight junction and Adhesion junction pathways by transcriptomic analysis. After further analysis, it was found that fish fed FOS had upregulated expression of genes related to apoptosis, antigen presentation, and the T-cell-mediated immune response in the intestine compared with those in the A. hydrophila group, which may be related to changes in the intestinal microbiome.}, }
@article {pmid37742728, year = {2023}, author = {Ciernikova, S and Sevcikova, A and Drgona, L and Mego, M}, title = {Modulating the gut microbiota by probiotics, prebiotics, postbiotics, and fecal microbiota transplantation: An emerging trend in cancer patient care.}, journal = {Biochimica et biophysica acta. Reviews on cancer}, volume = {}, number = {}, pages = {188990}, doi = {10.1016/j.bbcan.2023.188990}, pmid = {37742728}, issn = {1879-2561}, abstract = {Treatment resistance, together with acute and late adverse effects, represents critical issues in the management of cancer patients. Promising results from preclinical and clinical research underline the emerging trend of a microbiome-based approach in oncology. Favorable bacterial species and higher gut diversity are associated with increased treatment efficacy, mainly in chemo- and immunotherapy. On the other hand, alterations in the composition and activity of gut microbial communities are linked to intestinal dysbiosis and contribute to high treatment-induced toxicity. In this Review, we provide an overview of studies concerning gut microbiota modulation in patients with solid and hematologic malignancies with a focus on probiotics, prebiotics, postbiotics, and fecal microbiota transplantation. Targeting the gut microbiome might bring clinical benefits and improve patient outcomes. However, a deeper understanding of mechanisms and large clinical trials concerning microbiome and immunological profiling is warranted to identify safe and effective ways to incorporate microbiota-based interventions in routine clinical practice.}, }
@article {pmid37742503, year = {2023}, author = {Meng, H and Xu, D and Wang, Q and Liu, L and Liu, W and Wang, J}, title = {Maintaining immune homeostasis with Coptis Chinensis water extract to mitigate sepsis severity via modulating gut microbiome and metabolism.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {236}, number = {}, pages = {115719}, doi = {10.1016/j.jpba.2023.115719}, pmid = {37742503}, issn = {1873-264X}, abstract = {Sepsis arises from an uncontrolled inflammatory response to infection that can lead to organ failure. The gut microbiome is increasingly recognized as a key modulator of sepsis progression. This study investigated whether Coptis chinensis water extract (CCWE) could attenuate sepsis by modulating the gut microbiome and immune response. A rat model of sepsis induced by cecum ligation and perforation was used. 16 S ribosomal ribonucleic acid (rRNA) sequencing, proton nuclear magnetic resonance ([1]H NMR) metabolomics and flow cytometry assays were used to evaluate microbial, metabolic and immune profiles. CCWE treatment reversed sepsis-induced loss of beneficial bacteria like Firmicutes and Bacteroidetes and restored gut microbial balance. CCWE increased short-chain fatty acids, carnitine and phenylacetate, which provide energy and curb inflammation. By enhancing immune homeostasis and maintaining regulatory T cells (Tregs), CCWE treatment also exerted bidirectional regulation on T cells for initially suppressing hyperactivation then enabling recovery. Overall, CCWE may benefit sepsis by regulating the gut-microbiome-immune axis. By restoring microbiome balance, improving metabolism, and modulating immunity, CCWE treatment shows potential for alleviating sepsis severity and progression. The increases in beneficial bacteria, Tregs, and anti-inflammatory metabolites coupled with decreases in opportunistic pathogens likely contributed collectively to CCWE's protective effects. CCWE may emerge as an alternative or adjunctive option for managing disorders of dangerous inflammation like sepsis. Future research should explore CCWE's mechanisms of action clinically to determine its potential as a safe, effective means of modulating health through natural regulation of the gut microbiome and immune function.}, }
@article {pmid37742499, year = {2023}, author = {Johnson, CA and Snelling, TJ and Huntington, JA and Taylor-Pickard, J and Warren, HE and Sinclair, LA}, title = {Effect of feeding Yucca schidigera extract and a live yeast on the rumen microbiome and performance of dairy cows fed a diet excess in rumen degradable nitrogen.}, journal = {Animal : an international journal of animal bioscience}, volume = {17}, number = {10}, pages = {100967}, doi = {10.1016/j.animal.2023.100967}, pmid = {37742499}, issn = {1751-732X}, abstract = {Nitrogen (N) loss from livestock agriculture via ammonia and nitrous oxide can reduce feed efficiency, production and negatively affect the environment. One option to reduce N loss is to add dietary supplements such as Yucca schidigera extract which has ammonia-binding properties and contains antimicrobial steroidal saponins, or Saccharomyces cerevisiae yeast, which can stabilise rumen pH and promote fibre degradation, increasing microbial growth and demand for degradable N. To determine the effect of Yucca schidigera extract when fed alone or in combination with a live yeast on the performance, rumen metabolism, microbiome and N balance, six rumen cannulated dairy cows were fed a mixed ration (C), mixed ration with Y. schidigera extract (De-Odorase®, Alltech®; 5 g/cow/day; D), or mixed ration with Y. schidigera extract (5 g/day) and Saccharomyces cerevisiae (Yea-Sacc®, Alltech®, 1 g/cow per day; DY), in a 3 × 3 Latin rectangle design study with three periods of 49-day duration. Digesta samples were collected via the ruminal cannula during the final week of each period and separated into liquid (LPD) and solid (SPD) phases for microbiome analysis using 16S rRNA amplicon sequencing. DM intake was 0.8 kg/d lower (P < 0.05) in cows fed DY than C or D, with milk protein concentration 1.7 g/kg higher in C than D or DY. There was a beta diversity (Bray Curtis) clustering of the LPD in cows fed D or DY compared to C (P < 0.05), driven by an increase in Prevotella ruminicola-related operational taxonomic units (OTUs), and a decrease in P. brevis and P. bryantii OTUs. A methanogen OTU, Methanobrevibacter olleyae, was decreased in cows fed D or DY and an unclassified species of Gammaproteobacteria was increased in DY (LDA > 2.0, P < 0.05) compared to C. Rumen pH, ammonia and total VFA concentration were not affected by treatment (P > 0.05) but the concentration of propionate and iso-butyrate were lower at 1700 and 2000 h in cows fed DY compared to C (P < 0.05). Measurements of N balance were unaffected by supplementation with D or DY, and there was no effect of treatment on slurry pH. In conclusion, supplementing with an extract of Yucca schidigera either alone or in combination with a live yeast had only a small effect on performance, with Yucca schidigera altering species associated with carbohydrate and protein metabolism, and reduced Methanobrevibacter olleyae which is involved in methanogenesis.}, }
@article {pmid37742216, year = {2023}, author = {Metras, BN and Oba, PM and Miller, MJ and Swanson, KS}, title = {Effects of Commercial and Traditional Kefir Supplementation on Apparent Total Tract Macronutrient Digestibility and the Fecal Characteristics, Metabolites, and Microbiota of Healthy Adult Dogs.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skad316}, pmid = {37742216}, issn = {1525-3163}, abstract = {Kefir is a fermented dairy beverage that has been consumed by humans for centuries, but poorly studied in pets. The objective of this study was to determine the effects of commercial or traditional kefir supplementation on apparent total tract macronutrient digestibility (ATTD) and fecal characteristics, microbiota populations, and metabolite and immunoglobulin (Ig) A concentrations of healthy adult dogs. Twelve healthy adult dogs (5.67±1.72 y, 7.27±1.15 kg) were used in a replicated 3x3 Latin square design (n=12/group). All dogs were fed a commercial diet and allotted to 1 of 3 treatments (60 mL/d): 2% reduced-fat milk treated with lactase [CNTL; 4.57E+03 lactic acid bacteria (LAB) colony-forming units (CFU)/mL], commercial kefir (C-Kefir; 6.95E+04 LAB CFU/mL), or traditional kefir brewed daily from 2% reduced-fat milk and kefir grains (T-Kefir; 1.79E+09 LAB CFU/mL). The experiment was composed of three 28-d periods, with each consisting of a 22-d transition phase, a 5-d fecal collection phase, and 1 d for blood collection. Fecal samples were collected for determination of ATTD and fecal pH, dry matter, microbiota, and metabolite and IgA concentrations. Data were analyzed using the Mixed Models procedure of SAS 9.4. The main effects of treatment were tested, with significance set at p≤0.05 and trends set at p≤0.10. Kefir products differed in microbial density and profile, but fecal microbiota populations were weakly impacted. Bacterial alpha diversity tended to be greater (p=0.10) in dogs fed T-Kefir than those fed CNTL. Bacterial beta diversity analysis identified a difference (p<0.0004) between dogs fed CNTL and those fed C-Kefir. Dogs fed C-Kefir tended to have a greater (p=0.06) relative abundance of Fusobacteriota than those fed CNTL or T-Kefir. Dogs fed T-Kefir had a greater (p<0.0001) relative abundance of Lactococcus than those fed CNTL or C-Kefir. Dogs fed T-Kefir also tended to have a lower (p=0.09) relative abundance of Escherichia-Shigella and greater (p=0.09) relative abundance of Candidatus stoquefichus than dogs fed CNTL or C-Kefir. Dogs fed C-Kefir tended to have lower (p=0.08) fecal valerate concentrations than those fed CNTL or T-Kefir. All other measures were unaffected by kefir treatments. Our results suggest that kefir supplementation had minor effects on the fecal microbiota populations and fecal metabolite concentrations of healthy adult dogs without impacting ATTD, fecal characteristics, or fecal IgA concentrations.}, }
@article {pmid37742185, year = {2023}, author = {Kemter, AM and Patry, RT and Arnold, J and Hesser, LA and Campbell, E and Ionescu, E and Mimee, M and Wang, S and Nagler, CR}, title = {Commensal bacteria signal through TLR5 and AhR to improve barrier integrity and prevent allergic responses to food.}, journal = {Cell reports}, volume = {42}, number = {10}, pages = {113153}, doi = {10.1016/j.celrep.2023.113153}, pmid = {37742185}, issn = {2211-1247}, abstract = {The increasing prevalence of food allergies has been linked to reduced commensal microbial diversity. In this article, we describe two features of allergy-protective Clostridia that contribute to their beneficial effects. Some Clostridial taxa bear flagella (a ligand for TLR5) and produce indole (a ligand for the aryl hydrocarbon receptor [AhR]). Lysates and flagella from a Clostridia consortium induced interleukin-22 (IL-22) secretion from ileal explants. IL-22 production is abrogated in explants from mice in which TLR5 or MyD88 signaling is deficient either globally or conditionally in CD11c[+] antigen-presenting cells. AhR signaling in RORγt[+] cells is necessary for the induction of IL-22. Mice deficient in AhR in RORγt[+] cells exhibit increased intestinal permeability and are more susceptible to an anaphylactic response to food. Our findings implicate TLR5 and AhR signaling in a molecular mechanism by which commensal Clostridia protect against allergic responses to food.}, }
@article {pmid37741901, year = {2023}, author = {Yuan, T and Zhang, S and He, S and Ma, Y and Chen, J and Gu, J}, title = {Bacterial lipopolysaccharide related genes signature as potential biomarker for prognosis and immune treatment in gastric cancer.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15916}, pmid = {37741901}, issn = {2045-2322}, abstract = {The composition of microbial microenvironment is an important factor affecting the development of tumor diseases. However, due to the limitations of current technological levels, we are still unable to fully study and elucidate the depth and breadth of the impact of microorganisms on tumors, especially whether microorganisms have an impact on cancer. Therefore, the purpose of this study is to conduct in-depth research on the role and mechanism of prostate microbiome in gastric cancer (GC) based on the related genes of bacterial lipopolysaccharide (LPS) by using bioinformatics methods. Through comparison in the Toxin Genomics Database (CTD), we can find and screen out the bacterial LPS related genes. In the study, Venn plots and lasso analysis were used to obtain differentially expressed LPS related hub genes (LRHG). Afterwards, in order to establish a prognostic risk score model and column chart in LRHG features, we used univariate and multivariate Cox regression analysis for modeling and composition. In addition, we also conducted in-depth research on the clinical role of immunotherapy with TMB, MSI, KRAS mutants, and TIDE scores. We screened 9 LRHGs in the database. We constructed a prognostic risk score and column chart based on LRHG, indicating that low risk scores have a protective effect on patients. We particularly found that low risk scores are beneficial for immunotherapy through TIDE score evaluation. Based on LPS related hub genes, we established a LRHG signature, which can help predict immunotherapy and prognosis for GC patients. Bacterial lipopolysaccharide related genes can also be biomarkers to predict progression free survival in GC patients.}, }
@article {pmid37741856, year = {2023}, author = {Wang, A and Diana, A and Rahmannia, S and Gibson, RS and Houghton, LA and Slupsky, CM}, title = {Impact of milk secretor status on the fecal metabolome and microbiota of breastfed infants.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2257273}, doi = {10.1080/19490976.2023.2257273}, pmid = {37741856}, issn = {1949-0984}, abstract = {Maternal secretor status has been shown to be associated with the presence of specific fucosylated human milk oligosaccharides (HMOs), and the impact of maternal secretor status on infant gut microbiota measured through 16s sequencing has previously been reported. None of those studies have confirmed exclusive breastfeeding nor investigated the impact of maternal secretor status on gut microbial fermentation products. The present study focused on exclusively breastfed (EBF) Indonesian infants, with exclusive breastfeeding validated through the stable isotope deuterium oxide dose-to-mother (DTM) technique, and the impact of maternal secretor status on the infant fecal microbiome and metabolome. Maternal secretor status did not alter the within-community (alpha) diversity, between-community (beta) diversity, or the relative abundance of bacterial taxa at the genus level. However, infants fed milk from secretor (Se+) mothers exhibited a lower level of fecal succinate, amino acids and their derivatives, and a higher level of 1,2-propanediol when compared to infants fed milk from non-secretor (Se-) mothers. Interestingly, for infants consuming milk from Se+ mothers, there was a correlation between the relative abundance of Bifidobacterium and Streptococcus, and between each of these genera and fecal metabolites that was not observed in infants receiving milk from Se- mothers. Our findings indicate that the secretor status of the mother impacts the gut microbiome of the exclusively breastfed infant.}, }
@article {pmid37741805, year = {2023}, author = {Wicaksono, WA and Cernava, T and Wassermann, B and Abdelfattah, A and Soto-Giron, MJ and Toledo, GV and Virtanen, SM and Knip, M and Hyöty, H and Berg, G}, title = {The edible plant microbiome: evidence for the occurrence of fruit and vegetable bacteria in the human gut.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2258565}, doi = {10.1080/19490976.2023.2258565}, pmid = {37741805}, issn = {1949-0984}, mesh = {Humans ; Vegetables ; Plants, Edible ; Fruit ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Bacteria/genetics ; }, abstract = {Diversity of the gut microbiota is crucial for human health. However, whether fruit and vegetable associated bacteria contribute to overall gut bacterial diversity is still unknown. We reconstructed metagenome-assembled genomes from 156 fruit and vegetable metagenomes to investigate the prevalence of associated bacteria in 2,426 publicly available gut metagenomes. The microbiomes of fresh fruits and vegetables and the human gut are represented by members in common such as Enterobacterales, Burkholderiales, and Lactobacillales. Exposure to bacteria via fruit and vegetable consumption potentially has a beneficial impact on the functional diversity of gut microbiota particularly due to the presence of putative health-promoting genes for the production of vitamin and short-chain fatty acids. In the human gut, they were consistently present, although at a low abundance, approx. 2.2%. Host age, vegetable consumption frequency, and the diversity of plants consumed were drivers favoring a higher proportion. Overall, these results provide one of the primary links between the human microbiome and the environmental microbiome. This study revealed evidence that fruit and vegetable-derived microbes could be found in the human gut and contribute to gut microbiome diversity.}, }
@article {pmid37741740, year = {2023}, author = {Hirt, H and Boukcim, H and Ducousso, M and Saad, MM}, title = {Engineering carbon sequestration on arid lands.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2023.08.009}, pmid = {37741740}, issn = {1878-4372}, abstract = {To limit the effects of global warming, arid lands, which constitute approximately one-third of terrestrial surfaces and are not utilized for agriculture, could serve as an effective method for long-term carbon (C) storage. We propose that soil-plant-microbiome engineering with oxalogenic plants and oxalotrophic microbes could facilitate C sequestration on a global scale.}, }
@article {pmid37741508, year = {2023}, author = {Muhammad, A and Zhang, N and He, J and Shen, X and Zhu, X and Xiao, J and Qian, Z and Sun, C and Shao, Y}, title = {Multiomics analysis reveals the molecular basis for increased body weight in silkworms (Bombyx mori) exposed to environmental concentrations of polystyrene micro- and nanoplastics.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2023.09.010}, pmid = {37741508}, issn = {2090-1224}, abstract = {INTRODUCTION: Micro- and nanoplastics (MNPs) are emerging environmental pollutants that have raised serious concerns about their potential impact on ecosystem and organism health. Despite increasing efforts to investigate the impacts of micro- and nanoplastics (MNPs) on biota little is known about their potential impacts on terrestrial organisms, especially insects, at environmental concentrations.<br><br>OBJECTIVES: To address this gap, we used an insect model, silkworm Bombyx mori to examine the potential long-term impacts of different sizes of polystyrene (PS) MNPs at environmentally realistic concentrations (0.25 to 1.0 &#x3bc;g/mL).<br><br>METHODS: After exposure to PS-MNPs over most of the larval lifetime (from second to last instar), the endpoints were examined by an integrated physiological (growth and survival) and multiomics approach (metabolomics, 16S rRNA, and transcriptomics).<br><br>RESULTS: Our results indicated that dietary exposures to PS-MNPs had no lethal effect on survivorship, but interestingly, increased host body weight. Multiomics analysis revealed that PS-MNPs exposure significantly altered multiple pathways, particularly lipid metabolism, leading to enriched energy reserves. Furthermore, the exposure changed the structure and composition of the gut microbiome and increased the abundance of gut bacteria Acinetobacter and Enterococcus. Notably, the predicted functional profiles and metabolite expressions were significantly correlated with bacterial abundance. Importantly, these observed effects were particle size-dependent and were ranked as PS-S (91.92 nm) > PS-M (5.69 &#xb5;m) > PS-L (9.7 &#xb5;m).<br><br>CONCLUSION: Overall, PS-MNPs at environmentally realistic concentrations exerted stimulatory effects on energy metabolism that subsequently enhanced body weight in silkworms, suggesting that chronic PS-MNPs exposure might trigger weight gain in animals and humans by influencing host energy and microbiota homeostasis.}, }
@article {pmid37741461, year = {2023}, author = {Fu, W and Xu, L and Chen, Z and Kan, L and Ma, Y and Qian, H and Wang, W}, title = {Recent advances on emerging nanomaterials for diagnosis and treatment of inflammatory bowel disease.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jconrel.2023.09.033}, pmid = {37741461}, issn = {1873-4995}, abstract = {Inflammatory bowel disease (IBD) is a chronic idiopathic inflammatory disorder that affects the entire gastrointestinal tract and is associated with an increased risk of colorectal cancer. Mainstream clinical testing methods are time-consuming, painful for patients, and insufficiently sensitive to detect early symptoms. Currently, there is no definitive cure for IBD, and frequent doses of medications with potentially severe side effects may affect patient response. In recent years, nanomaterials have demonstrated considerable potential for IBD management due to their diverse structures, composition, and physical and chemical properties. In this review, we provide an overview of the advances in nanomaterial-based diagnosis and treatment of IBD in recent five years. Multi-functional bio-nano platforms, including contrast agents, near-infrared (NIR) fluorescent probes, and bioactive substance detection agents have been developed for IBD diagnosis. Based on a series of pathogenic characteristics of IBD, the therapeutic strategies of antioxidant, anti-inflammatory, and intestinal microbiome regulation of IBD based on nanomaterials are systematically introduced. Finally, the future challenges and prospects in this field are presented to facilitate the development of diagnosis and treatment of IBD.}, }
@article {pmid37741374, year = {2023}, author = {Quan, Z and Zhao, Z and Liu, Z and Wang, W and Yao, S and Liu, H and Lin, X and Li, QX and Yan, H and Liu, X}, title = {Biodegradation of polystyrene microplastics by superworms (larve of Zophobas atratus): Gut microbiota transition, and putative metabolic ways.}, journal = {Chemosphere}, volume = {343}, number = {}, pages = {140246}, doi = {10.1016/j.chemosphere.2023.140246}, pmid = {37741374}, issn = {1879-1298}, abstract = {Superworm (larve of Zophobas atratus) could consume foams of expanded polystyrene plastics. However, there is no sufficient understanding of the impact of microplastics on superworms and the degradation pathways of polystyrene. Herein, we explored the weight and survival change of superworms while fed with polystyrene microplastics, and found that survival rate and mean weight would reduce. In terms of gut microbial community structure of surperworms, significant shifts were detected with the relative abundance of Hafnia-Obesumbacterium sp. increasing. In addition, we domesticated two microbiota from the gut of superworms, and confirmed their ability to degrade PS in vitro. The last but most important, 1291 metabolites were identified by HPLC-TOF-MS/MS, and six metabolites related to polystyrene degradation were identified through comparative metabolomic analysis. According to the content and pathways of these metabolites, three metabolic pathways of polystyrene were (a) styrene-phenylacetyl-CoA-L-2-aminoadipic acid; (b) styrene-phenylacetyl-CoA-benzaldehyde; (c) styrene-2-hydroxyacetophenone. These results would help to further screen bacteria of PS degradation and investigate PS metabolic pathways in invertebrates.}, }
@article {pmid37741304, year = {2023}, author = {Cheng, Y and An, N and Ishaq, HM and Xu, J}, title = {Ocular microbial dysbiosis and its linkage with infectious keratitis patients in Northwest China: A cross-sectional study.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {106371}, doi = {10.1016/j.micpath.2023.106371}, pmid = {37741304}, issn = {1096-1208}, abstract = {OBJECTIVES: To evaluate the alteration of ocular surface microbiome of patients with infectious keratitis in northwest of China.<br><br>METHODS: The corneal scrapings, eyelid margin and conjunctiva samples were collected from 57 participants, who were divided into bacterial keratitis, fungal keratitis, viral keratitis and control group. The V3-V4 region of bacterial 16S rDNA in each sample was amplified and sequenced on the Illumina HiSeq 2500 sequencing platform, and the differences among different groups were compared bioinformatically.<br><br>RESULTS: Significant alterations of the microbiome were observed in alpha-diversity and beta-diversity analysis between the keratitis groups and the control group (p&#x202f;<&#x202f;0.05). There was no significant differences between eyelid margin and conjunctiva samples in Alpha-Diversity analysis, but a significant difference between eyelid margin and corneal scraping samples in the keratitis group (p&#x202f;<&#x202f;0.05, independent t-test). The abundances of Bacillus, Megamonas, Acinetobacter, and Rhodococcu were significantly elevated, while the abundance of Staphylococcus was decreased in the keratitis group compared to the control group.<br><br>CONCLUSIONS: The abundance of the ocular microbiome in patients with bacterial keratitis, fungal keratitis, or viral keratitis was significantly higher than those in the control group. Keratitis patients may have ecological disorder on ocular surface microbiome compared with controls. We believe that the conjunctiva and eyelid margin microbiome combined analysis can more comprehensively reflect the composition and abundance of ocular surface microbiome.}, }
@article {pmid37741298, year = {2023}, author = {Liu, Z and Sun, M and Jin, C and Sun, X and Feng, F and Niu, X and Wang, B and Zhang, Y and Wang, J}, title = {Naringenin confers protection against experimental autoimmune encephalomyelitis through modulating the gut-brain axis: A multi-omics analysis.}, journal = {The Journal of nutritional biochemistry}, volume = {}, number = {}, pages = {109448}, doi = {10.1016/j.jnutbio.2023.109448}, pmid = {37741298}, issn = {1873-4847}, abstract = {Multiple sclerosis (MS) is a disease of the central nervous system that involves the immune system attacking the protective covering of nerve fibers. This disease can be influenced by both environmental and genetic factors. Evidence has highlighted the critical role of the intestinal microbiota in MS and its animal model, experimental autoimmune encephalomyelitis (EAE). The composition of gut microflora is mainly determined by dietary components, which, in turn, modulate host homeostasis. A diet rich in naringenin at 0.5% can effectively mitigate the severity of EAE in mice. However, there is little direct data on the impact of naringenin at optimal doses on EAE development, as well as its intestinal microbiota and metabolites. Our study revealed that 2.0% naringenin resulted in the lowest clinical score and pathological changes in EAE mice, and altered the gene expression profiles associated with inflammation and immunity in spinal cord tissue. We then used untargeted metabolomics and 16S rRNA gene sequence to identify metabolites and intestinal microbiota, respectively. Naringenin supplementation enriched gut microbiota in EAE mice, including increasing the abundance of Paraprevotellaceae and Comamonadaceae, while decreasing the abundance of Deltaproteobacteria, RF39, and Desulfovibrionaceae. Furthermore, the changes in gut microbiota affected the production of metabolites in the feces and brain, suggesting a role in regulating the gut-brain axis. Finally, we conducted a fecal transplantation experiment to validate that gut microbiota partly mediates the effect of naringenin on EAE alleviation. In conclusion, naringenin has potential immunomodulatory effects that are influenced to some extent by the gut microbiome.}, }
@article {pmid37741254, year = {2023}, author = {Gao, C and Ni, B and Lu, X and Guo, C and Wei, G}, title = {An integrated investigation of 16S rRNA gene sequencing and proteomics to elucidate the mechanism of Corydalis bungeana Turcz. on dextran sulfate sodium-induced colitis.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {167}, number = {}, pages = {115550}, doi = {10.1016/j.biopha.2023.115550}, pmid = {37741254}, issn = {1950-6007}, abstract = {Corydalis bungeana Turcz. (CBT) is frequently used to treat inflammatory illnesses, the mechanisms underlying its use to ulcerative colitis (UC) remain unclear. A dextran sulfate sodium (DSS)-induced UC mice model was established. The disease activity index (DAI), colonic length, histological inspection by hematoxylin-eosin staining, the cytokines levels in the colon, proteomics and intestinal flora in mice were investigated to evaluate the effect of CBT. The results showed that CBT can significantly reduce the DAI, increase the length of colon, improve the pathological injury of colon tissue, decrease the level of TNF-α, IL-6, IL-1β and increase the level of IL-10 in UC mice. Gut microbe sequencing showed that CBT could enhance the abundance of the intestinal microbiome, decrease possibly harmful bacteria and promote potentially helpful microbes. Proteomics investigation showed that 20 overlapping differentially expressed proteins (DEPs) were discovered in the control, model, and CBT administration groups. The DEPs in the CBT administration group were connected to biological procedures mainly involving detoxification. Extracellular matrix (ECM) receptor-associated proteins such as Col6a1 and CD36 may be important targets for CBT treatment of UC. Overall, this integrated methodology identified a comprehensive multi-omics network, composed of a certain set of gut microbiota and proteins, which may be potential targets for CBT treatment with UC.}, }
@article {pmid37741201, year = {2023}, author = {Haight, PJ and Kistenfeger, Q and Riedinger, CJ and Khadraoui, W and Backes, FJ and Bixel, KL and Copeland, LJ and Cohn, DE and Cosgrove, CM and O'Malley, DM and Nagel, CI and Spakowicz, DJ and Chambers, LM}, title = {The impact of antibiotic and proton pump inhibitor use at the time of adjuvant platinum-based chemotherapy on survival in patients with endometrial cancer.}, journal = {Gynecologic oncology}, volume = {178}, number = {}, pages = {14-22}, doi = {10.1016/j.ygyno.2023.09.005}, pmid = {37741201}, issn = {1095-6859}, abstract = {OBJECTIVE: We sought to assess the impact of antibiotic (ABX) and proton-pump inhibitor (PPI) use on progression-free (PFS) and overall survival (OS) in patients treated with adjuvant platinum-based chemotherapy (PC) for endometrial cancer (EC).<br><br>METHODS: A retrospective, single-institution cohort study of EC patients treated with &#x2265;four cycles of adjuvant PC following surgical staging from 2014 to 2020. Demographics and clinicopathologic features, including ABX and PPI use, were compared using &#x3c7;[2] and Fisher's exact tests. Univariate and multivariable analyses were performed, and survival outcomes were compared using the log-rank test.<br><br>RESULTS: Of 325 patients, 95 (29%) received ABX, and 80 (24.6%) received PPI. ABX were associated with decreased 3-year PFS (49.9% vs. 66%; p&#xa0;=&#xa0;0.0237) but not 3-year OS (68.9% vs. 79.9%; p&#xa0;=&#xa0;0.0649). ABX targeting gram-positive bacteria were associated with decreased 3-year PFS (21.2% vs. 66.0% vs. 55.4%; p&#xa0;=&#xa0;0.0038) and 3-year OS (36.5% vs. 79.9% vs. 75.6%; p&#xa0;=&#xa0;0.0014) compared to no ABX and other ABX, respectively. PPI use was associated with decreased 3-year PFS (46.9% vs. 66.0%; p&#xa0;=&#xa0;0.0001) and 3-year OS (60.7% vs. 81.9%; p&#xa0;=&#xa0;0.0041) compared to no PPI. On multivariable regression analysis controlling for confounders including stage, histology, grade, radiation, and co-morbidities, PPI use was independently associated with worse PFS (HR 1.96, 95% CI 1.25-3.08; p&#xa0;=&#xa0;0.0041) and OS (HR 2.06, 95% CI 1.01-4.18, p&#xa0;=&#xa0;0.04).<br><br>CONCLUSION: In this retrospective cohort study, we demonstrate that PPI use is independently associated with worse PFS and OS in patients with EC treated with PC. ABX use was associated with worse PFS on univariate analysis only. There is an unmet need to understand how PPI, ABX, and, potentially, the microbiome impact the effectiveness of chemotherapy in EC patients.}, }
@article {pmid37740880, year = {2023}, author = {Sagada, G and Wang, L and Xu, B and Sun, Y and Shao, Q}, title = {Interactive Effect of Dietary Heat-Killed Lactobacillus Plantarum L-137 and Berberine Supplementation on Intestinal Mucosa and Microbiota of Juvenile Black Sea Bream (Acanthopagrus Schlegelii).}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {37740880}, issn = {1867-1314}, support = {2020YFD0900801//Ministry of Science and Technology of the People's Republic of China/ ; 2015C02020//Zhejiang Provincial Bureau of Science and Technology/ ; }, abstract = {To compare the synergistic impact of dietary heat-killed Lactobacillus plantarum and berberine supplementation on intestinal health of juvenile black sea bream, the test fish (5.67 ± 0.05 g) were fed three diets: a basal control diet designated as Con; basal diet supplemented with 400 mg/kg L. plantarum, labelled LP; and basal diet supplemented with 400 mg/kg L. plantarum + 50 mg/k berberine, labelled LPBB. After 56 days of feeding, the control fish had significantly lower intestinal villus height (VH), villus surface area (VSA), and muscularis mucosae (MS) thickness than the rest of the groups (P < 0.05). The LPBB fish had significantly higher VH than the control fish, and wider MS and VSA than the rest of the groups (P < 0.05). Occludin was significantly upregulated in the LPBB fish, and heat shock protein 90 was upregulated in the control fish (P < 0.05). The abundance of Proteobacteria family was significantly higher in the intestinal microbiome of the control and LP fish, the LPBB fish had higher abundance of Cyanobacteria and Spirochaetes, and the LP group had higher Bacteroidetes abundance (P < 0.05). Potentially beneficial Delftia and Brevinema were the significantly abundant genera in the LP and LPBB fish, respectively; potentially pathogenic Elizabethkingia was abundant in the LP fish; and the control fish had higher abundance of potentially pathogenic Burkholderia-Caballeronia-Paraburkholderia (P < 0.05). According to these results, there is possible synergy between L. plantarum and berberine as dietary supplements in fostering healthy intestine for black sea bream than L. plantarum alone.}, }
@article {pmid37740532, year = {2023}, author = {}, title = {Correction to: The microbiome of the sponge Aplysina caissara in two sites with different levels of anthropogenic impact.}, journal = {FEMS microbiology letters}, volume = {370}, number = {}, pages = {}, doi = {10.1093/femsle/fnad094}, pmid = {37740532}, issn = {1574-6968}, }
@article {pmid37740322, year = {2023}, author = {Zanardi, KR and Grancieri, M and Silva, CW and Trivillin, LO and Viana, ML and Costa, AGV and Costa, NMB}, title = {Functional effects of yacon (Smallanthus sonchifolius) and kefir on systemic inflammation, antioxidant activity, and intestinal microbiome in rats with induced colorectal cancer.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d3fo02599c}, pmid = {37740322}, issn = {2042-650X}, abstract = {Colorectal cancer (CRC) is one of the most common cancers with high morbidity and mortality. The modulation of intestinal health through the administration of pro- and prebiotics may be a viable alternative to reduce the risk of CRC. This study aimed to evaluate the functional effects of yacon and kefir, isolated or associated, in rats with colorectal cancer. Adult Wistar rats were divided into five groups (n = 8): HC (healthy control AIN-93M diet), CC (CCR + AIN-93M diet), Y (CCR + AIN-93 M + yacon diet), K (CCR + AIN-93-M + kefir diet) and YK (CCR + AIN-93 M + yacon + kefir diet). Colorectal carcinogenesis was induced in groups CC, Y, K, and YK with 1,2-dimethylhydrazine (55 mg kg[-1], subcutaneously) for 5 weeks. From the 6[th] week onwards, the experimental groups were fed the respective diets. In the 15[th] week, urine was collected for analysis of intestinal permeability and then the animals were euthanized. Yacon increased acetate levels, reduced pH and carcinogenic neoplastic lesions, and increased the abundance of bacteria related to the fermentation of non-digestible carbohydrates, such as the genera Dorea, Collinsela, and Bifidobacteria. On the other hand, kefir increased macroscopic neoplastic lesions and increased the abundance of Firmicutes and Clostridium. The association of yacon + kefir increased the number of carcinogenic lesions, despite a reduction in pH and beneficial bacteria prevalence. Thus, it is concluded that yacon, unlikely kefir, is a promising alternative to mitigate the manifestations of induced carcinogenesis in rats.}, }
@article {pmid37740056, year = {2023}, author = {Acuña, AM and Olive, MF}, title = {Influence of gut microbiome metabolites on cocaine demand and cocaine-seeking behavior.}, journal = {Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology}, volume = {}, number = {}, pages = {}, pmid = {37740056}, issn = {1740-634X}, support = {AA025590//U.S. Department of Health &amp; Human Services | NIH | National Institute on Alcohol Abuse and Alcoholism (NIAAA)/ ; AA030061//U.S. Department of Health &amp; Human Services | NIH | National Institute on Alcohol Abuse and Alcoholism (NIAAA)/ ; DA043172//U.S. Department of Health &amp; Human Services | NIH | National Institute on Drug Abuse (NIDA)/ ; DA055153//U.S. Department of Health &amp; Human Services | NIH | National Institute on Drug Abuse (NIDA)/ ; }, }
@article {pmid37739940, year = {2023}, author = {Bao, Y and Ma, Y and Liu, W and Li, X and Li, Y and Zhou, P and Feng, Y and Delgado-Baquerizo, M}, title = {Innovative strategy for the conservation of a millennial mausoleum from biodeterioration through artificial light management.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {69}, pmid = {37739940}, issn = {2055-5008}, support = {42177297//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42207365//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Carbon ; Light ; *Microbiota ; Nitrogen ; }, abstract = {Artificial lights can cause critical microbial biodeterioration of heritage monuments by promoting the outbreak of phototrophic microbiomes when they are used for touristic viewing. Here, with the ultimate aim of providing innovative solutions for the conservation and visiting of such monuments, we conducted a pioneering two-year in situ manipulative experiment to evaluate the impacts of different artificial light wavelengths (i.e., blue, green and red lights compared to white light) on the phototrophic microbiome of a millennial Chinese imperial mausoleum. Our results show that artificial light can shape the ecophysiological features of the phototrophic bacteriome in this monument and reduce its potential for further biodeterioration. In general, Cyanobacteria dominated (42.0% of the total relative abundance) the phototrophic bacteriome of this cultural relic; however, they were also very sensitive to the choice of artificial light. Compared to white light, monochromatic light, especially green light, reduced Cyanobacteria abundances (18.6%) by decreasing photosynthetic pigment abundances (42.9%); decreased the abundances of heterotrophic species belonging to Proteobacteria (4.5%) and the proportion of genes (6.1%) associated with carbon (i.e., carbon fixation), nitrogen (i.e., denitrification), and sulfur (i.e., dissimilatory sulfate reduction) cycling; and further decreased organic acid (10.1-14.1%) production of the phototrophic bacteriome, which is known to be involved in biodeterioration. Taken together, our findings constitute a major advancement in understanding how light wavelengths influence the phototrophic microbiome in cultural relics, and we found that artificial lights with certain wavelengths (e.g., green light) can help long-term conservation while allowing tourism activities.}, }
@article {pmid37739710, year = {2023}, author = {Kabir, MH and Rahman, SA and Kamruzzaman, M}, title = {General and abdominal obesity and dietary nutrient intake among university students in Bangladesh: A cross-sectional study targeting potential risk factors.}, journal = {Clinical nutrition ESPEN}, volume = {57}, number = {}, pages = {587-597}, doi = {10.1016/j.clnesp.2023.08.006}, pmid = {37739710}, issn = {2405-4577}, mesh = {Infant, Newborn ; Female ; Male ; Pregnancy ; Humans ; Young Adult ; Adult ; Obesity, Abdominal/epidemiology ; Cross-Sectional Studies ; Overweight/epidemiology ; Bangladesh/epidemiology ; *Diabetes, Gestational ; Retrospective Studies ; Universities ; *Premature Birth ; Obesity/epidemiology ; Eating ; Risk Factors ; Nutrients ; }, abstract = {BACKGROUND &amp; AIMS: The overall national increase in the prevalence of overweight and obesity has emerged among university students in Bangladesh. Though, poor dietary habits and lifestyle is quite common among university students, their dietary nutrient intake level, obesity prevalence and potential risk factors has hitherto given little priority. This study aimed to understand the prevalence and factors associated with general and abdominal obesity and level of dietary nutrient intake among university students in Bangladesh.<br><br>METHODS: Data from 320 unselected tertiary level students (81.6% males, 18.4% females; average age 22.7&#xb1;3.0, BMI 22.4&#xb1;3.1 and waist-hip ratio (WHR) 0.88&#xa0;&#xb1;&#xa0;0.1) was collected randomly, in a single visit, from Islamic University, Kushtia, Bangladesh. Basic demographic and anthropometric information were collected. Twenty-four hour (24H) dietary recall and food frequency questionnaire (FFQ) was used to collect dietary nutrient level retrospectively. Descriptive statistics, chi-square test, t-test, ANOVA, and binomial logistic regression analysis were done.<br><br>RESULTS: Around 3% and 42% student were reported to be obese and overweight respectively. Whereas abdominal obesity was prevalent among &#x223c;52% and more than 67% of student were reportedly obese/overweight by either BMI or WHR or WHtR category. Energy and carbohydrate (CHO) intake were reported to be significantly higher (P&#xa0;<&#xa0;0.05) among overweight who born by C-section delivery and were fed formula milk than those were normal weight and born by vaginal-birth and were breastfed. The overweight individual with a history of preterm birth was reported to intake significantly higher (P&#xa0;<&#xa0;0.05) carbohydrates compared to normal-weight individuals with a history of term birth. While total fat intake was significantly higher (P&#xa0;<&#xa0;0.05) among overweight individuals with their mother had gestational diabetes than those with normal weight individuals with mother without gestational diabetes.<br><br>CONCLUSIONS: General and abdominal obesity is common among university students and possibly associated with mode of birth, gestational duration, gestational diabetes, and breastfeeding practice.}, }
@article {pmid37739225, year = {2023}, author = {Patel, PA and Teherani, MF and Xiang, Y and Bernardo, V and Chandrakasan, S and Goggin, KP and Haight, A and Horwitz, E and Liang, WH and Parikh, SH and Schoettler, ML and Spencer, K and Stenger, E and Watkins, B and Williams, KM and Leung, K and Jaggi, P and Qayed, M}, title = {Short-course empiric antibiotics in children undergoing allogeneic hematopoietic cell transplant.}, journal = {Transplantation and cellular therapy}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtct.2023.09.011}, pmid = {37739225}, issn = {2666-6367}, abstract = {BACKGROUND: Fever is common in children undergoing hematopoietic cell transplant (HCT). Empiric antibiotics (EA) are initiated and often continued until neutrophil engraftment. Prolonged antibiotic exposure reduces microbiome diversity and causes overgrowth of pathogenic organisms, leading to complications such as infections from antibiotic-resistant organisms and Clostridium difficile colitis. Shorter courses of EA have been studied in adults undergoing HCT without significant safety concerns but data in children are lacking.<br><br>OBJECTIVE: We instituted a single-center pre-/post-intervention quality improvement (QI) project to assess the feasibility of short-course EA for first fever in patients undergoing HCT. We aimed to reduce the median duration of broad-spectrum antibiotic use in eligible patients from 20 days in 2020 to 10 days in 2021.<br><br>METHODS: Patients were eligible for the intervention, limiting EA to 7 days for first fever, if admitted for their first allogeneic HCT, afebrile for >24 hours, had no infection requiring systemic treatment, and were hemodynamically stable. Outcome measures included days of EA for first fever and total broad-spectrum antibiotic use during the hospitalization period, defined as the start of the conditioning regimen to 30 days after HCT or hospital discharge, whichever occurred first. Balancing measures included bloodstream infection (BSI), fever, and ICU admission within 3 days of stopping EAT. Project criteria were applied retrospectively to patients transplanted in 2020 to construct a pre-intervention short-course eligible cohort.<br><br>RESULTS: During the intervention period, 41 patients underwent allogeneic HCT with 17 (41%) eligible for short-course EA. Among eligible patients, the median age was 5.3 years, 47% had an underlying malignancy, and 88% received myeloablative conditioning. There were no differences in demographics or HCT characteristics between patients eligible for short-course EA during the intervention and pre-intervention period (n=24). Short-course EA was adhered to in 14 of the 17 eligible patients (82%). The duration of EA for first fever and total broad-spectrum antibiotic use significantly decreased in the short-course EA eligible patients compared to the pre-intervention cohort from a median of 17 days to 8 days and 20 days to 10 days respectively (p<0.01). Of the 14 patients adhering to short-course EA, 2 experienced a balancing measure of recurrent fever requiring resumption of EA, but no infection was identified. There were no BSIs, ICU admissions, or deaths during the hospitalization period in patients who underwent short-course EA.<br><br>CONCLUSIONS: In this single-center QI project, short-course EA for initial fever was successfully applied to children undergoing allogeneic HCT using strict criteria and led to a significant decrease in broad-spectrum antibiotic use during hospitalization. These results should be validated in a prospective clinical trial to include the impact of short-course EA on antibiotic-resistant organisms, the intestinal microbiome and HCT outcomes.}, }
@article {pmid37739156, year = {2023}, author = {Du, L and Gao, X and Zhao, L and Zhu, X and Wang, L and Zhang, K and Li, D and Ji, J and Luo, J and Cui, J}, title = {Assessment of the risk of imidaclothiz to the dominant aphid parasitoid Binodoxys communis (Hymenoptera: Braconidae).}, journal = {Environmental research}, volume = {}, number = {}, pages = {117165}, doi = {10.1016/j.envres.2023.117165}, pmid = {37739156}, issn = {1096-0953}, abstract = {The neonicotinoid of imidaclothiz insecticide with low resistance and high efficiency, has great potential for application in pest control in specifically cotton field. In this systematically evaluate the effects of sublethal doses of imidaclothiz (LC10: 11.48 mg/L; LC30: 28.03 mg/L) on the biology, transcriptome, and microbiome of Binodoxys communis, the predominant primary parasitic natural enemy of aphids. The findings indicated that imidaclothiz has significant deleterious effects on the survival rate, parasitic rate, and survival time of B. communis. Additionally, there was a marked reduction in the survival rate and survival time of the F1 generation, that is, the negative effect of imidaclothiz on B. communis was continuous and trans-generational. Transcriptome analysis revealed that imidaclothiz treatment elicited alterations in the expression of genes associated with energy and detoxification metabolism. In addition, 16S rRNA analysis revealed a significant increase in the relative abundance of Rhodococcus and Pantoea, which are associated with detoxification metabolism, due to imidaclothiz exposure. These findings provide evidence that B. communis may regulate gene expression in conjunction with symbiotic bacteria to enhance adaptation to imidaclothiz. Finally, this study precise evaluation of imidaclothiz's potential risk to B. communis and provides crucial theoretical support for increasing the assessment of imidaclothiz in integrated pest management.}, }
@article {pmid37739152, year = {2023}, author = {Gao, X and Hu, F and Cui, H and Zhu, X and Wang, L and Zhang, K and Li, D and Ji, J and Luo, J and Cui, J}, title = {Glyphosate decreases survival, increases fecundity, and alters the microbiome of the natural predator Harmonia axyridis (ladybird beetle).}, journal = {Environmental research}, volume = {}, number = {}, pages = {117174}, doi = {10.1016/j.envres.2023.117174}, pmid = {37739152}, issn = {1096-0953}, abstract = {Glyphosate is a widely-used herbicide that shows toxicity to non-target organisms. The predatory natural enemy Harmonia axyridis may ingest glyphosate present in pollen and aphid prey. The present study characterized the responses of adult H. axyridis to environmentally relevant concentrations of glyphosate (5, 10, and 20 mg/L) for one or five days. There were no obvious effects on adult H. axyridis survival rates or fecundity in response to 5 or 10 mg/L glyphosate. However, exposure to 20 mg/L glyphosate significantly reduced the survival rate and increased fecundity. Analysis of the adult H. axyridis microbiota with 16S rRNA sequencing demonstrated changes in the relative and/or total abundance of specific taxa, including Serratia, Enterobacter, Staphylococcus, and Hafnia-Obesumbacterium. These changes in symbiotic bacterial abundance may have led to changes in survival rates or fecundity of this beetle. This is the first report of herbicide-induced stimulation of fecundity in a non-target predatory natural enemy, reflecting potentially unexpected risks of glyphosate exposure in adult H. axyridis. Although glyphosate resistant crops have been widely planted, the results of this study indicate a need to strengthen glyphosate management to prevent over-use, which could cause glyphosate toxicity and threaten environmental and human health.}, }
@article {pmid37738628, year = {2023}, author = {Prajapati, SK and Shah, R and Alford, N and Mishra, SP and Jain, S and Hansen, B and Sanburg, P and Molina, AJA and Yadav, H}, title = {The Triple Alliance: Microbiome, Mitochondria, and Metabolites in the Context of Age-Related Cognitive Decline and Alzheimer's Disease.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {}, number = {}, pages = {}, doi = {10.1093/gerona/glad226}, pmid = {37738628}, issn = {1758-535X}, abstract = {Alzheimer's disease (AD) is a progressive, age-related neurodegenerative disorder that affects a large proportion of the elderly population. It currently lacks effective treatments, placing a heavy burden on patients, families, healthcare systems, and society. This is mainly due to our limited comprehension of the pathophysiology of AD progression, as well as the lack of effective drug targets and intervention timing to address the underlying pathology. AD is a multifactorial condition, and emerging evidence suggests that abnormalities in the gut microbiota play a significant role as environmental and multifaceted contributors to AD, although the exact mechanisms are yet to be fully explored. Changes in the composition of microbiota influence host neuronal health through their metabolites. These metabolites regulate intestinal epithelia, blood-brain barrier (BBB) permeability and neuroinflammation by impacting mitochondrial function. The decline in the proportion of beneficial microbes and their essential metabolites during aging and AD is directly linked to poor mitochondrial function, although the specific mechanisms remain unclear. In this review, we discuss recent developments in understanding the impact of the microbiome and its metabolites on various cell types, their influence on the integrity of the gut and BBB barriers, systemic and brain inflammation, and cell-specific effects in AD pathology. This information is expected to pave the way for a new understanding of the interactions between microbiota and mitochondria in AD, providing a foundation for the development of novel treatments for AD.}, }
@article {pmid37738402, year = {2023}, author = {Cho, H and Qu, Y and Liu, C and Tang, B and Lyu, R and Lin, BM and Roach, J and Azcarate-Peril, MA and Aguiar Ribeiro, A and Love, MI and Divaris, K and Wu, D}, title = {Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {5}, pages = {}, pmid = {37738402}, issn = {1477-4054}, support = {R03 DE028983/DE/NIDCR NIH HHS/United States ; U01 DE025046/DE/NIDCR NIH HHS/United States ; }, mesh = {Child ; Humans ; Child, Preschool ; *Benchmarking ; Biofilms ; Computer Simulation ; Lactic Acid ; *Stomatognathic Diseases ; }, abstract = {Understanding the function of the human microbiome is important but the development of statistical methods specifically for the microbial gene expression (i.e. metatranscriptomics) is in its infancy. Many currently employed differential expression analysis methods have been designed for different data types and have not been evaluated in metatranscriptomics settings. To address this gap, we undertook a comprehensive evaluation and benchmarking of 10 differential analysis methods for metatranscriptomics data. We used a combination of real and simulated data to evaluate performance (i.e. type I error, false discovery rate and sensitivity) of the following methods: log-normal (LN), logistic-beta (LB), MAST, DESeq2, metagenomeSeq, ANCOM-BC, LEfSe, ALDEx2, Kruskal-Wallis and two-part Kruskal-Wallis. The simulation was informed by supragingival biofilm microbiome data from 300 preschool-age children enrolled in a study of childhood dental disease (early childhood caries, ECC), whereas validations were sought in two additional datasets from the ECC study and an inflammatory bowel disease study. The LB test showed the highest sensitivity in both small and large samples and reasonably controlled type I error. Contrarily, MAST was hampered by inflated type I error. Upon application of the LN and LB tests in the ECC study, we found that genes C8PHV7 and C8PEV7, harbored by the lactate-producing Campylobacter gracilis, had the strongest association with childhood dental disease. This comprehensive model evaluation offers practical guidance for selection of appropriate methods for rigorous analyses of differential expression in metatranscriptomics. Selection of an optimal method increases the possibility of detecting true signals while minimizing the chance of claiming false ones.}, }
@article {pmid37744088, year = {2021}, author = {Gerke, J and Köhler, AM and Wennrich, JP and Große, V and Shao, L and Heinrich, AK and Bode, HB and Chen, W and Surup, F and Braus, GH}, title = {Biosynthesis of Antibacterial Iron-Chelating Tropolones in Aspergillus nidulans as Response to Glycopeptide-Producing Streptomycetes.}, journal = {Frontiers in fungal biology}, volume = {2}, number = {}, pages = {777474}, pmid = {37744088}, issn = {2673-6128}, abstract = {The soil microbiome comprises numerous filamentous fungi and bacteria that mutually react and challenge each other by the production of bioactive secondary metabolites. Herein, we show in liquid co-cultures that the presence of filamentous Streptomycetes producing antifungal glycopeptide antibiotics induces the production of the antibacterial and iron-chelating tropolones anhydrosepedonin (1) and antibiotic C (2) in the mold Aspergillus nidulans. Additionally, the biosynthesis of the related polyketide tripyrnidone (5) was induced, whose novel tricyclic scaffold we elucidated by NMR and HRESIMS data. The corresponding biosynthetic polyketide synthase-encoding gene cluster responsible for the production of these compounds was identified. The tropolones as well as tripyrnidone (5) are produced by genes that belong to the broad reservoir of the fungal genome for the synthesis of different secondary metabolites, which are usually silenced under standard laboratory conditions. These molecules might be part of the bacterium-fungus competition in the complex soil environment, with the bacterial glycopeptide antibiotic as specific environmental trigger for fungal induction of this cluster.}, }
@article {pmid37738222, year = {2023}, author = {Price, JT and McLachlan, RH and Jury, CP and Toonen, RJ and Wilkins, MJ and Grottoli, AG}, title = {Long-term coral microbial community acclimatization is associated with coral survival in a changing climate.}, journal = {PloS one}, volume = {18}, number = {9}, pages = {e0291503}, pmid = {37738222}, issn = {1932-6203}, abstract = {The plasticity of some coral-associated microbial communities under stressors like warming and ocean acidification suggests the microbiome has a role in the acclimatization of corals to future ocean conditions. Here, we evaluated the acclimatization potential of coral-associated microbial communities of four Hawaiian coral species (Porites compressa, Porites lobata, Montipora capitata, and Pocillopora acuta) over 22-month mesocosm experiment. The corals were exposed to one of four treatments: control, ocean acidification, ocean warming, or combined future ocean conditions. Over the 22-month study, 33-67% of corals died or experienced a loss of most live tissue coverage in the ocean warming and future ocean treatments while only 0-10% died in the ocean acidification and control. Among the survivors, coral-associated microbial communities responded to the chronic future ocean treatment in one of two ways: (1) microbial communities differed between the control and future ocean treatment, suggesting the potential capacity for acclimatization, or (2) microbial communities did not significantly differ between the control and future ocean treatment. The first strategy was observed in both Porites species and was associated with higher survivorship compared to M. capitata and P. acuta which exhibited the second strategy. Interestingly, the microbial community responses to chronic stressors were independent of coral physiology. These findings indicate acclimatization of microbial communities may confer resilience in some species of corals to chronic warming associated with climate change. However, M. capitata genets that survived the future ocean treatment hosted significantly different microbial communities from those that died, suggesting the microbial communities of the survivors conferred some resilience. Thus, even among coral species with inflexible microbial communities, some individuals may already be tolerant to future ocean conditions. These findings suggest that coral-associated microbial communities could play an important role in the persistence of some corals and underlie climate change-driven shifts in coral community composition.}, }
@article {pmid37737900, year = {2023}, author = {Suarez Arbelaez, MC and Monshine, J and Porto, JG and Shah, K and Singh, PK and Roy, S and Amin, K and Marcovich, R and Herrmann, TRW and Shah, HN}, title = {The emerging role of the urinary microbiome in benign noninfectious urological conditions: an up-to-date systematic review.}, journal = {World journal of urology}, volume = {}, number = {}, pages = {}, pmid = {37737900}, issn = {1433-8726}, abstract = {PURPOSE: The goal of this systematic review was to examine the current literature on the urinary microbiome and its associations with noninfectious, nonmalignant, urologic diseases. Secondarily, we aimed to describe the most common bioinformatics used to analyze the urinary microbiome.<br><br>METHODS: A comprehensive literature search of Ovid MEDLINE using the keywords "microbiota" AND "prostatic hyperplasia," "microbiota" AND "urinary bladder, overactive," "microbiota" AND "pelvic pain," and "microbiota" AND "urolithiasis" OR "nephrolithiasis" OR "urinary calculi" AND "calcium oxalate" was performed to identify relevant clinical microbiome studies associated with noninfectious benign urological conditions published from 2010 to 2022. We included human studies that evaluated the urinary, stone, or semen microbiota, or any combination of the above-mentioned locations.<br><br>RESULTS: A total of 25 human studies met the inclusion criteria: 4 on benign prostatic hyperplasia (BPH), 9 on overactive bladder (OAB), 8 on calcium oxalate stones, and 4 on chronic pelvic pain syndrome (CPPS). Specific taxonomic profiles in the urine microbiome were associated with each pathology, and evaluation of alpha- and beta-diversity and relative abundance was accounted for most of the studies. Symptom prevalence and severity were also analyzed and showed associations with specific microbes.<br><br>CONCLUSION: The study of the urogenital microbiome is rapidly expanding in urology. Noninfectious benign urogenital diseases, such as BPH, calcium oxalate stones, CPPS, and OAB were found to be associated with specific microbial taxonomies. Further research with larger study populations is necessary to solidify the knowledge of the urine microbiome in these conditions and to facilitate the creation of microbiome-based diagnostic and therapeutic approaches.}, }
@article {pmid37737730, year = {2023}, author = {Ahmad, AF and Caparrós-Martin, JA and Gray, N and Lodge, S and Wist, J and Lee, S and O'Gara, F and Shah, A and Ward, NC and Dwivedi, G}, title = {Insights into the associations between the gut microbiome, its metabolites and heart failure.}, journal = {American journal of physiology. Heart and circulatory physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpheart.00436.2023}, pmid = {37737730}, issn = {1522-1539}, abstract = {Heart failure (HF) is the end stage of most cardiovascular diseases and remains a significant health problem globally. We aimed to assess whether patients with left ventricular ejection fraction ≤45% had alterations in both the gut microbiome profile and production of associated metabolites when compared to a healthy cohort. We also examined the associated inflammatory, metabolomic, and lipidomic profiles of HF patients. This single centre, observational study, recruited 73 HF patients and 59 healthy volunteers. Blood and stool samples were collected at baseline and 6-month follow-up, along with anthropometric and clinical data. Compared to healthy controls, HF patients had reduced gut bacterial alpha diversity at follow-up (p =0.004) but not at baseline. The stool microbiota of HF patients was characterized by a depletion of operational taxonomic units representing commensal Clostridia at both baseline and follow-up. HF patients also had significantly elevated baseline plasma acetate (p =0.007), plasma TMAO (p =0.003), serum sCD14 (p =0.005) and sCD163 (p =0.004) levels compared to healthy controls. Furthermore, HF patients had a distinct metabolomic and lipidomic profile at baseline when compared to healthy controls. Differences in the composition of the gut microbiome and the levels of associated metabolites were observed in patients with HF when compared to a healthy cohort. This was also associated with an altered metabolomic and lipidomic profile. Our study identifies microorganisms and metabolites that could represent new therapeutic targets and diagnostic tools in the pathogenesis of HF.}, }
@article {pmid37737631, year = {2023}, author = {Fanfan, D and Mulligan, CJ and Groer, M and Mai, V and Weaver, M and Huffman, F and Lyon, DE}, title = {The intersection of social determinants of health, the microbiome, and health outcomes in immigrants: A scoping review.}, journal = {American journal of biological anthropology}, volume = {}, number = {}, pages = {}, doi = {10.1002/ajpa.24850}, pmid = {37737631}, issn = {2692-7691}, support = {1K23NR020222-01A1/NR/NINR NIH HHS/United States ; }, abstract = {In the present scoping review, we explore whether existing evidence supports the premise that social determinants of health (SDoH) affect immigrant health outcomes through their effects on the microbiome. We adapt the National Institute on Minority Health and Health Disparities' research framework to propose a conceptual model that considers the intersection of SDoH, the microbiome, and health outcomes in immigrants. We use this conceptual model as a lens through which to explore recent research about SDoH, biological factors associated with changes to immigrants' microbiomes, and long-term health outcomes. In the 17 articles reviewed, dietary acculturation, physical activity, ethnicity, birthplace, age at migration and length of time in the host country, socioeconomic status, and social/linguistic acculturation were important determinants of postmigration microbiome-related transformations. These factors are associated with progressive shifts in microbiome profile with time in host country, increasing the risks for cardiometabolic, mental, immune, and inflammatory disorders and antibiotic resistance. The evidence thus supports the premise that SDoH influence immigrants' health postmigration, at least in part, through their effects on the microbiome. Omission of important postmigration social-ecological variables (e.g., stress, racism, social/family relationships, and environment), limited research among minoritized subgroups of immigrants, complexity and inter- and intra-individual differences in the microbiome, and limited interdisciplinary and biosocial collaboration restrict our understanding of this area of study. To identify potential microbiome-based interventions and promote immigrants' well-being, more research is necessary to understand the intersections of immigrant health with factors from the biological, behavioral/psychosocial, physical/built environment, and sociocultural environment domains at all social-ecological levels.}, }
@article {pmid37737617, year = {2023}, author = {London, LY and Lim, CH and Modliszewski, JL and Siddiqui, NY and Sysoeva, TA}, title = {Draft genomes of Lactobacillus delbrueckii and Klebsiella pneumoniae coexisting within a female urinary bladder.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0030523}, doi = {10.1128/MRA.00305-23}, pmid = {37737617}, issn = {2576-098X}, abstract = {Here, we present the draft genome sequences of Lactobacillus delbrueckii and Klebsiella pneumoniae, both isolated from the urinary bladder of an asymptomatic post-menopausal female patient with a diagnosis of recurrent urinary tract infections. These genomes will facilitate analyses of interbacterial interactions in the urinary microbiome.}, }
@article {pmid37737559, year = {2023}, author = {Effandie, E and Gupte, GL}, title = {Chronic Liver Disease - What's New?.}, journal = {Indian journal of pediatrics}, volume = {}, number = {}, pages = {}, pmid = {37737559}, issn = {0973-7693}, abstract = {Chronic liver disease (CLD) is a persistent public health burden, with over one billion cases reported worldwide. In most cases, the progression of CLD is slow and undulating with end-stage liver disease developing at variable time points depending on the underlying etiology of the disease. The concept of reversibility or halting progression to end stage liver disease is recent and various medications are in the pipeline which influence the progression of CLD. Non-invasive tests for monitoring of CLD may have the potential to avoid the morbidity and mortality related to invasive procedures. However, their applicability and validation in pediatrics requires further development and a coordinated effort by large pediatric liver centres. Recent advances in metabolomics and modern molecular technologies have led to an understanding of the interaction between gut microbiome liver axis and gut dysbiosis contributing to liver diseases. In the future, modifying the gut microbiome has the potential to change the outcome and significantly reduce the morbidity associated with CLD. This article focuses on newer modalities and concepts in the management of CLD, which may help develop strategies to prevent its progression to end-stage liver disease and associated morbidity/mortality.}, }
@article {pmid37737528, year = {2023}, author = {Kalayci, FNC and Ozen, S}, title = {Possible Role of Dysbiosis of the Gut Microbiome in SLE.}, journal = {Current rheumatology reports}, volume = {}, number = {}, pages = {}, pmid = {37737528}, issn = {1534-6307}, abstract = {PURPOSE OF REVIEW: The resident gut microbiota serves as a double-edged sword that aids the host in multiple ways to preserve a healthy equilibrium and serve as early companions and boosters for the gradual evolution of our immune defensive layers; nevertheless, the perturbation of the symbiotic resident intestinal communities has a profound impact on autoimmunity induction, particularly in systemic lupus erythematosus (SLE). Herein, we seek to critically evaluate the microbiome research in SLE with a focus on intestinal dysbiosis.<br><br>RECENT FINDINGS: SLE is a complex and heterogeneous disorder with self-attack due to loss of tolerance, and there is aberrant excessive immune system activation. There is mounting evidence suggesting that intestinal flora disturbances may accelerate the formation and progression of SLE, presumably through a variety of mechanisms, including intestinal barrier dysfunction and leaky gut, molecular mimicry, bystander activation, epitope spreading, gender bias, and biofilms. Gut microbiome plays a critical role in SLE pathogenesis, and additional studies are warranted to properly define the impact of gut microbiome in SLE, which can eventually lead to new and potentially safer management approaches for this debilitating disease.}, }
@article {pmid37737154, year = {2023}, author = {Luan, M and Niu, M and Yang, P and Han, D and Zhang, Y and Li, W and He, Q and Zhao, Y and Mao, B and Chen, J and Mou, K and Li, P}, title = {Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {265}, pmid = {37737154}, issn = {1471-2180}, support = {2020QN-31//Institutional Foundation of The First Affiliated Hospital of Xi'an Jiaotong University/ ; 2022SF-248//the Science and Technology Research and Development Program of Shaanxi Province of China/ ; 81972935//National Natural Sciences Foundation of China/ ; 2023-JC-YB-665//the Natural Science Basis Research Plan in Shaanxi Province of China/ ; }, abstract = {BACKGROUND: Vitiligo has been correlated with an abnormal gut microbiota. We aimed to systematically identify characteristics of the gut microbial compositions, genetic functions, and potential metabolic features in patients with non-segmental vitiligo.<br><br>METHODS: Twenty-five patients with non-segmental vitiligo and 25 matched healthy controls (HCs) were enrolled. Metagenomic sequencing and bioinformatic analysis were performed to determine the gut microbiota profiles. Differences in gut microbiota diversity and composition between patients with vitiligo and HCs were analyzed. Gene functions and gut metabolic modules were predicted with the Kyoto Encyclopedia of Gene and Genomes (KEGG) and MetaCyc databases.<br><br>RESULTS: Compared with HCs, alpha diversity of intestinal microbiome in vitiligo patients was significantly reduced. At the species level, the relative abundance of Staphylococcus thermophiles was decreased, and that of Bacteroides fragilis was increased in patients with vitiligo compared with those of the HCs. Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed representative microbial markers of Lachnospiraceae_bacterium_BX3, Massilioclostridium_coli, TM7_phylum_sp_oral_taxon_348 and Bacteroides_fragilis for patients with vitiligo. KEGG gene function analysis showed that the NOD-like receptor signaling pathway was significantly enriched in patients with vitiligo. Gut metabolic modules (GMMs) analysis showed that cysteine degradation was significantly down-regulated, and galactose degradation was up-regulated in patients with vitiligo. A panel of 28 microbial features was constructed to distinguish patients with vitiligo from HCs.<br><br>CONCLUSIONS: The gut microbial profiles and genetic functions of patients with vitiligo were distinct from those of the HCs. The identified gut microbial markers may potentially be used for earlier diagnosis and treatment targets.}, }
@article {pmid37737046, year = {2023}, author = {Lasagna, A and Mascaro, F and Figini, S and Basile, S and Gambini, G and Klersy, C and Lenti, MV and Di Sabatino, A and Di Benedetto, A and Calvi, M and Bruno, R and Sacchi, P and Pedrazzoli, P}, title = {Impact of proton pump inhibitors on the onset of gastrointestinal immune-related adverse events during immunotherapy.}, journal = {Cancer medicine}, volume = {}, number = {}, pages = {}, doi = {10.1002/cam4.6565}, pmid = {37737046}, issn = {2045-7634}, support = {Ricerca Corrente grant no 41087/2017//Fondazione IRCCS Policlinico San Matteo/ ; }, abstract = {INTRODUCTION: The gut microbiota (GM) can influence the pathogenesis of immune-mediated adverse events (irAEs). Proton pump inhibitors (PPIs) can affect the integrity of GM, but their role in promoting irAEs is still poorly understood.<br><br>METHODS: In this retrospective single-center cohort study, the primary endpoint was the evaluation of the incidence of gastrointestinal (GI) irAEs in cancer patients on PPIs (exposed) versus cancer patients who were not on PPIs (unexposed).<br><br>RESULTS: Three hundred and sixty three patients' records (248&#x2009;M/115F, median age 69) were reviewed. Twenty-three exposed patients (92%) developed GI irAEs while only two unexposed patients (8%) developed GI irAEs (hazard ratio [HR] 13.22, 95% confidence interval [CI] 3.11-56.10, p&#x2009;<&#x2009;0.000). This HR was confirmed after weighting for the propensity score (HR15.13 95% CI 3.22-71.03, p&#x2009;<&#x2009;0.000).<br><br>CONCLUSION: Chronic PPI use is associated with an increased risk of GI irAES.}, }
@article {pmid37737033, year = {2023}, author = {Moreno Jiménez, E and Ferrol, N and Corradi, N and Peñalosa, JM and Rillig, MC}, title = {The potential of arbuscular mycorrhizal fungi to enhance metallic micronutrient uptake and mitigate food contamination in agriculture: prospects and challenges.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19269}, pmid = {37737033}, issn = {1469-8137}, support = {//Alexander von Humboldt-Stiftung/ ; MCIN/AEI/ 10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n/ ; RGPAS-2020-00033//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN2020-05643//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Optimizing agroecosystems and crops for micronutrient uptake while reducing issues with inorganic contaminants (metal(loid)s) is a challenging task. One promising approach is to use arbuscular mycorrhizal fungi (AMF) and investigate the physiological, molecular and epigenetic changes that occur in their presence and that lead to changes in plant metal(loid) concentration (biofortification of micronutrients or mitigation of contaminants). Moreover, it is important to understand these mechanisms in the context of the soil microbiome, particularly those interactions of AMF with other soil microbes that can further shape crop nutrition. To address these challenges, a two-pronged approach is recommended: exploring molecular mechanisms and investigating microbiome management and engineering. Combining both approaches can lead to benefits in human health by balancing nutrition and contamination caused by metal(loid)s in the agro-ecosystem.}, }
@article {pmid37737029, year = {2023}, author = {Revillini, D and David, AS and Reyes, AL and Knecht, LD and Vigo, C and Allen, P and Searcy, CA and Afkhami, ME}, title = {Allelopathy-selected microbiomes mitigate chemical inhibition of plant performance.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19249}, pmid = {37737029}, issn = {1469-8137}, support = {DEB-1922521//National Science Foundation/ ; }, abstract = {Allelopathy is a common and important stressor that shapes plant communities and can alter soil microbiomes, yet little is known about the direct effects of allelochemical addition on bacterial and fungal communities or the potential for allelochemical-selected microbiomes to mediate plant performance responses, especially in habitats naturally structured by allelopathy. Here, we present the first community-wide investigation of microbial mediation of allelochemical effects on plant performance by testing how allelopathy affects soil microbiome structure and how these microbial changes impact germination and productivity across 13 plant species. The soil microbiome exhibited significant changes to 'core' bacterial and fungal taxa, bacterial composition, abundance of functionally important bacterial and fungal taxa, and predicted bacterial functional genes after the addition of the dominant allelochemical native to this habitat. Furthermore, plant performance was mediated by the allelochemical-selected microbiome, with allelopathic inhibition of plant productivity moderately mitigated by the microbiome. Through our findings, we present a potential framework to understand the strength of plant-microbial interactions in the presence of environmental stressors, in which frequency of the ecological stress may be a key predictor of microbiome-mediation strength.}, }
@article {pmid37737001, year = {2023}, author = {Bernadus, JBB and Pelealu, J and Kandou, GD and Pinaria, AG and Mamahit, JME and Tallei, TE}, title = {Metagenomic Insight into the Microbiome and Virome Associated with Aedes aegypti Mosquitoes in Manado (North Sulawesi, Indonesia).}, journal = {Infectious disease reports}, volume = {15}, number = {5}, pages = {549-563}, pmid = {37737001}, issn = {2036-7430}, abstract = {The aim of this study was to investigate the microbial diversity encompassing bacteria, fungi, and viruses within the composite microbial community associated with Aedes aegypti mosquitoes in Manado, Indonesia, using a whole-genome shotgun metagenomics approach. Female mosquitoes were collected and grouped into pools of 50 individuals, from which genomic DNA (gDNA) and RNA were extracted separately. Whole-genome shotgun metagenomics were performed on gDNA samples. The bioinformatics analysis encompassed quality assessment, taxonomic classification, and visualization. The evaluation of the microbial community entailed an assessment of taxa abundance and diversity using Kraken version 2.1.2. The study delineated the prevalence of dominant bacterial phyla, including Proteobacteria, with varying abundance of Firmicutes, Bacteroidota, and Actinobacteria, and notable occurrence of Tenericutes. Furthermore, the presence of the fungal phylum Ascomycota was also detected. Among the identified barcodes, Barcode04 emerged as the most abundant and diverse, while Barcode06 exhibited greater evenness. Barcode03, 05, and 07 displayed moderate richness and diversity. Through an analysis of the relative abundance, a spectrum of viruses within Ae. aegypti populations was unveiled, with Negarnaviricota constituting the most prevalent phylum, followed by Nucleocytoviricota, Uroviricota, Artverviricota, Kitrinoviricota, Peploviricota, Phixviricota, and Cossaviricota. The presence of Negarnaviricota viruses raises pertinent public health concerns. The presence of other viral phyla underscores the intricate nature of virus-mosquito interactions. The analysis of viral diversity provides valuable insights into the range of viruses carried by Ae. aegypti. The community exhibits low biodiversity, with a few dominant species significantly influencing its composition. This has implications for healthcare and ecological management, potentially simplifying control measures but also posing risks if the dominant species are harmful. This study enriches our comprehension of the microbiome and virome associated with Ae. aegypti mosquitoes, emphasizing the importance of further research to fully comprehend their ecological significance and impact on public health. The findings shed light on the microbial ecology of Ae. aegypti, offering potential insights into mosquito biology, disease transmission, and strategies for vector control. Future studies should endeavor to establish specific associations with Ae. aegypti, elucidate the functional roles of the identified microbial and viral species, and investigate their ecological implications.}, }
@article {pmid37736791, year = {2023}, author = {Nie, S and Ge, Y}, title = {The link between the gut microbiome, inflammation, and Parkinson's disease.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37736791}, issn = {1432-0614}, support = {SKLURE2022-1-3//State Key Laboratory of Urban and Regional Ecology/ ; }, abstract = {As our society ages, the growing number of people with Parkinson's disease (PD) puts tremendous pressure on our society. Currently, there is no effective treatment for PD, so there is an urgent need to find new treatment options. In recent years, increasing studies have shown a strong link between gut microbes and PD. In this review, recent advances in research on gut microbes in PD patients were summarized. Increased potential pro-inflammatory microbes and decreased potential anti-inflammatory microbes are prominent features of gut microbiota in PD patients. These changes may lead to an increase in pro-inflammatory substances (such as lipopolysaccharide and H2S) and a decrease in anti-inflammatory substances (such as short-chain fatty acids) to promote inflammation in the gut. This gut microbiota-mediated inflammation will lead to pathological α-synuclein accumulation in the gut, and the inflammation and α-synuclein can spread to the brain via the microbiota-gut-brain axis, thereby promoting neuroinflammation, apoptosis of dopaminergic neurons, and ultimately the development of PD. This review also showed that therapies based on gut microbiota may have a bright future for PD. However, more research and new approaches are still needed to clarify the causal relationship between gut microbes and PD and to determine whether therapies based on gut microbiota are effective in PD patients. KEY POINTS: • There is a strong association between gut microbes and PD. • Inflammation mediated by gut microbes may promote the development of PD. • Therapies based on the gut microbiome provide a promising strategy for PD prevention.}, }
@article {pmid37736613, year = {2023}, author = {Wu, L and Weston, LA and Zhu, S and Zhou, X}, title = {Editorial: Rhizosphere interactions: root exudates and the rhizosphere microbiome.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1281010}, pmid = {37736613}, issn = {1664-462X}, }
@article {pmid37736590, year = {2023}, author = {Kim, SH and Lee, SH}, title = {Updates on ankylosing spondylitis: pathogenesis and therapeutic agents.}, journal = {Journal of rheumatic diseases}, volume = {30}, number = {4}, pages = {220-233}, pmid = {37736590}, issn = {2233-4718}, abstract = {Ankylosing spondylitis (AS) is an autoinflammatory disease that manifests with the unique feature of enthesitis. Gut microbiota, HLA-B*27, and biomechanical stress mutually influence and interact resulting in setting off a flame of inflammation. In the HLA-B*27 positive group, dysbiosis in the gut environment disrupts the barrier to exogenous bacteria or viruses. Additionally, biomechanical stress induces inflammation through enthesial resident or gut-origin immune cells. On this basis, innate and adaptive immunity can propagate inflammation and lead to chronic disease. Finally, bone homeostasis is regulated by cytokines, by which the inflamed region is substituted into new bone. Agents that block cytokines are constantly being developed to provide diverse therapeutic options for preventing the progression of inflammation. In addition, some antibodies have been shown to distinguish disease selectively, which support the involvement of autoimmune immunity in AS. In this review, we critically analyze the complexity and uniqueness of the pathogenesis with updates on the findings of immunity and provide new information about biologics and biomarkers.}, }
@article {pmid37736390, year = {2023}, author = {Dweh, TJ and Pattnaik, S and Sahoo, JP}, title = {Assessing the impact of meta-genomic tools on current cutting-edge genome engineering and technology.}, journal = {International journal of biochemistry and molecular biology}, volume = {14}, number = {4}, pages = {62-75}, pmid = {37736390}, issn = {2152-4114}, abstract = {Metagenomics is defined as the study of the genome of the total microbiota found in nature and is often referred to as microbial environmental genomics because it entails the examination of a group of genetic components (genomes) from a diverse community of organisms in a particular setting. It is a sub-branch of omics technology that encompasses Deoxyribonucleic Acid (DNA), Ribonucleic acid (DNA), proteins, and various components associated with comprehensive analysis of all aspects of biological molecules in a system-wide manner. Clustered regularly interspaced palindromic repeats and its endonuclease, CRISPR-associated protein which forms a complex called CRISPR-cas9 technology, though it is a different technique used to make precise changes to the genome of an organism, it can be used in conjunction with metagenomic approaches to give a better, rapid, and more accurate description of genomes and sequence reads. There have been ongoing improvements in sequencing that have deepened our understanding of microbial genomes forever. From the time when only a small amount of gene could be sequenced using traditional methods (e.g., "the plus and minus" method developed by Allan and Sanger and the "chemical cleavage" method that is known for its use in the sequencing the phiX174 bacteriophage genome via radio-labeled DNA polymerase-primer in a polymerization reaction aided by polyacrylamide gel) to the era of total genomes sequencing which includes "sequencing-by-ligation" and the "sequencing-by-synthesis" that detects hydrogen ions when new DNA is synthesized (Second Generation) and then Next Generation Sequencing technologies (NGS). With these technologies, the Human Genome Project (HGP) was made possible. The study looks at recent advancements in metagenomics in plants and animals by examining findings from randomly selected research papers. All selected case studies examined the functional and taxonomical analysis of different microbial communities using high-throughput sequencing to generate different sequence reads. In animals, five studies indicated how Zebrafish, Livestock, Poultry, cattle, niches, and the human microbiome were exploited using environmental samples, such as soil and water, to identify microbial communities and their functions. It has also been used to study the microbiome of humans and other organisms, including gut microbiomes. Recent studies demonstrated how these technologies have allowed for faster and more accurate identification of pathogens, leading to improved disease diagnostics. They have also enabled the development of personalized medicine by allowing for the identification of genetic variations that can impact drug efficacy and toxicity. Continued advancements in sequencing techniques and the refinement of CRISPR-Cas9 tools offer even greater potential for transformative breakthroughs in scientific research and applications. On the other hand, metagenomic data are always large and uneasy to handle. The complexity of taxonomical profiling, functional annotation, and mechanisms of complex interaction still needs better bioinformatics tools. Current review focuses on better (e.g., AI-driven algorithms) tools that can predict metabolic pathways and interactions, and manipulate complex data to address potential bias for accurate interpretation.}, }
@article {pmid37736325, year = {2023}, author = {Hammond, TC and Green, SJ and Jacobs, Y and Chlipala, GE and Xing, X and Heil, S and Chen, A and Aware, C and Flemister, A and Stromberg, A and Balchandani, P and Lin, AL}, title = {Gut microbiome association with brain imaging markers, APOE genotype, calcium and vegetable intakes, and obesity in healthy aging adults.}, journal = {Frontiers in aging neuroscience}, volume = {15}, number = {}, pages = {1227203}, pmid = {37736325}, issn = {1663-4365}, abstract = {INTRODUCTION: Advanced age is a significant factor in changes to brain physiology and cognitive functions. Recent research has highlighted the critical role of the gut microbiome in modulating brain functions during aging, which can be influenced by various factors such as apolipoprotein E (APOE) genetic variance, body mass index (BMI), diabetes, and dietary intake. However, the associations between the gut microbiome and these factors, as well as brain structural, vascular, and metabolic imaging markers, have not been well explored.<br><br>METHODS: We recruited 30 community dwelling older adults between age 55-85 in Kentucky. We collected the medical history from the electronic health record as well as the Dietary Screener Questionnaire. We performed APOE genotyping with an oral swab, gut microbiome analysis using metagenomics sequencing, and brain structural, vascular, and metabolic imaging using MRI.<br><br>RESULTS: Individuals with APOE e2 and APOE e4 genotypes had distinct microbiota composition, and higher level of pro-inflammatory microbiota were associated higher BMI and diabetes. In contrast, calcium- and vegetable-rich diets were associated with microbiota that produced short chain fatty acids leading to an anti-inflammatory state. We also found that important gut microbial butyrate producers were correlated with the volume of the thalamus and corpus callosum, which are regions of the brain responsible for relaying and processing information. Additionally, putative proinflammatory species were negatively correlated with GABA production, an inhibitory neurotransmitter. Furthermore, we observed that the relative abundance of bacteria from the family Eggerthellaceae, equol producers, was correlated with white matter integrity in tracts connecting the brain regions related to language, memory, and learning.<br><br>DISCUSSION: These findings highlight the importance of gut microbiome association with brain health in aging population and could have important implications aimed at optimizing healthy brain aging through precision prebiotic, probiotic or dietary interventions.}, }
@article {pmid37736099, year = {2023}, author = {Schaft, N and Dörrie, J and Schuler, G and Schuler-Thurner, B and Sallam, H and Klein, S and Eisenberg, G and Frankenburg, S and Lotem, M and Khatib, A}, title = {The future of affordable cancer immunotherapy.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1248867}, pmid = {37736099}, issn = {1664-3224}, abstract = {The treatment of cancer was revolutionized within the last two decades by utilizing the mechanism of the immune system against malignant tissue in so-called cancer immunotherapy. Two main developments boosted cancer immunotherapy: 1) the use of checkpoint inhibitors, which are characterized by a relatively high response rate mainly in solid tumors; however, at the cost of serious side effects, and 2) the use of chimeric antigen receptor (CAR)-T cells, which were shown to be very efficient in the treatment of hematologic malignancies, but failed to show high clinical effectiveness in solid tumors until now. In addition, active immunization against individual tumors is emerging, and the first products have reached clinical approval. These new treatment options are very cost-intensive and are not financially compensated by health insurance in many countries. Hence, strategies must be developed to make cancer immunotherapy affordable and to improve the cost-benefit ratio. In this review, we discuss the following strategies: 1) to leverage the antigenicity of "cold tumors" with affordable reagents, 2) to use microbiome-based products as markers or therapeutics, 3) to apply measures that make adoptive cell therapy (ACT) cheaper, e.g., the use of off-the-shelf products, 4) to use immunotherapies that offer cheaper platforms, such as RNA- or peptide-based vaccines and vaccines that use shared or common antigens instead of highly personal antigens, 5) to use a small set of predictive biomarkers instead of the "sequence everything" approach, and 6) to explore affordable immunohistochemistry markers that may direct individual therapies.}, }
@article {pmid37735944, year = {2023}, author = {Farooq, MZ and Wang, X and Yan, X}, title = {Effects of Aeriscardovia aeriphila on growth performance, antioxidant functions, immune responses, and gut microbiota in broiler chickens.}, journal = {Journal of Zhejiang University. Science. B}, volume = {}, number = {}, pages = {1-13}, doi = {10.1631/jzus.B2200621}, pmid = {37735944}, issn = {1862-1783}, support = {31925037//the National Natural Science Foundation of China/ ; }, abstract = {Aeriscardovia aeriphila, also known as Bifidobacterium aerophilum, was first isolated from the caecal contents of pigs and the faeces of cotton-top tamarin. Bifidobacterium species play important roles in preventing intestinal infections, decreasing cholesterol levels, and stimulating the immune system. In this study, we isolated a strain of bacteria from the duodenal contents of broiler chickens, which was identified as A. aeriphila, and then evaluated the effects of A. aeriphila on growth performance, antioxidant functions, immune functions, and gut microbiota in commercial broiler chickens. Chickens were orally gavaged with A. aeriphila (1×10[9] CFU/mL) for 21 d. The results showed that A. aeriphila treatment significantly increased the average daily gain and reduced the feed conversion ratio (P<0.001). The levels of serum growth hormone (GH) and insulin-like growth factor 1 (IGF-1) were significantly increased following A. aeriphila treatment (P<0.05). Blood urea nitrogen and aspartate aminotransferase levels were decreased, whereas glucose and creatinine levels increased as a result of A. aeriphila treatment. Furthermore, the levels of serum antioxidant enzymes, including catalase (P<0.01), superoxide dismutase (P<0.001), and glutathione peroxidase (P<0.05), and total antioxidant capacity (P<0.05) were enhanced following A. aeriphila treatment. A. aeriphila treatment significantly increased the levels of serum immunoglobulin A (IgA) (P<0.05), IgG (P<0.01), IgM (P<0.05), interleukin-1 (IL-1) (P<0.05), IL-4 (P<0.05), and IL-10 (P<0.05). The broiler chickens in the A. aeriphila group had higher secretory IgA (SIgA) levels in the duodenum (P<0.01), jejunum (P<0.001), and cecum (P<0.001) than those in the control group. The messenger RNA (mRNA) relative expression levels of IL-10 (P<0.05) and IL-4 (P<0.001) in the intestinal mucosa of chickens were increased, while nuclear factor-‍κB (NF‍-‍κB) (P<0.001) expression was decreased in the A. aeriphila group compared to the control group. Phylum-level analysis revealed Firmicutes as the main phylum, followed by Bacteroidetes, in both groups. The data also found that Phascolarctobacterium and Barnesiella were increased in A. aeriphila-treated group. In conclusion, oral administration of A. aeriphila could improve the growth performance, serum antioxidant capacity, immune modulation, and gut health of broilers. Our findings may provide important information for the application of A. aeriphila in poultry production.}, }
@article {pmid37735685, year = {2023}, author = {Newman, NK and Zhang, Y and Padiadpu, J and Miranda, CL and Magana, AA and Wong, CP and Hioki, KA and Pederson, JW and Li, Z and Gurung, M and Bruce, AM and Brown, K and Bobe, G and Sharpton, TJ and Shulzhenko, N and Maier, CS and Stevens, JF and Gombart, AF and Morgun, A}, title = {Reducing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {208}, pmid = {37735685}, issn = {2049-2618}, support = {5R01AT009168/NH/NIH HHS/United States ; 5R01AT009168/NH/NIH HHS/United States ; 5R01AT009168/NH/NIH HHS/United States ; 5R01AT009168/NH/NIH HHS/United States ; DK103761/DK/NIDDK NIH HHS/United States ; }, abstract = {BACKGROUND: The gut microbiota contributes to macrophage-mediated inflammation in adipose tissue with consumption of an obesogenic diet, thus driving the development of metabolic syndrome. There is a need to identify and develop interventions that abrogate this condition. The hops-derived prenylated flavonoid xanthohumol (XN) and its semi-synthetic derivative tetrahydroxanthohumol (TXN) attenuate high-fat diet-induced obesity, hepatosteatosis, and metabolic syndrome in C57Bl/6J mice. This coincides with a decrease in pro-inflammatory gene expression in the gut and adipose tissue, together with alterations in the gut microbiota and bile acid composition.<br><br>RESULTS: In this study, we integrated and interrogated multi-omics data from different organs with fecal 16S rRNA sequences and systemic metabolic phenotypic data using a Transkingdom Network Analysis. By incorporating cell type information from single-cell RNA-seq data, we discovered TXN attenuates macrophage inflammatory processes in adipose tissue. TXN treatment also reduced levels of inflammation-inducing microbes, such as Oscillibacter valericigenes, that lead to adverse metabolic phenotypes. Furthermore, in vitro validation in macrophage cell lines and in vivo mouse supplementation showed addition of O. valericigenes supernatant induced the expression of metabolic macrophage signature genes that are downregulated by TXN in vivo.<br><br>CONCLUSIONS: Our findings establish an important mechanism by which TXN mitigates adverse phenotypic outcomes of diet-induced obesity and metabolic syndrome. TXN primarily reduces the abundance of pro-inflammatory gut microbes that can otherwise promote macrophage-associated inflammation in white adipose tissue. Video Abstract.}, }
@article {pmid37735572, year = {2023}, author = {Castonguay-Paradis, S and Perron, J and Flamand, N and Lamarche, B and Raymond, F and Di Marzo, V and Veilleux, A}, title = {Dietary food patterns as determinants of the gut microbiome-endocannabinoidome axis in humans.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15702}, pmid = {37735572}, issn = {2045-2322}, support = {CERC-04//Canada Research Excellence Chair in the Microbiome-Endocannabinoidome Axis in Metabolic Health/ ; 33219//Fonds de recherche du Qu&#xe9;bec-Sant&#xe9;/ ; }, abstract = {The gut microbiota and the endocannabinoidome (eCBome) play important roles in regulating energy homeostasis, and both are closely linked to dietary habits. However, the complex and compositional nature of these variables has limited our understanding of their interrelationship. This study aims to decipher the interrelation between dietary intake and the gut microbiome-eCBome axis using two different approaches for measuring dietary intake: one based on whole food and the other on macronutrient intakes. We reveal that food patterns, rather than macronutrient intakes, were associated with the gut microbiome-eCBome axis in a sample of healthy men and women (n = 195). N-acyl-ethanolamines (NAEs) and gut microbial families were correlated with intakes of vegetables, refined grains, olive oil and meats independently of adiposity and energy intakes. Specifically, higher intakes in vegetables and olive oil were associated with increased relative abundance of Clostridiaceae, Veillonellaceae and Peptostreptococaceae, decreased relative abundance of Acidominococaceae, higher circulating levels of NAEs, and higher HDL and LDL cholesterol levels. Our findings highlight the relative importance of food patterns in determining the gut microbiome-eCBome axis. They emphasize the importance of recognizing the contribution of dietary habits in these systems to develop personalized dietary interventions for preventing and treating metabolic disorders through this axis.}, }
@article {pmid37735460, year = {2023}, author = {Schnell, LJ and Khan, F and Hart, M and Davis, MC}, title = {Loop-mediated isothermal amplification identifies nematode Leidynema in the hindgut of non-pest cockroach.}, journal = {BMC research notes}, volume = {16}, number = {1}, pages = {227}, pmid = {37735460}, issn = {1756-0500}, abstract = {Cockroach microbiome studies generally focus on pest cockroach species belonging to the Blattidae and Ectobiidae families. There are no reports characterizing the gut microbiome of non-pest cockroach species Blaberus discoidalis (family Blaberidae), which is commonly used as a food source for insectivorous animals. We discovered the parasitic nematode Leidynema appendiculata in the B. discoidalis hindgut during initial work characterizing the gut microbiome of this organism. To determine the proportion of the B. discoidalis colony that was colonized by L. appendiculata, 28 S rDNA was amplified using two Methods: endpoint polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP). B. discoidalis colonies were raised on three diet types (control, high fibre, and high fat and salt) for 21 days before dissection. Each individual was sexed during dissection to identify potential sex-based effects of colonization. Data collected were analysed to determine if diet and sex impacted parasite colonization patterns. LAMP detected a higher proportion of parasite positive samples when compared to endpoint PCR. No sex- or diet-based differences in L. appendiculata colonization were found. This study adds to the limited existing knowledge of the B. discoidalis gut microbiome.}, }
@article {pmid37735458, year = {2023}, author = {Pinnow, N and Chibani, CM and Güllert, S and Weiland-Bräuer, N}, title = {Microbial community changes correlate with impaired host fitness of Aurelia aurita after environmental challenge.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {45}, pmid = {37735458}, issn = {2524-4671}, abstract = {Climate change globally endangers certain marine species, but at the same time, such changes may promote species that can tolerate and adapt to varying environmental conditions. Such acclimatization can be accompanied or possibly even be enabled by a host's microbiome; however, few studies have so far directly addressed this process. Here we show that acute, individual rises in seawater temperature and salinity to sub-lethal levels diminished host fitness of the benthic Aurelia aurita polyp, demonstrated by up to 34% reduced survival rate, shrinking of the animals, and almost halted asexual reproduction. Changes in the fitness of the polyps to environmental stressors coincided with microbiome changes, mainly within the phyla Proteobacteria and Bacteroidota. The absence of bacteria amplified these effects, pointing to the benefit of a balanced microbiota to cope with a changing environment. In a future ocean scenario, mimicked by a combined but milder rise of temperature and salinity, the fitness of polyps was severely less impaired, together with condition-specific changes in the microbiome composition. Our results show that the effects on host fitness correlate with the strength of environmental stress, while salt-conveyed thermotolerance might be involved. Further, a specific, balanced microbiome of A. aurita polyps supports the host's acclimatization. Microbiomes may provide a means for acclimatization, and microbiome flexibility can be a fundamental strategy for marine animals to adapt to future ocean scenarios and maintain biodiversity and ecosystem functioning.}, }
@article {pmid37735195, year = {2023}, author = {Malukiewicz, J and D'arc, M and Dias, CA and Cartwright, RA and Grativol, AD and Moreira, SB and Souza, AR and Tavares, MCH and Pissinatti, A and Ruiz-Miranda, CR and Santos, AFA}, title = {Bifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15679}, pmid = {37735195}, issn = {2045-2322}, support = {grant 313005/2020-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; E26/211.040/2019//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; E-26/211.355/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; E-26/201.193/2022//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; }, abstract = {Gut microbiome disruptions may lead to adverse effects on wildlife fitness and viability, thus maintaining host microbiota biodiversity needs to become an integral part of wildlife conservation. The highly-endangered callitrichid golden lion tamarin (GLT-Leontopithecus rosalia) is a rare conservation success, but allochthonous callitrichid marmosets (Callithrix) serve as principle ecological GLT threats. However, incorporation of microbiome approaches to GLT conservation is impeded by limited gut microbiome studies of Brazilian primates. Here, we carried out analysis of gut metagenomic pools from 114 individuals of wild and captive GLTs and marmosets. More specifically, we analyzed the bacterial component of ultra filtered samples originally collected as part of a virome profiling study. The major findings of this study are consistent with previous studies in showing that Bifidobacterium, a bacterial species important for the metabolism of tree gums consumed by callitrichids, is an important component of the callitrichid gut microbiome - although GTLs and marmosets were enriched for different species of Bifidobacterium. Additionally, the composition of GLT and marmoset gut microbiota is sensitive to host environmental factors. Overall, our data expand baseline gut microbiome data for callitrichids to allow for the development of new tools to improve their management and conservation.}, }
@article {pmid37734611, year = {2023}, author = {Khalid, M and Liu, X and Ur Rahman, S and Rehman, A and Zhao, C and Li, X and Yucheng, B and Hui, N}, title = {Responses of microbial communities in rhizocompartments of king grass to phytoremediation of cadmium-contaminated soil.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167226}, doi = {10.1016/j.scitotenv.2023.167226}, pmid = {37734611}, issn = {1879-1026}, abstract = {King grass has been recognized as a potential phytoremediation plant species due to its high biomass and resistance to heavy metals (HMs). However, the possible impacts of cadmium (Cd) contamination on rhizocompartments' microbial activities in association with king grass have not been extensively explored. The utilization of 16S rRNA gene and ITS sequencing was carried out to examine alterations in the bacterial and fungal communities in the rhizosphere and rhizoplane of king grass in response to low and high Cd stress. Results demonstrated that both bacterial and fungal communities' diversity and richness were negatively impacted by Cd stress, regardless of its concentration. However, evenness did not exhibit any significant response to either of the concentrations. Additionally, nonmetric multidimensional scaling (NMDS) ordination demonstrated a significant difference (p < 0.001) in microbial communities under different treatments. The abundance of bacterial taxa such as Steroibacter, Nitrospira, Pseudoxanthomonas, Cellvirio, Phenylobacterium, Mycobacterium, Pirellula and Aquicella was adversely affected under Cd stress while Flavobacterium, Gemmata, Thiobacillus and Gemmatimonas showed no prominent response, indicating their resistance to Cd stress. Like that, certain fungal taxa for instance, Cladosporium, Cercophora, Acremonium, Mortierella, Aspergillus, Penicillium, Glomus and Sebacina were also highly reduced by low and high Cd stress. In contrast, Fusarium, Thanatephorus, Botrytis and Curvularia did not show any response to Cd stress. The identified taxa may have a crucial role in the growth of king grass under heavy metal contamination, making them promising candidates for developing bioinoculants to encourage plant performance and phytoremediation capability in HM-contaminated soils.}, }
@article {pmid37734505, year = {2023}, author = {Martinez, G and Zhu, J and Takser, L and Baccarelli, AA and Bellenger, JP}, title = {Complementarity of plasma and stool for the characterization of children's exposure to halogenated flame retardants: Update on analytical methods and application to a Canadian cohort.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {140222}, doi = {10.1016/j.chemosphere.2023.140222}, pmid = {37734505}, issn = {1879-1298}, abstract = {Sixteen halogenated flame retardants including Polybrominated diphenyl ethers (PBDEs), Dechlorane-like compounds, and emerging halogenated flame retardants were measured in stool and plasma samples from children aged 8.9-13.8 years old. Samples were obtained from a Canadian cohort investigating the effect of contaminants on children's neurodevelopment in the Estrie region, Québec, Canada. The method for stool analysis developed for this study showed good recovery for all targeted compounds (73%-93%) with associated relative standard deviation (RSD) in the range of 16.0%-30.7% for most compounds except for the thermosensitive BDE209, OBTMBI, and BTBPE, which showed slightly higher RSD, i.e., 49.3%, 37.2%, and 34.9% respectively. Complementarity investigation of stool and blood samples allowed us to better characterize human exposure to these halogenated flame retardants. Exposure patterns differed significantly between stool and blood, notably in the relative abundance of BDE47, BDE100, BDE99, and BDE153 and the detection frequencies of BDE209, syn-DP, anti-DP, and DBDPE. There was no correlation between the two matrices' PBDEs concentration levels except for BDE153 (rho = 0.44, p < 0.01). Our results indicate that future epidemiological studies may benefit from the use of stool as a complementary matrix to blood, especially investigations into chemical impacts on the gut microbiome. Results also revealed that children from the GESTE cohort, an Eastern Canadian semi-rural cohort, are exposed to both historical and emergent flame retardants.}, }
@article {pmid37734144, year = {2023}, author = {Chicas, RC and Wang, Y and Jennifer Weil, E and Elon, L and Xiuhtecutli, N and C Houser, M and Jones, DP and M Sands, J and Hertzberg, V and McCauley, L and Liang, D}, title = {The impact of heat exposures on biomarkers of AKI and plasma metabolome among agricultural and non-agricultural workers.}, journal = {Environment international}, volume = {180}, number = {}, pages = {108206}, doi = {10.1016/j.envint.2023.108206}, pmid = {37734144}, issn = {1873-6750}, abstract = {BACKGROUND: Agricultural workers are consistently exposed to elevated heat exposures and vulnerable to acute kidney injury. The underlying pathophysiology and detailed molecular mechanisms of AKI among agricultural workers, and the disproportionate burden of HRI and heat stress exposure are not well understood, especially at the level of cellular metabolism.<br><br>OBJECTIVE: The aim of this study was to examine the impact of heat exposures on renal biomarkers and on the human metabolome via untargeted high-resolution metabolomics among agricultural and non-agricultural workers.<br><br>METHODS: Blood and urine samples were collected pre- and post-work shift from 63 agricultural workers and 27 non- agricultural workers. We evaluated pre- and post-work shift renal biomarkers and completed untargeted metabolomics using high-resolution mass spectrometry with liquid chromatography. Metabolome-wide association studies (MWAS) models identified the metabolic features differentially expressed between agricultural workers and non-agricultural workers.<br><br>RESULTS: Median values of pre-shift creatinine and osteopontin (p&#xa0;<&#xa0;0.05) were higher for agricultural workers than non-agricultural workers. Metabolic pathway enrichment analyses revealed 27 diverse pathways differed between agricultural workers and non-agricultural workers (p&#xa0;<&#xa0;0.05) including TCA cycle and urea cycle, carbohydrate metabolism, histidine metabolism and evidence for altered microbiome shikimate pathway.<br><br>CONCLUSION: This is the first investigation on the metabolic pathways that are affected among agricultural workers who are exposed to heat compared to non-heat exposed workers. This study shows extensive responses of central metabolic systems to heat exposures that impact human health.}, }
@article {pmid37734107, year = {2023}, author = {}, title = {Association of the Cervicovaginal Microbiome With Contraceptive Methods in Hispanic Women Living in Puerto Rico [ID: 1376364]: Correction.}, journal = {Obstetrics and gynecology}, volume = {142}, number = {4}, pages = {996}, pmid = {37734107}, issn = {1873-233X}, }
@article {pmid37733741, year = {2023}, author = {Beller, ZW and Wesener, DA and Seebeck, TR and Guruge, JL and Byrne, AE and Henrissat, S and Terrapon, N and Henrissat, B and Rodionov, DA and Osterman, AL and Suarez, C and Bacalzo, NP and Chen, Y and Couture, G and Lebrilla, CB and Zhang, Z and Eastlund, ER and McCann, CH and Davis, GD and Gordon, JI}, title = {Inducible CRISPR-targeted "knockdown" of human gut Bacteroides in gnotobiotic mice discloses glycan utilization strategies.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {39}, pages = {e2311422120}, doi = {10.1073/pnas.2311422120}, pmid = {37733741}, issn = {1091-6490}, support = {R01DK70977//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; F30DK123838//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; K99 AT0113774//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; }, abstract = {Understanding how members of the human gut microbiota prioritize nutrient resources is one component of a larger effort to decipher the mechanisms defining microbial community robustness and resiliency in health and disease. This knowledge is foundational for development of microbiota-directed therapeutics. To model how bacteria prioritize glycans in the gut, germfree mice were colonized with 13 human gut bacterial strains, including seven saccharolytic Bacteroidaceae species. Animals were fed a Western diet supplemented with pea fiber. After community assembly, an inducible CRISPR-based system was used to selectively and temporarily reduce the absolute abundance of Bacteroides thetaiotaomicron or B. cellulosilyticus by 10- to 60-fold. Each knockdown resulted in specific, reproducible increases in the abundances of other Bacteroidaceae and dynamic alterations in their expression of genes involved in glycan utilization. Emergence of these "alternate consumers" was associated with preservation of community saccharolytic activity. Using an inducible system for CRISPR base editing in vitro, we disrupted translation of transporters critical for utilizing dietary polysaccharides in Phocaeicola vulgatus, a B. cellulosilyticus knockdown-responsive taxon. In vitro and in vivo tests of the resulting P. vulgatus mutants allowed us to further characterize mechanisms associated with its increased fitness after knockdown. In principle, the approach described can be applied to study utilization of a range of nutrients and to preclinical efforts designed to develop therapeutic strategies for precision manipulation of microbial communities.}, }
@article {pmid37733209, year = {2023}, author = {Perna, A and Montine, KS and White, LR and Montine, TJ and Cholerton, BA}, title = {Paradigm Shift: Multiple Potential Pathways to Neurodegenerative Dementia.}, journal = {Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics}, volume = {}, number = {}, pages = {}, pmid = {37733209}, issn = {1878-7479}, support = {UF1 AG057707/AG/NIA NIH HHS/United States ; UF1 AG053983/AG/NIA NIH HHS/United States ; }, abstract = {Neurodegenerative dementia can result from multiple underlying abnormalities, including neurotransmitter imbalances, protein aggregation, and other neurotoxic events. A major complication in identifying effective treatment targets is the frequent co-occurrence of multiple neurodegenerative processes, occurring either in parallel or sequentially. The path towards developing effective treatments for Alzheimer's disease (AD) and other dementias has been relatively slow and until recently has focused on disease symptoms. Aducanumab and lecanemab, recently approved by the FDA, are meant to target disease structures but have only modest benefit on symptom progression and remain unproven in reversing or preventing dementia. A third, donanemab, appears more promising but awaits FDA approval. Ongoing trials include potential cognition enhancers, new combinations of known drugs for synergistic effects, prodrugs with less toxicity, and increasing interest in drugs targeting neuroinflammation or microbiome. Scientific and technological advances offer the opportunity to move in new therapy directions, such as modifying microglia to prevent or suppress underlying disease. A major challenge, however, is that underlying comorbidities likely influence the effectiveness of therapies. Indeed, the full range of comorbidity, today only definitively identified postmortem, likely contributes to failed clinical trials and overmedication of older adults, since it is difficult to exclude (during life) people unlikely to respond. Our current knowledge thus signals that a paradigm shift towards individualized and multimodal treatments is necessary to effectively advance the field of dementia therapeutics.}, }
@article {pmid37733190, year = {2023}, author = {Pal, P and Shastry, RP}, title = {Correction to: Exploring the complex role of gut microbiome in the development of precision medicine strategies for targeting microbial imbalance-induced colon cancer.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12223-023-01094-4}, pmid = {37733190}, issn = {1874-9356}, }
@article {pmid37732569, year = {2023}, author = {O'Brien, PA and Tan, S and Frade, PR and Robbins, SJ and Engelberts, JP and Bell, SC and Vanwonterghem, I and Miller, DJ and Webster, NS and Zhang, G and Bourne, DG}, title = {Validation of key sponge symbiont pathways using genome-centric metatranscriptomics.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16509}, pmid = {37732569}, issn = {1462-2920}, support = {//Beijing Genomics Institute/ ; //Earthwatch Institute/ ; //Mitsubishi International Corporation/ ; //AIMS@JCU/ ; }, abstract = {The sponge microbiome underpins host function through provision and recycling of essential nutrients in a nutrient poor environment. Genomic data suggest that carbohydrate degradation, carbon fixation, nitrogen metabolism, sulphur metabolism and supplementation of B-vitamins are central microbial functions. However, validation beyond the genomic potential of sponge symbiont pathways is rarely explored. To evaluate metagenomic predictions, we sequenced the metagenomes and metatranscriptomes of three common coral reef sponges: Ircinia ramosa, Ircinia microconulosa and Phyllospongia foliascens. Multiple carbohydrate active enzymes were expressed by Poribacteria, Bacteroidota and Cyanobacteria symbionts, suggesting these lineages have a central role in assimilating dissolved organic matter. Expression of entire pathways for carbon fixation and multiple sulphur compound transformations were observed in all sponges. Gene expression for anaerobic nitrogen metabolism (denitrification and nitrate reduction) were more common than aerobic metabolism (nitrification), where only the I. ramosa microbiome expressed the nitrification pathway. Finally, while expression of the biosynthetic pathways for B-vitamins was common, the expression of additional transporter genes was far more limited. Overall, we highlight consistencies and disparities between metagenomic and metatranscriptomic results when inferring microbial activity, while uncovering new microbial taxa that contribute to the health of their sponge host via nutrient exchange.}, }
@article {pmid37732273, year = {2023}, author = {Tsamir-Rimon, M and Borenstein, E}, title = {A Manifold-Based Framework for Studying the Dynamics of the Vaginal Microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37732273}, abstract = {The vaginal bacterial community plays a crucial role in preventing infections. The composition of this community can be classified into five main groups, termed community state types (CSTs). Four of these CSTs, which are primarily consisted of Lactobacillus species, are considered healthy, while the fifth, which is composed of non-Lactobacillus populations, is considered less protective. This latter CST is often considered to represent a state termed Bacterial vaginosis (BV) - a common disease condition associated with unpleasant symptoms and increased susceptibility to sexually transmitted diseases. However, the exact mechanisms underlying BV development are not yet fully understood, including specifically, the dynamics of the vaginal microbiome in BV, and the possible routes it may take from a healthy to a BV state. This study aims to identify the progression from healthy Lactobacillus-dominant populations to symptomatic BV by analyzing 8,026 vaginal samples and using a manifold-detection framework. This approach is inspired by single-cell analysis and aims to identify low-dimensional trajectories in the high-dimensional composition space. This framework further order samples along these trajectories and assign a score (pseudo-time) to each sample based on its proximity to the BV state. Our results reveal distinct routes of progression between healthy and BV state for each CST, with pseudo-time scores correlating with community diversity and quantifying the health state of each sample. BV indicators, including Nugent score, positive Amsel's test, and several Amsel's criteria, can also be successfully predicted based on pseudo-time scores. Additionally, Gardnerella vaginalis can be identified as a key taxon in BV development using this approach, with increased abundance in samples with high pseudo-time, indicating an unhealthier state across all BV-development routes on the manifold. Taken together, these findings demonstrate how manifold detection can be used to successfully characterizes the progression from healthy Lactobacillus-dominant populations to BV and to accurately quantify the health condition of new samples along the route of BV development.}, }
@article {pmid37732141, year = {2023}, author = {Fang, M and Hu, W and Liu, B}, title = {Effects of nano-selenium on cecum microbial community and metabolomics in chickens challenged with Ochratoxin A.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1228360}, pmid = {37732141}, issn = {2297-1769}, abstract = {INTRODUCTION: Ochratoxin A (OTA) is a widely distributed mycotoxin. Nano-selenium (Nano-Se) is an emerging form of selenium known for its superior bioavailability, remarkable catalytic efficiency, and robust adsorbing capacity. Despite these characteristics, its impact on the microbial community and metabolomics in the cecum of chickens exposed to OTA has been infrequently investigated. This research examined the microbiota and metabolomic alterations linked to OTA in chickens, with or without Nano-Se present.<br><br>METHODS: A cohort of 80 healthy chickens at the age of 1 day was randomly distributed into four groups of equal numbers, namely the Se cohort (1 mg/kg Nano-Se), the OTA cohort (50 &#x3bc;g/kg OTA), the OTA-Se cohort (50 &#x3bc;g/kg OTA&#x2009;+&#x2009;1 mg/kg Nano-Se), and the control group. Each chicken group's caecal microbiome and metabolome were characterized using 16S rRNA sequencing and Liquid chromatography coupled with mass spectrometry (LC-MS) analyses.<br><br>RESULTS AND DISCUSSION: Our results showed that the on day 21, the final body weight was significantly reduced in response to OTA treatments (p < 0.05), the average daily gain in the OTA group was found to be inferior to the other groups (p < 0.01). In addition, Nano-Se supplementation could reduce the jejunum and liver pathological injuries caused by OTA exposure. The 16S rRNA sequencing suggest that Nano-Se supplementation in OTA-exposed chickens mitigated gut microbiota imbalances by promoting beneficial microbiota and suppressing detrimental bacteria. Moreover, untargeted metabolomics revealed a significant difference in caecal metabolites by Nano-Se pretreatment. Collectively, the dataset outcomes highlighted that Nano-Se augmentation regulates intestinal microbiota and associated metabolite profiles, thus influencing critical metabolic pathways, and points to a possible food-additive product.}, }
@article {pmid37732131, year = {2023}, author = {Ji, J and Ye, Y and Sheng, L and Sun, J and Hong, Q and Liu, C and Ding, J and Geng, S and Xu, D and Zhang, Y and Sun, X}, title = {Sleep Promotion by 3-Hydroxy-4-Iminobutyric Acid in Walnut Diaphragma juglandis Fructus.}, journal = {Research (Washington, D.C.)}, volume = {6}, number = {}, pages = {0216}, pmid = {37732131}, issn = {2639-5274}, abstract = {Insufficient sleep can produce a multitude of deleterious repercussions on various domains of human well-being. Concomitantly, the walnut (Juglans mandshurica) confers numerous salutary biological activities pertaining to sleep. Nevertheless, the sedative and hypnotic capacities of walnut's functional constituents remain obscure. In this investigation, we analyzed the sedative and hypnotic components of the walnut Diaphragma juglandis fructus and innovatively discovered a compound, defined as 3-hydroxy-4-iminobutyric acid (HIBA), which disrupts motor activity and enhances sleep duration by regulating the neurotransmitters (GABA, DA, etc.) within the brain and serum of mice. Subsequently, a metabolomics approach of the serum, basal ganglia, hypothalamus, and hippocampus as well as the gut microbiota was undertaken to unravel the underlying molecular mechanisms of sleep promotion. Our data reveal that HIBA can regulate the metabolism of basal ganglia (sphingolipids, acylcarnitines, etc.), possibly in relation to HIBA's influence on the gut microbiome (Muribaculum, Bacteroides, Lactobacillus, etc.). Therefore, we introduce a novel natural product, HIBA, and explicate the modulation of sleep promotion in mice based on the microbiota-gut-brain axis. This study contributes fresh insights toward natural product-based sleep research.}, }
@article {pmid37731926, year = {2023}, author = {Dikareva, E and Matharu, D and Lahtinen, E and Kolho, KL and De Vos, WM and Salonen, A and Ponsero, AJ}, title = {An extended catalog of integrated prophages in the infant and adult fecal microbiome shows high prevalence of lysogeny.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1254535}, pmid = {37731926}, issn = {1664-302X}, abstract = {BACKGROUND AND AIMS: The acquisition and gradual maturation of gut microbial communities during early childhood is central to an individual's healthy development. Bacteriophages have the potential to shape the gut bacterial communities. However, the complex ecological interactions between phages and their bacterial host are still poorly characterized. In this study, we investigated the abundance and diversity of integrated prophages in infant and adult gut bacteria by detecting integrated prophages in metagenome assembled genomes (MAGs) of commensal bacteria.<br><br>METHODS: Our study included 88 infants sampled at 3&#x2009;weeks, 3&#x2009;months, 6&#x2009;months, and 12&#x2009;months (n&#x2009;=&#x2009;323 total samples), and their parents around delivery time (n&#x2009;=&#x2009;138 total samples). Fecal DNA was extracted and characterized by using shotgun metagenomic sequencing, and a collection of prokaryotic MAGs was generated. The MAG collection was screened for the presence of integrated bacteriophage sequences, allowing their taxonomic and functional characterization.<br><br>RESULTS: A large collection of 6,186 MAGs from infant and adult gut microbiota was obtained and screened for integrated prophages, allowing the identification of 7,165 prophage sequences longer than 10&#x2009;kb. Strikingly, more than 70% of the near-complete MAGs were identified as lysogens. The prevalence of prophages in MAGs varied across bacterial families, with a lower prevalence observed among Coriobacteriaceae, Eggerthellaceae, Veillonellaceae and Burkholderiaceae, while a very high prevalence of lysogen MAGs were observed in Oscillospiraceae, Enterococcaceae, and Enterobacteriaceae. Interestingly for several bacterial families such as Bifidobacteriaceae and Bacteroidaceae, the prevalence of prophages in MAGs was higher in early infant time point (3&#x2009;weeks and 3&#x2009;months) than in later sampling points (6 and 12&#x2009;months) and in adults. The prophage sequences were clustered into 5,616 species-like vOTUs, 77% of which were novel. Finally, we explored the functional repertoire of the potential auxiliary metabolic genes carried by these prophages, encoding functions involved in carbohydrate metabolism and degradation, amino acid metabolism and carbon metabolism.<br><br>CONCLUSION: Our study provides an enhanced understanding of the diversity and prevalence of lysogens in infant and adult gut microbiota and suggests a complex interplay between prophages and their bacterial hosts.}, }
@article {pmid37731925, year = {2023}, author = {Xiong, M and Jiang, W and Zou, S and Kang, D and Yan, X}, title = {Microbial carbohydrate-active enzymes influence soil carbon by regulating the of plant- and fungal-derived biomass decomposition in plateau peat wetlands under differing water conditions.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1266016}, pmid = {37731925}, issn = {1664-302X}, abstract = {Peatlands are important carbon sinks and water sources in terrestrial ecosystems. It is important to explore their microbial-driven water-carbon synergistic mechanisms to understand the driving mechanisms of carbon processes in peatlands. Based on macrogenomic sequencing techniques, located on the peatland of the eastern margin of the Tibetan Plateau with similar stand and different water conditions, we taken soil properties, microbiome abundance, CAZyme abundance and enzyme gene pathways as the object of study, investigated the characterization of soil microbial carbohydrate-active enzymes (CAZymes) under different water gradients in peatland. According to the results, these three phyla (Chloroflexi, Gemmatimonadetes, and Verrucomicrobia) differed significantly between water gradients. Under dried wetlands, the abundance of CAZymes involved in hemicellulose and glucan degradation increased by 3.0 × 10[-5] and 3.0 × 10[-6], respectively. In contrast, the abundance of CAZymes involved in chitin degradation decreased by 1.1 × 10[-5] (p < 0.05). It highlights that regulating plant- and fungus-derived carbon metabolism processes by soil microorganisms in highland peatlands is a crucial mechanism for their response to water changes. Most plant-derived carbon fractions are regulated by soil enzymes (endo-beta 1,4-xylanase, alpha-L-arabinofuranosidase, and alpha-L-fucosidase) containing CAZymes functional genes. Additional findings in this enzyme gene pathway indicate that water changes that affect soil carbon fractions indirectly influence the three enzyme gene metabolic pathways related to plant carbon sources (the glycolysis/gluconeogenesis, other glycan degradation and amino sugar, and nucleotide sugar metabolism). Overall, this study highlights the significance of microbial CAZymes in highland peatland soil carbon processes and indicates that microbial conversion of plant and fungal biomass carbon is more sensitive to water changes.}, }
@article {pmid37731924, year = {2023}, author = {Wu, J and Tian, C and Jiao, J and Yan, Q and Zhou, C and Tan, Z}, title = {The epithelial transcriptome and mucosal microbiota are altered for goats fed with a low-protein diet.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1237955}, pmid = {37731924}, issn = {1664-302X}, abstract = {INTRODUCTION: Feeding low protein (LP) diet to animals impose severe challenge to animals' immune homeostasis. However, limited knowledge about the underlying adaption mechanism of host and ruminal microbiota responding to LP diet were well understood. Herein, this study was performed to examine the changes in relative abundance of ruminal microbiota and host ruminal mucosal transcriptome profiles in response to a LP diet.<br><br>METHODS: A total of twenty-four female Xiangdong balck goats with similar weight (20.64 &#xb1; 2.40 kg) and age (8 &#xb1; 0.3 months) were randomly assigned into two groups, LP (5.52% crude protein containing diet) and CON (10.77% crude protein containing diet) groups. Upon completion of the trial, all goats were slaughtered after a 16-hour fasting period in LiuYang city (N 28&#xb0;15', E 113&#xb0;63') in China. HE staining, free amino acids measurement, transcriptome analysis and microbiome analysis were applied to detect the morphology alterations, free amino acids profile alterations and the shift in host ruminal mucosal transcriptome and ruminal microbiota communities.<br><br>RESULTS: Firstly, the results showed that feeding LP diet to goats decreased the rumen papilla width (P = 0.043), surface area (P = 0.013) and total ruminal free amino acids concentration (P = 0.016). Secondly, microbiome analysis indicated that 9 microbial genera, including Eubacterium and Prevotella, were enriched in LP group while 11 microbial genera, including Butyrivibrio and Ruminococcus, were enriched in CON group. Finally, in terms of immune-related genes, the expression levels of genes involved in tight junction categories (e.g., MYH11, PPP2R2C, and MYL9) and acquired immunity (e.g., PCP4 and CXCL13) were observed to be upregulated in the LP group when compared to the CON group.<br><br>CONCLUSION: Under the LP diet, the rumen exhibited increased relative abundance of pathogenic microbiota and VFA-degrading microbiota, leading to disruptions in immune homeostasis within the host's ruminal mucosa. These findings indicate that the ruminal microbiota interacts with host results in the disruption in animals' immune homeostasis under LP diet challenge.}, }
@article {pmid37731918, year = {2023}, author = {Liu, H and Zhang, H and Yu, Q and Zhang, S and Tu, X and Zhuang, F and Fu, S}, title = {Lead induced structural and functional damage and microbiota dysbiosis in the intestine of crucian carp (Carassius auratus).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1239323}, pmid = {37731918}, issn = {1664-302X}, abstract = {Lead (Pb) is a hazardous pollutant in water environments that can cause significant damage to aquatic animals and humans. In this study, crucian carp (Carassius auratus) were exposed to waterborne Pb for 96 h; then, histopathological analysis, quantitative qPCR analysis, and 16S high-throughput sequencing were performed to explore the effects of Pb on intestinal bioaccumulation, structural damage, oxidative stress, immune response, and microbiota imbalance of C. auratus. After Pb exposure, the intestinal morphology was obviously damaged, including significantly increasing the thickness of the intestinal wall and the number of goblet cells and reducing the depth of intestinal crypts. Pb exposure reduced the mRNA expressions of Claudin-7 and villin-1 while significantly elevated the level of GST, GSH, CAT, IL-8, IL-10, IL-1, and TNF-α. Furthermore, 16S rRNA analysis showed that the Shannon and Simpson indices decreased at 48 h after Pb exposure, and the abundance of pathogenic bacteria (Erysipelotrichaceae, Weeksellaceae, and Vibrionaceae) increased after Pb exposure. In addition, the correlation network analysis found that Proteobacteria were negatively correlated with Firmicutes and positively correlated with Bacteroidetes. Functional prediction analysis of bacteria speculated that the change in intestinal microbiota led to the PPAR signaling pathway and peroxisome function of the intestine of crucian carp was increased, while the immune system and membrane transport function were decreased. Finally, canonical correlation analysis (CCA) found that there were correlations between the intestinal microbiota, morphology, antioxidant factors, and immune factors of crucian carp after Pb exposure. Taken together, our results demonstrated that intestinal flora dysbiosis, morphological disruption, oxidative stress, and immune injury are involved in the toxic damage of Pb exposure to the intestinal structure and function of crucian carp. Meanwhile, Pb exposure rapidly increased the abundance of pathogenic bacteria, leading to intestinal disorders, further aggravating the damage of Pb to intestinal structure and function. These findings provide us a basis for the link between gut microbiome changes and heavy metal toxicity, and gut microbiota can be used as biomarkers for the evaluation of heavy metal pollution in future.}, }
@article {pmid37731597, year = {2023}, author = {Molina, MA and Melchers, WJG and Andralojc, KM and Leenders, WPJ and Huynen, MA}, title = {Longitudinal analysis on the ecological dynamics of the cervicovaginal microbiome in hrHPV infection.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {4424-4431}, pmid = {37731597}, issn = {2001-0370}, abstract = {The cervicovaginal microbiome (CVM) is a dynamic continuous microenvironment that can be clustered in microbial community state types (CSTs) and is associated with women's cervical health. Lactobacillus-depleted communities particularly associate with an increased susceptibility for persistence of high-risk human papillomavirus (hrHPV) infections and progression of disease, but the long-term ecological dynamics of CSTs after hrHPV infection diagnosis remain poorly understood. To determine such dynamics, we examined the CVM of our longitudinal cohort of 141 women diagnosed with hrHPV infection at baseline with collected cervical smears at two timepoints six-months apart. Here we describe that the long-term microbiome dissimilarity has a positive correlation with microbial diversity at both visits and that women with high abundance and dominance for Lactobacillus iners at baseline exhibit more similar microbiome composition at second visit than women with Lactobacillus-depleted communities at baseline. We further show that the species Lactobacillus acidophilus and Megasphaera genomosp type 1 associate with CST changes between both visits. Lastly, we also observe that Gardnerella vaginalis is associated with the stability of Lactobacillus-depleted communities while L. iners is associated with the instability of Megasphaera genomosp type 1-dominated communities. Our data suggest dynamic patterns of cervicovaginal CSTs during hrHPV infection, which could be potentially used to develop microbiome-based therapies against infection progression towards disease.}, }
@article {pmid37731574, year = {2023}, author = {Zyoud, SH and Shakhshir, M and Abushanab, AS and Koni, A and Shahwan, M and Jairoun, AA and Abu Taha, A and Al-Jabi, SW}, title = {Unveiling the hidden world of gut health: Exploring cutting-edge research through visualizing randomized controlled trials on the gut microbiota.}, journal = {World journal of clinical cases}, volume = {11}, number = {26}, pages = {6132-6146}, pmid = {37731574}, issn = {2307-8960}, abstract = {BACKGROUND: The gut microbiota plays a crucial role in gastrointestinal and overall health. Randomized clinical trials (RCTs) play a crucial role in advancing our knowledge and evaluating the efficacy of therapeutic interventions targeting the gut microbiota.<br><br>AIM: To conduct a comprehensive bibliometric analysis of the literature on RCTs involving the gut microbiota.<br><br>METHODS: Using bibliometric tools, a descriptive cross-sectional investigation was conducted on scholarly publications concentrated on RCTs related to gut microbiota, spanning the years 2003 to 2022. The study used VOSviewer version 1.6.9 to examine collaboration networks between different countries and evaluate the frequently employed terms in the titles and abstracts of the retrieved publications. The primary objective of this analysis was to identify key research areas and focal points associated with RCTs involving the gut microbiota.<br><br>RESULTS: A total of 1061 relevant articles were identified from the 24758 research articles published between 2003 and 2022. The number of publications showed a notable increase over time, with a positive correlation (R[2] = 0.978, P < 0.001). China (n = 276, 26.01%), the United States (n = 254, 23.94%), and the United Kingdom (n = 97, 9.14%) were the leading contributing countries. K&#xf8;benhavns Universitet (n = 38, 3.58%) and Dankook University (n = 35, 3.30%) were the top active institutions. The co-occurrence analysis shows current gut microbiota research trends and important topics, such as obesity interventions targeting the gut microbiota, the efficacy and safety of fecal microbiota transplantation, and the effects of dietary interventions on humans.<br><br>CONCLUSION: The study highlights the rapid growth and importance of research on RCTs that involve the gut microbiota. This study provides valuable insight into research trends, identifies key players, and outlines potential future directions in this field. Additionally, the co-occurrence analysis identified important topics that play a critical role in the advancement of science and provided insights into future research directions in this field.}, }
@article {pmid37731336, year = {2023}, author = {Aizpurua, O and Dunn, RR and Hansen, LH and Gilbert, MTP and Alberdi, A}, title = {Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data.}, journal = {Critical reviews in biotechnology}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/07388551.2023.2254933}, pmid = {37731336}, issn = {1549-7801}, abstract = {Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.}, }
@article {pmid37731320, year = {2023}, author = {Easter, QT and Matuck, BF and Warner, BM and Byrd, KM}, title = {Biogeographical Impacts of Dental, Oral, and Craniofacial Microbial Reservoirs.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345231191115}, doi = {10.1177/00220345231191115}, pmid = {37731320}, issn = {1544-0591}, abstract = {The human mouth, or oral cavity, is at the crossroads of our external and internal environments, and it is increasingly evident that local colonization of dental, oral, and craniofacial (DOC) tissues and cells by bacteria and viruses may also have systemic effects across myriad diseases and disorders. Better understanding of this phenomenon will require a holistic understanding of host-microbial interactions in both spatiotemporal and biogeographical contexts while also considering person-, organ-, tissue-, cell-, and molecular-level variation. After the acute phase interaction with microbes, the establishment of site-specific reservoirs constitutes an important relationship to understand within the human body; however, despite a preliminary understanding of how viral reservoirs originate and persist across the human body, the landscape of single-cell and spatial multiomic tools has challenged our current understanding of what cells and niches can support microbial reservoirs. The lack of complete understanding impacts research into these relevant topics and implementing precision care for microbial-induced or microbial-influenced diseases. Here, via the lens of acute and chronic microbial infections of the DOC tissues, the goal of this review is to highlight and link the emerging spatiotemporal biogeography of host-viral interactomics at 3 levels: (1) DOC cell types in distinct tissues, (2) DOC-associated microbes, and (3) niche-specific DOC pathologies. Further, we will focus on the impact of postacute infectious syndromes such as long COVID, neurodegenerative disorders, and other underappreciated postviral conditions. We will provide hypotheses about how DOC tissues may play roles systemically in these conditions. Throughout, we will underscore how COVID-19 has catalyzed a new understanding of these biological questions, discuss future directions to study these phenomena, and highlight the utility of noninvasive oral biofluids in screening, monitoring, and intervening to prevent and/or ameliorate human infectious diseases.}, }
@article {pmid37730461, year = {2023}, author = {Pacheco-Yanes, J and Reynolds, E and Li, J and Mariño, E}, title = {Microbiome-targeted interventions for the control of oral-gut dysbiosis and chronic systemic inflammation.}, journal = {Trends in molecular medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molmed.2023.08.006}, pmid = {37730461}, issn = {1471-499X}, abstract = {Recent research has confirmed the strong connection between imbalances in the oral and gut microbiome (oral-gut dysbiosis), periodontitis, and inflammatory conditions such as diabetes, Alzheimer's disease, and cardiovascular diseases. Microbiome modulation is crucial for preventing and treating several autoimmune and inflammatory diseases, including periodontitis. However, the causal relationships between the microbiome and its derived metabolites that mediate periodontitis and chronic inflammation constitute a notable knowledge gap. Here we review the mechanisms involved in the microbiome-host crosstalk, and describe novel precision medicine for the control of systemic inflammation. As microbiome-targeted therapies begin to enter clinical trials, the success of these approaches relies upon understanding these reciprocal microbiome-host interactions, and it may provide new therapeutic avenues to reduce the risk of periodontitis-associated diseases.}, }
@article {pmid37730180, year = {2023}, author = {Yu, Z and Cantet, JM and Paz, HA and Kaufman, JD and Orellano, MS and Ipharraguerre, IR and Ríus, AG}, title = {Heat stress-associated changes in the intestinal barrier, inflammatory signals, and microbiome communities in dairy calves.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2023-23873}, pmid = {37730180}, issn = {1525-3198}, abstract = {Recent studies indicate that heat stress pathophysiology is associated with intestinal barrier dysfunction, local and systemic inflammation, and gut dysbiosis. However, inconclusive results and a poor description of tissue specific changes must be addressed to identify potential intervention targets against heat stress illness in growing calves. Therefore, the objective of this study was to evaluate components of the intestinal barrier, pro- and anti-inflammatory signals, and microbiota community composition in Holstein bull calves exposed to heat stress. Animals (mean age = 12-week-old, mean body weight = 122 kg) penned individually in temperature-controlled rooms were assigned to 1) thermoneutral conditions (constant room temperature at 19.5°C) and restricted offer of feed (TNR, n = 8), or, 2) heat stress conditions (cycles of room temperatures ranging from 20 to 37.8°C) along with ad libitum offer of feed (HS, n = 8) for 7 d. Upon treatment completion, sections of the jejunum, ileum, and colon were collected and snap-frozen immediately to evaluate gene and protein expression, cytokine concentrations, and myeloperoxidase (MPO) activity. Digesta aliquots of the ileum, colon, and rectum were collected to assess bacterial communities. Plasma was harvested on d 2, 5, and 7 to determine cytokine concentrations. Overall, results showed a section-specific impact of HS on intestinal integrity. Jejunal mRNA expression of TJP1 was decreased by 70% in HS relative to TNR calves. In agreement, jejunal expression of heat shock transcription factor-1 protein (HSF-1), a known tight junction protein expression regulator, decreased by 48% in HS calves. Jejunal analyses showed that HS decreased concentrations of interleukin-1 α by 36.6% and tended to decrease the concentration of interleukin-17A. Conversely, HS elicited a 3.5-fold increase in jejunal concentration of anti-inflammatory interleukin-36 receptor antagonist. Plasma analysis of pro-inflammatory cytokines showed that interleukin-6 decreased by 51% in HS relative to TNR calves. Heat stress alteration of the large intestine bacterial communities was characterized by increased genus Butyrivibrio_3, a known butyrate-producing organism, and changes in bacteria metabolism of energy and amino acids. A strong positive correlation between the rectal temperature and pro-inflammatory Eggerthii spp. was detected in HS calves. In conclusion, this work indicates that HS impairs the intestinal barrier function of jejunum. The pro- and anti-inflammatory signal changes may be part of a broader response to restore intestinal homeostasis in jejunum. The changes in large intestine bacterial communities favoring butyrate-producing organisms e.g., Butyrivibrio spp. may be part of a successful response to maintain the integrity of the colonic mucosa of HS calves. The alteration of intestinal homeostasis should be the target for heat stress therapies to restore biological functions, and, thus highlights the relevance of this work.}, }
@article {pmid37729875, year = {2023}, author = {Oldfield, L and Costello, E}, title = {Where the metabolome meets the microbiome for pancreatic cancer detection.}, journal = {Cell reports. Medicine}, volume = {4}, number = {9}, pages = {101011}, doi = {10.1016/j.xcrm.2023.101011}, pmid = {37729875}, issn = {2666-3791}, mesh = {Humans ; Pancreas ; *Pancreatic Neoplasms/diagnosis ; *Microbiota ; Metabolome ; }, abstract = {Risk prediction tools for pancreatic cancer are urgently sought to facilitate screening. Irajizad et al.[1] describe the performance of a risk predication model based on circulating microbial- and non-microbial metabolites for assessment of 5-year pancreatic cancer risk.}, }
@article {pmid37729870, year = {2023}, author = {Irajizad, E and Kenney, A and Tang, T and Vykoukal, J and Wu, R and Murage, E and Dennison, JB and Sans, M and Long, JP and Loftus, M and Chabot, JA and Kluger, MD and Kastrinos, F and Brais, L and Babic, A and Jajoo, K and Lee, LS and Clancy, TE and Ng, K and Bullock, A and Genkinger, JM and Maitra, A and Do, KA and Yu, B and Wolpin, BM and Hanash, S and Fahrmann, JF}, title = {A blood-based metabolomic signature predictive of risk for pancreatic cancer.}, journal = {Cell reports. Medicine}, volume = {4}, number = {9}, pages = {101194}, doi = {10.1016/j.xcrm.2023.101194}, pmid = {37729870}, issn = {2666-3791}, support = {U01 CA210171/CA/NCI NIH HHS/United States ; P50 CA127003/CA/NCI NIH HHS/United States ; U01 CA196403/CA/NCI NIH HHS/United States ; U01 CA200468/CA/NCI NIH HHS/United States ; P50 CA221707/CA/NCI NIH HHS/United States ; }, mesh = {Male ; Humans ; *CA-19-9 Antigen ; *Pancreatic Neoplasms/diagnosis ; Pancreas ; Metabolomics ; }, abstract = {Emerging evidence implicates microbiome involvement in the development of pancreatic cancer (PaCa). Here, we investigate whether increases in circulating microbial-related metabolites associate with PaCa risk by applying metabolomics profiling to 172 sera collected within 5 years prior to PaCa diagnosis and 863 matched non-subject sera from participants in the Prostate, Lung, Colorectal, and Ovarian (PLCO) cohort. We develop a three-marker microbial-related metabolite panel to assess 5-year risk of PaCa. The addition of five non-microbial metabolites further improves 5-year risk prediction of PaCa. The combined metabolite panel complements CA19-9, and individuals with a combined metabolite panel + CA19-9 score in the top 2.5th percentile have absolute 5-year risk estimates of >13%. The risk prediction model based on circulating microbial and non-microbial metabolites provides a potential tool to identify individuals at high risk of PaCa that would benefit from surveillance and/or from potential cancer interception strategies.}, }
@article {pmid37729713, year = {2023}, author = {Qian, Y and Hu, P and Lang-Yona, N and Xu, M and Guo, C and Gu, JD}, title = {Global landfill leachate characteristics: Occurrences and abundances of environmental contaminants and the microbiome.}, journal = {Journal of hazardous materials}, volume = {461}, number = {}, pages = {132446}, doi = {10.1016/j.jhazmat.2023.132446}, pmid = {37729713}, issn = {1873-3336}, abstract = {Landfill leachates are complex mixtures containing very high concentrations of biodegradable and recalcitrant toxic compounds. Understanding the major contaminant components and microbial community signatures in global landfill leachates is crucial for timely decision-making regarding contaminant management and treatment. Therefore, this study analyzed leachate data from 318 landfill sites primarily used for municipal solid waste disposal, focusing on their chemical and microbiological characteristics. The most prevalent and dominant components in landfill leachates are the chemical oxygen demand (COD, 3.7-75.9 × 10[3] mg/L) and NH4[+] (0.03-0.81 × 10[4] mg/L), followed by salt species such as SO4[2-] (0.03-5.25 × 10[3] mg/L), Cl[-] (3.2-7.8 × 10[3] mg/L), K[+] (0.58-4.20 × 10[3] mg/L), Na[+] (1.3-13.0 × 10[3] mg/L) and Ca[2+] (2.35-230.23 × 10[3] mg/L), which exhibit significant fluctuations. Heavy metals and metalloids are widely distributed in most landfill leachates but at relatively low concentrations (<182.8 mg/L) compared to conventional parameters. Importantly, there is a distinct global variation in the occurrence of emerging environmental contaminants (ECs). Among these compounds, perfluorooctanoic acid (PFOA, 0.02-7.50 × 10[3] μg/L) of per- and poly-fluoroalkyl substances (PFAS), bisphenol A (BPA, 0.01-33.46 × 10[3] μg/L) belonged to endocrine-disrupting compounds (EDCs), together with di-ethyltoluamide (DEET, 1.0-1.0 × 10[3] μg/L) affiliated to pharmaceuticals and personal care products (PPCPs) are the most frequently detected in landfill leachates. Additionally, the microbial community compositions in most leachates are primarily dominated by Proteobacteria, Bacteroidota, Firmicutes, and Chloroflexi, and some of their abundances are correlated with the concentrations of NH4[+], NO3[-], Cl[-], Na[+] and Cr. Notably, the leading microbes driving advanced removal of inorganic nitrogen in the treatment systems are Candidatus Brocadia (anammox), denitrifying Thauera, nitrite-oxidizing bacteria Nitrospira, along with ammonia-oxidizing bacteria Nitrosomonas and Nitrosospira. The findings of this work provide a deeper insight into the leachate characteristics and the sustainable management of landfill leachates, especially presenting a snapshot of the global distribution of pollutants and also the microbiome.}, }
@article {pmid37729536, year = {2023}, author = {Gong, S and Liang, J and Jin, X and Xu, L and Zhao, M and Yu, K}, title = {Unfolding the secrets of microbiome (Symbiodiniaceae and bacteria) in cold-water coral.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0131523}, doi = {10.1128/spectrum.01315-23}, pmid = {37729536}, issn = {2165-0497}, abstract = {Recent deep-ocean exploration has uncovered a variety of cold-water coral (CWC) ecosystems around the world ocean, but it remains unclear how microbiome is associated with these corals at a molecular levels. This study utilized metabarcoding, tissue section observation, and metatranscriptomes to investigate the microbiome (Symbiodiniaceae and bacteria) of CWC species (Narella versluysi, Heterogorgia uatumani, and Muriceides sp.) from depths ranging from 260 m to 370 m. Warm-water coral (WWC) species (Acropora pruinosa, Pocillopora damicornis, and Galaxea fascicularis) were used as control groups. Results revealed that CWC host diverse bacteria and Symbiodiniaceae cells were observed in endoderm of CWC tissues. Several new candidate bacterial phyla were found in both CWC and WWC, including Coralsanbacteria, Coralqiangbacteria, Coralgsqaceae, Coralgongineae, etc. Both the 16S rRNA gene sequencing and metatranscriptomes revealed that Actinobacteria and Proteobacteria were abundant bacterial phyla in CWC. At the gene transcription level, the CWC-associated Symbiodiniaceae community showed a low-level transcription of genes involved in photosynthesis, CO2 fixation, glycolysis, citric acid cycle, while bacteria associated with CWC exhibited a high-level transcription of genes for carbon fixation via the Wood-Lijungdahl pathway, short chain fatty acids production, nitrogen, and sulfur cycles. IMPORTANCE This study shed new light on the functions of both Symbiodiniaceae and bacteria in cold-water coral (CWC). The results demonstrated that Symbiodiniaceae can survive and actively transcribe genes in CWC, suggesting a possible symbiotic or parasitic relationship with the host. This study also revealed complete non-photosynthetic CO2 fixation pathway of bacteria in CWC, as well as their roles in short chain fatty acids production and assimilation of host-derived organic nitrogen and sulfur. These findings highlight the important role of bacteria in the carbon, nitrogen sulfur cycles in CWC, which were possibly crucial for CWC survival in in deep-water environments.}, }
@article {pmid37728606, year = {2023}, author = {Naasko, KI and Naylor, D and Graham, EB and Couvillion, SP and Danczak, R and Tolic, N and Nicora, C and Fransen, S and Tao, H and Hofmockel, KS and Jansson, JK}, title = {Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry.}, journal = {mBio}, volume = {}, number = {}, pages = {e0175823}, doi = {10.1128/mbio.01758-23}, pmid = {37728606}, issn = {2150-7511}, abstract = {Climate change is causing an increase in drought in many soil ecosystems and a loss of soil organic carbon. Calcareous soils may partially mitigate these losses via carbon capture and storage. Here, we aimed to determine how irrigation-supplied soil moisture and perennial plants impact biotic and abiotic soil properties that underpin deep soil carbon chemistry in an unfertilized calcareous soil. Soil was sampled up to 1 m in depth from irrigated and planted field treatments and was analyzed using a suite of omics and chemical analyses. The soil microbial community composition was impacted more by irrigation and plant cover treatments than by soil depth. By contrast, metabolomes, lipidomes, and proteomes differed more with soil depth than treatments. Deep soil (>50 cm) had higher soil pH and calcium concentrations and higher levels of organic acids, bicarbonate, and triacylglycerides. By contrast, surface soil (0-5 cm) had higher concentrations of soil organic matter, organic carbon, oxidizable carbon, and total nitrogen. Surface soils also had higher amounts of sugars, sugar alcohols, phosphocholines, and proteins that reflect osmotic and oxidative stress responses. The lipidome was more responsive to perennial tall wheatgrass treatments compared to the metabolome or proteome, with a striking change in diacylglyceride composition. Permanganate oxidizable carbon was more consistently correlated to metabolites and proteins than soil organic and inorganic carbon and soil organic matter. This study reveals specific compounds that reflect differences in organic, inorganic, and oxidizable soil carbon fractions that are impacted by interactions between irrigation-supplied moisture and plant cover in calcareous soil profiles. IMPORTANCE Carbon is cycled through the air, plants, and belowground environment. Understanding soil carbon cycling in deep soil profiles will be important to mitigate climate change. Soil carbon cycling is impacted by water, plants, and soil microorganisms, in addition to soil mineralogy. Measuring biotic and abiotic soil properties provides a perspective of how soil microorganisms interact with the surrounding chemical environment. This study emphasizes the importance of considering biotic interactions with inorganic and oxidizable soil carbon in addition to total organic carbon in carbonate-containing soils for better informing soil carbon management decisions.}, }
@article {pmid37728579, year = {2023}, author = {Qu, L and Li, Y and Liu, F and Fang, Y and He, J and Ma, J and Xu, T and Wang, L and Lei, P and Dong, H and Jin, L and Yang, Q and Wu, W and Sun, D}, title = {Microbiota-Gut-Brain Axis Dysregulation in Alzheimer's Disease: Multi-Pathway Effects and Therapeutic Potential.}, journal = {Aging and disease}, volume = {}, number = {}, pages = {}, doi = {10.14336/AD.2023.0823-2}, pmid = {37728579}, issn = {2152-5250}, abstract = {An essential regulator of neurodegenerative conditions like Alzheimer's disease (AD) is the gut microbiota. Alterations in intestinal permeability brought on by gut microbiota dysregulation encourage neuroinflammation, central immune dysregulation, and peripheral immunological dysregulation in AD, as well as hasten aberrant protein aggregation and neuronal death in the brain. However, it is unclear how the gut microbiota transmits information to the brain and how it influences brain cognition and function. In this review, we summarized the multiple pathways involved in the gut microbiome in AD and provided detailed treatment strategies based on the gut microbiome. Based on these observations, this review also discusses the problems, challenges, and strategies to address current therapeutic strategies.}, }
@article {pmid37728335, year = {2023}, author = {Mancabelli, L and Taurino, G and Ticinesi, A and Ciociola, T and Vacondio, F and Milani, C and Fontana, F and Lugli, GA and Tarracchini, C and Alessandri, G and Viappiani, A and Bianchi, M and Nouvenne, A and Chetta, AA and Turroni, F and Meschi, T and Mor, M and Bussolati, O and Ventura, M}, title = {Disentangling the interactions between nasopharyngeal and gut microbiome and their involvement in the modulation of COVID-19 infection.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0219423}, doi = {10.1128/spectrum.02194-23}, pmid = {37728335}, issn = {2165-0497}, abstract = {The human organism is inhabited by trillions of microorganisms, known as microbiota, which are considered to exploit a pivotal role in the regulation of host health and immunity. Recent investigations have suggested a relationship between the composition of the human microbiota and COVID-19 infection, highlighting a possible role of bacterial communities in the modulation of the disease severity. In this study, we performed a shotgun metagenomics analysis to explore and compare the nasopharyngeal microbiota of 38 hospitalized Italian patients with and without COVID-19 infection during the third and fourth pandemic waves. In detail, the metagenomic analysis combined with specific correlation analyses suggested a positive association of several microbial species, such as S. parasanguinis and P. melaninogenica, with the severity of COVID-19 infection. Furthermore, the comparison of the microbiota composition between the nasopharyngeal and their respective fecal samples highlighted an association between these different compartments represented by a sharing of several bacterial species. Additionally, lipidomic and deep-shotgun functional analyses of the fecal samples suggested a metabolic impact of the microbiome on the host's immune response, indicating the presence of key metabolic compounds in COVID-19 patients, such as lipid oxidation end products, potentially related to the inflammatory state. Conversely, the patients without COVID-19 displayed enzymatic patterns associated with the biosynthesis and degradation of specific compounds like lysine (synthesis) and phenylalanine (degradation) that could positively impact disease severity and contribute to modulating COVID-19 infection. IMPORTANCE The human microbiota is reported to play a major role in the regulation of host health and immunity, suggesting a possible impact on the severity of COVID-19 disease. This preliminary study investigated the possible correlation between nasopharyngeal microbiota and COVID-19 infection. In detail, the analysis of the nasopharyngeal microbiota of hospitalized Italian patients with and without COVID-19 infection suggested a positive association of several microbial species with the severity of the disease and highlighted a sharing of several bacteria species with the respective fecal samples. Moreover, the metabolic analyses suggested a possible impact of the microbiome on the host's immune response and the disease severity.}, }
@article {pmid37727856, year = {2023}, author = {Meng, D and Yuan, MM and Li, J}, title = {Editorial: Microbe assisted plant resistance to abiotic stresses.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1277682}, pmid = {37727856}, issn = {1664-462X}, }
@article {pmid37727808, year = {2023}, author = {Herzog, EL and Kreuzer, M and Zinkernagel, MS and Zysset-Burri, DC}, title = {Challenges and insights in the exploration of the low abundance human ocular surface microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1232147}, pmid = {37727808}, issn = {2235-2988}, mesh = {Humans ; *Nylons ; Reproducibility of Results ; Face ; Conjunctiva ; *Microbiota ; }, abstract = {PURPOSE: The low microbial abundance on the ocular surface results in challenges in the characterization of its microbiome. The purpose of this study was to reveal factors introducing bias in the pipeline from sample collection to data analysis of low-abundant microbiomes.<br><br>METHODS: Lower conjunctiva and lower lid swabs were collected from six participants using either standard cotton or flocked nylon swabs. Microbial DNA was isolated with two different kits (with or without prior host DNA depletion and mechanical lysis), followed by whole-metagenome shotgun sequencing with a high sequencing depth set at 60 million reads per sample. The relative microbial compositions were generated using the two different tools MetaPhlan3 and Kraken2.<br><br>RESULTS: The total amount of extracted DNA was increased by using nylon flocked swabs on the lower conjunctiva. In total, 269 microbial species were detected. The most abundant bacterial phyla were Actinobacteria, Firmicutes and Proteobacteria. Depending on the DNA extraction kit and tool used for profiling, the microbial composition and the relative abundance of viruses varied.<br><br>CONCLUSION: The microbial composition on the ocular surface is not dependent on the swab type, but on the DNA extraction method and profiling tool. These factors have to be considered in further studies about the ocular surface microbiome and other sparsely colonized microbiomes in order to improve data reproducibility. Understanding challenges and biases in the characterization of the ocular surface microbiome may set the basis for microbiome-altering interventions for treatment of ocular surface associated diseases.}, }
@article {pmid37727718, year = {2023}, author = {Del Giglio, A and Atui, FC}, title = {Fecal transplantation in patient with metastatic melanoma refractory to immunotherapy: A case report.}, journal = {World journal of clinical cases}, volume = {11}, number = {24}, pages = {5830-5834}, pmid = {37727718}, issn = {2307-8960}, abstract = {BACKGROUND: Immunotherapy has revolutionized the treatment of metastatic melanoma, but a significant proportion of patients still experience treatment resistance. Fecal microbiota transplantation (FMT) has emerged as a potential strategy to overcome immunotherapy resistance by modulating the gut microbiome.<br><br>CASE SUMMARY: We present a case report of a 57-year-old male with metastatic melanoma refractory to immunotherapy who received FMT in combination with anti-programmed death-ligand 1 (PD-L1) immunotherapy (pembrolizumab). After failing multiple lines of treatment, the patient underwent a single FMT procedure by colonoscopy using fecal material from a female metastatic melanoma donor who successfully responded to immunotherapy. Following FMT, the patient demonstrated a response with decreased subcutaneous disease and subsequently underwent surgery to remove the residual disease. Despite a subsequent recurrence in the small bowel that was resected, the patient remained on pembrolizumab without evidence of melanoma recurrence at the time of writing.<br><br>CONCLUSION: The favorable clinical and long-lasting effect we saw in our patient without significant toxicity suggests that this procedure should be considered in similar patients with immunotherapy refractory melanomas.}, }
@article {pmid37727689, year = {2023}, author = {de Freitas, STF and Faria, G and Silva, FG and Batista, MA and Augusto, DSS and Dyszy, FH and Vitorino, LC}, title = {The morphoanatomy of Serjania erecta Radlk (Sapindaceae) provides evidence of biotrophic interactions by endophytic fungi within leaves.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15980}, pmid = {37727689}, issn = {2167-8359}, mesh = {*Sapindaceae ; Bipolaris ; Brazil ; Curvularia ; }, abstract = {BACKGROUND: The leaves of Serjania erecta Radlk (Sapindaceae) are renowned in ethnobotany for their medicinal properties and are significant as a medicinal resource for traditional Brazilian communities. As necrotic spots are common on these leaves, indicating interaction with phytopathogenic fungi, it was hypothesized that biotrophic fungal species colonize the leaf tissues of S. erecta.<br><br>METHODS: To test this hypothesis, we employed standard techniques in plant anatomy, which enabled us to investigate the interaction of fungal structures with plant tissues and describe the morphoanatomical and histochemical characteristics of the epidermis and limbus of S. erecta.<br><br>RESULTS: The anatomical analysis showed the existence of leaf teeth on the leaf tips. Additionally, hyphae, conidiospores, and spores of Bipolaris/Curvularia species were detected on the adaxial epidermis. Moreover, melanized microsclerotia were found in glandular areas of the leaf teeth and the phloem, providing evidence of biotrophic behavior. The hypothesis that biotrophic phytopathogenic fungi interact with S. erecta leaf tissues was confirmed, despite the presence of many bioactive compounds (such as flavonoids, alkaloids, and essential oils), as evidenced by histochemical analyses. The presence of tector, glandular, and scabiform trichomes on the leaf teeth and epidermis was also revealed. This study presents, for the first time, the synthesis of essential oils and alkaloids in the leaves of S. erecta. Additionally, it investigates previously unexplained aspects of the anatomy and histochemistry of the species, as well as its interaction with resident microorganisms. Therefore, it is recommended that future research focus on extracting and characterizing the oils and alkaloids of S. erecta, as well as exploring other aspects related to its microbiome and its relationship.}, }
@article {pmid37727634, year = {2023}, author = {Wilson, SMG and Peach, JT and Fausset, H and Miller, ZT and Walk, ST and Yeoman, CJ and Bothner, B and Miles, MP}, title = {Metabolic impact of polyphenol-rich aronia fruit juice mediated by inflammation status of gut microbiome donors in humanized mouse model.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1244692}, pmid = {37727634}, issn = {2296-861X}, abstract = {BACKGROUND: The Aronia melanocarpa fruit is emerging as a health food owing to its high polyphenolic content and associated antioxidant activity. Antioxidant-rich foods, such as Aronia fruit, may counter inflammatory stimuli and positively modulate the gut microbiome. However, a comprehensive study characterizing the impact of Aronia fruit supplementation has not been completed. Therefore, we completed analyses measuring the metabolic, microbial, and inflammatory effects of a diet supplemented with Aronia fruit juice.<br><br>METHOD: Humanized mice were generated by colonizing gnotobiotic mice with microbiomes from human donors presenting disparate inflammation levels. Blood and fecal samples were collected throughout the course of an 8-week dietary intervention with either Aronia juice or a carbohydrate-matched beverage alone (2&#x2009;weeks) or in combination with a high-fat diet to induce inflammation (6&#x2009;weeks). Samples were analyzed using 16S rRNA gene sequencing (stool) and liquid chromatography-mass spectrometry (serum).<br><br>RESULTS: We demonstrated transfer of microbiome composition and diversity and metabolic characteristics from humans with low and high inflammation levels to second-generation humanized mice. Aronia supplementation provided robust protection against high-fat diet induced metabolic and microbiome changes that were dependent in part on microbiome donor. Aronia induced increases in bacteria of the Eggerthellaceae genus (7-fold) which aligns with its known ability to metabolize (poly)phenols and in phosphatidylcholine metabolites which are consistent with improved gut barrier function. The gut microbiome from a low inflammation phenotype donor provided protection against high-fat diet induced loss of microbiome &#x3b2;-diversity and global metabolomic shifts compared to that from the high inflammation donor.<br><br>CONCLUSION: These metabolic changes elucidate pathway-specific drivers of reduced inflammation stemming from both Aronia and the gut microbiota.}, }
@article {pmid37727347, year = {2023}, author = {Cheng, X and Wang, M and Yuan, MM and Li, J and Xiong, W}, title = {Editorial: Rhizosphere microbiome engineering for crop cultivation.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1267442}, pmid = {37727347}, issn = {2296-4185}, }
@article {pmid37727327, year = {2023}, author = {Tendilla-Beltrán, H and Martín-Hernández, D}, title = {Editorial: Non-canonical pathways of psychiatric drugs: beyond their neurotransmitter action.}, journal = {Frontiers in neuroscience}, volume = {17}, number = {}, pages = {1278748}, pmid = {37727327}, issn = {1662-4548}, }
@article {pmid37727291, year = {2023}, author = {Jiang, X and Niu, M and Qin, K and Hu, Y and Li, Y and Che, C and Wang, C and Mu, C and Wang, H}, title = {The shared microbiome in mud crab (Scylla paramamosain) of Sanmen Bay, China: core gut microbiome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1243334}, pmid = {37727291}, issn = {1664-302X}, abstract = {INTRODUCTION: The mud crab, Scylla paramamosain, holds great commercial significance as a marine crustacean widely cultivated in the Indo-Pacific region. Understanding the core gut microbiota of aquatic animals is crucial for their overall health and growth, yet the core gut microbiota of mud crab remains poorly characterized.<br><br>METHODS: In this study, we gathered gut samples from mud crabs across five locations within Sanmen Bay, China. Through the utilization of high-throughput sequencing, we delved into the composition of the gut microbial community and identified the core gut microbiome of mud crab.<br><br>RESULTS: Our results demonstrate that the gut microbial diversity of mud crab did not exhibit significant variation among the five sampling sites, although there were some differences in community richness. At the phylum level, we identified 35 representative phyla, with Firmicutes, Proteobacteria, Bacteroidota, and Campilobacterota as the dominant phyla. Among the 815 representative genera, we discovered 19 core genera, which accounted for 65.45% of the total sequences. These core genera were distributed across 6 phyla, and among them, Photobacterium exhibited the highest average relative abundance.<br><br>DISCUSSION: Photobacterium has probiotic activity and may play a crucial role in enhancing the immune response of the host and maintaining the diversity of the gut microbiota. Moreover, we observed a positive correlation between the relative abundance of core genera and the stability of the gut microbial community. Furthermore, our findings revealed distinct differences in gut microbial composition and specific taxa between the sexes of mud crab. These differences subsequently influenced the functionality of the gut microbial community. Overall, our investigation sheds light on the core gut microbiota of mud crab, emphasizing the importance of core gut microbial communities in maintaining the health and growth of these commercially significant marine crustaceans.}, }
@article {pmid37727289, year = {2023}, author = {Volmer, JG and McRae, H and Morrison, M}, title = {The evolving role of methanogenic archaea in mammalian microbiomes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1268451}, pmid = {37727289}, issn = {1664-302X}, abstract = {Methanogenic archaea (methanogens) represent a diverse group of microorganisms that inhabit various environmental and host-associated microbiomes. These organisms play an essential role in global carbon cycling given their ability to produce methane, a potent greenhouse gas, as a by-product of their energy production. Recent advances in culture-independent and -dependent studies have highlighted an increased prevalence of methanogens in the host-associated microbiome of diverse animal species. Moreover, there is increasing evidence that methanogens, and/or the methane they produce, may play a substantial role in human health and disease. This review addresses the expanding host-range and the emerging view of host-specific adaptations in methanogen biology and ecology, and the implications for host health and disease.}, }
@article {pmid37727151, year = {2023}, author = {Manzano, C and Fuentes-Martín, &#xc1; and Zuil, M and Gil Barturen, M and González, J and Cilleruelo-Ramos, &#xc1;}, title = {[Questions and Answers in Lung Cancer].}, journal = {Open respiratory archives}, volume = {5}, number = {3}, pages = {100264}, pmid = {37727151}, issn = {2659-6636}, abstract = {Over the past 2 decades, scientific evidence has strongly supported the use of low-radiation dose chest computed tomography (CT) as a screening technique for lung cancer. This approach has resulted in a significant reduction in mortality rates by enabling the detection of early-stage lung cancer amenable to potentially curative treatments. Regarding diagnosis, there are also novel methods under study, such as liquid biopsy, identification of the pulmonary microbiome, and the use of artificial intelligence techniques, which will play a key role in the near future. At present, there is a growing trend towards less invasive surgical procedures, such as segmentectomy, as an alternative to lobectomy. This procedure is based on 2 recent clinical trials conducted on peripheral tumors measuring less than 2 cm. Although these approaches have demonstrated comparable survival rates, there remains controversy due to uncertainties surrounding recurrence rates and functional capacity preservation. With regard to adjuvant therapy, immunotherapy, either as a monotherapy or in conjunction with chemotherapy, has shown encouraging results in resectable stages of locally advanced lung cancer, demonstrating complete pathologic responses and improved overall survival.After surgery treatment, despite the lack of solid evidence for long-term follow-up of these patients, clinical practice recommends periodic CT scans during the early years.In conclusion, there have been significant advances in lung cancer that have improved diagnostic techniques using new technologies and screening programs. Furthermore, the treatment of lung cancer is increasingly personalized, resulting in an improvement in the survival of patients.}, }
@article {pmid37726739, year = {2023}, author = {Petrisko, TJ and Gargus, M and Chu, SH and Selvan, P and Whiteson, KL and Tenner, AJ}, title = {Influence of complement protein C1q or complement receptor C5aR1 on gut microbiota composition in wildtype and Alzheimer's mouse models.}, journal = {Journal of neuroinflammation}, volume = {20}, number = {1}, pages = {211}, pmid = {37726739}, issn = {1742-2094}, support = {T32 AG000096/NH/NIH HHS/United States ; AG060148/NH/NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Gastrointestinal Microbiome ; Complement C1q/genetics ; *Alzheimer Disease/genetics ; *Neurodegenerative Diseases ; Neuroinflammatory Diseases ; Receptors, Complement/genetics ; Disease Models, Animal ; }, abstract = {The contribution of the gut microbiome to neuroinflammation, cognition, and Alzheimer's disease progression has been highlighted over the past few years. Additionally, inhibition of various components of the complement system has repeatedly been demonstrated to reduce neuroinflammation and improve cognitive performance in AD mouse models. Whether the deletion of these complement components is associated with distinct microbiome composition, which could impact neuroinflammation and cognitive performance in mouse models has not yet been examined. Here, we provide a comprehensive analysis of conditional and constitutive knockouts, pharmacological inhibitors, and various housing paradigms for the animal models and wild-type controls at various ages. We aimed to determine the impact of C1q or C5aR1 inhibition on the microbiome in the Arctic and Tg2576 mouse models of AD, which develop amyloid plaques at different ages and locations. Analysis of fecal samples from WT and Arctic mice following global deletion of C1q demonstrated significant alterations to the microbiomes of Arctic but not WT mice, with substantial differences in abundances of Erysipelotrichales, Clostridiales and Alistipes. While no differences in microbiome diversity were detected between cohoused wildtype and Arctic mice with or without the constitutive deletion of the downstream complement receptor, C5aR1, a difference was detected between the C5aR1 sufficient (WT and Arctic) and deficient (C5ar1KO and ArcticC5aR1KO) mice, when the mice were housed segregated by C5aR1 genotype. However, cohousing of C5aR1 sufficient and deficient wildtype and Arctic mice resulted in a convergence of the microbiomes and equalized abundances of each identified order and genus across all genotypes. Similarly, pharmacologic treatment with the C5aR1 antagonist, PMX205, beginning at the onset of beta-amyloid plaque deposition in the Arctic and Tg2576 mice, demonstrated no impact of C5aR1 inhibition on the microbiome. This study demonstrates the importance of C1q in microbiota homeostasis in neurodegenerative disease. In addition, while demonstrating that constitutive deletion of C5aR1 can significantly alter the composition of the fecal microbiome, these differences are not present when C5aR1-deficient mice are cohoused with C5aR1-sufficient animals with or without the AD phenotype and suggests limited if any contribution of the microbiome to the previously observed prevention of cognitive and neuronal loss in the C5aR1-deficient AD models.}, }
@article {pmid37726418, year = {2023}, author = {Greten, TF and Villanueva, A and Korangy, F and Ruf, B and Yarchoan, M and Ma, L and Ruppin, E and Wang, XW}, title = {Biomarkers for immunotherapy of hepatocellular carcinoma.}, journal = {Nature reviews. Clinical oncology}, volume = {}, number = {}, pages = {}, pmid = {37726418}, issn = {1759-4782}, abstract = {Immune-checkpoint inhibitors (ICIs) are now widely used for the treatment of patients with advanced-stage hepatocellular carcinoma (HCC). Two different ICI-containing regimens, atezolizumab plus bevacizumab and tremelimumab plus durvalumab, are now approved standard-of-care first-line therapies in this setting. However, and despite substantial improvements in survival outcomes relative to sorafenib, most patients with advanced-stage HCC do not derive durable benefit from these regimens. Advances in genome sequencing including the use of single-cell RNA sequencing (both of tumour material and blood samples), as well as immune cell identification strategies and other techniques such as radiomics and analysis of the microbiota, have created considerable potential for the identification of novel predictive biomarkers enabling the accurate selection of patients who are most likely to derive benefit from ICIs. In this Review, we summarize data on the immunology of HCC and the outcomes in patients receiving ICIs for the treatment of this disease. We then provide an overview of current biomarker use and developments in the past 5 years, including gene signatures, circulating tumour cells, high-dimensional flow cytometry, single-cell RNA sequencing as well as approaches involving the microbiome, radiomics and clinical markers. Novel concepts for further biomarker development in HCC are then discussed including biomarker-driven trials, spatial transcriptomics and integrated 'big data' analysis approaches. These concepts all have the potential to better identify patients who are most likely to benefit from ICIs and to promote the development of new treatment approaches.}, }
@article {pmid37726374, year = {2023}, author = {Hansen, ZA and Vasco, K and Rudrik, JT and Scribner, KT and Zhang, L and Manning, SD}, title = {Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15524}, pmid = {37726374}, issn = {2045-2322}, support = {U19AI090872/NH/NIH HHS/United States ; U19AI090872/NH/NIH HHS/United States ; }, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/genetics ; Drug Resistance, Bacterial/genetics ; *Anti-Infective Agents ; Aminoglycosides ; }, abstract = {Enteric pathogens cause widespread foodborne illness and are increasingly resistant to important antibiotics yet their ecological impact on the gut microbiome and resistome is not fully understood. Herein, shotgun metagenome sequencing was applied to stool DNA from 60 patients (cases) during an enteric bacterial infection and after recovery (follow-ups). Overall, the case samples harbored more antimicrobial resistance genes (ARGs) with greater resistome diversity than the follow-up samples (p < 0.001), while follow-ups had more diverse gut microbiota (p < 0.001). Although cases were primarily defined by genera Escherichia, Salmonella, and Shigella along with ARGs for multi-compound and multidrug resistance, follow-ups had a greater abundance of Bacteroidetes and Firmicutes phyla and resistance genes for tetracyclines, macrolides, lincosamides, and streptogramins, and aminoglycosides. A host-tracking analysis revealed that Escherichia was the primary bacterial host of ARGs in both cases and follow-ups, with a greater abundance occurring during infection. Eleven distinct extended spectrum beta-lactamase (ESBL) genes were identified during infection, with some detectable upon recovery, highlighting the potential for gene transfer within the community. Because of the increasing incidence of disease caused by foodborne pathogens and their role in harboring and transferring resistance determinants, this study enhances our understanding of how enteric infections impact human gut ecology.}, }
@article {pmid37726348, year = {2023}, author = {Warner, BB and Rosa, BA and Ndao, IM and Tarr, PI and Miller, JP and England, SK and Luby, JL and Rogers, CE and Hall-Moore, C and Bryant, RE and Wang, JD and Linneman, LA and Smyser, TA and Smyser, CD and Barch, DM and Miller, GE and Chen, E and Martin, J and Mitreva, M}, title = {Social and psychological adversity are associated with distinct mother and infant gut microbiome variations.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5824}, pmid = {37726348}, issn = {2041-1723}, support = {R01 MH113883/MH/NIMH NIH HHS/United States ; }, mesh = {Female ; Pregnancy ; Humans ; Infant ; *Gastrointestinal Microbiome/genetics ; Mothers ; Case-Control Studies ; Bifidobacterium/genetics ; Cytokines ; Vitamins ; }, abstract = {Health disparities are driven by underlying social disadvantage and psychosocial stressors. However, how social disadvantage and psychosocial stressors lead to adverse health outcomes is unclear, particularly when exposure begins prenatally. Variations in the gut microbiome and circulating proinflammatory cytokines offer potential mechanistic pathways. Here, we interrogate the gut microbiome of mother-child dyads to compare high-versus-low prenatal social disadvantage, psychosocial stressors and maternal circulating cytokine cohorts (prospective case-control study design using gut microbiomes from 121 dyads profiled with 16 S rRNA sequencing and 89 dyads with shotgun metagenomic sequencing). Gut microbiome characteristics significantly predictive of social disadvantage and psychosocial stressors in the mothers and children indicate that different discriminatory taxa and related pathways are involved, including many species of Bifidobacterium and related pathways across several comparisons. The lowest inter-individual gut microbiome similarity was observed among high-social disadvantage/high-psychosocial stressors mothers, suggesting distinct environmental exposures driving a diverging gut microbiome assembly compared to low-social disadvantage/low-psychosocial stressors controls (P = 3.5 × 10[-5] for social disadvantage, P = 2.7 × 10[-15] for psychosocial stressors). Children's gut metagenome profiles at 4 months also significantly predicted high/low maternal prenatal IL-6 (P = 0.029), with many bacterial species overlapping those identified by social disadvantage and psychosocial stressors. These differences, based on maternal social and psychological status during a critical developmental window early in life, offer potentially modifiable targets to mitigate health inequities.}, }
@article {pmid37725594, year = {2023}, author = {Madison, JD and LaBumbard, BC and Woodhams, DC}, title = {Shotgun metagenomics captures more microbial diversity than targeted 16S rRNA gene sequencing for field specimens and preserved museum specimens.}, journal = {PloS one}, volume = {18}, number = {9}, pages = {e0291540}, pmid = {37725594}, issn = {1932-6203}, mesh = {Genes, rRNA ; *Metagenomics ; *Museums ; RNA, Ribosomal, 16S/genetics ; Benchmarking ; }, abstract = {The use of museum specimens for research in microbial evolutionary ecology remains an under-utilized investigative dimension with important potential. Despite this potential, there remain barriers in methodology and analysis to the wide-spread adoption of museum specimens for such studies. Here, we hypothesized that there would be significant differences in taxonomic prediction and related diversity among sample type (museum or fresh) and sequencing strategy (medium-depth shotgun metagenomic or 16S rRNA gene). We found dramatically higher predicted diversity from shotgun metagenomics when compared to 16S rRNA gene sequencing in museum and fresh samples, with this differential being larger in museum specimens. Broadly confirming these hypotheses, the highest diversity found in fresh samples was with shotgun sequencing using the Rep200 reference inclusive of viruses and microeukaryotes, followed by the WoL reference database. In museum-specimens, community diversity metrics also differed significantly between sequencing strategies, with the alpha-diversity ACE differential being significantly greater than the same comparisons made for fresh specimens. Beta diversity results were more variable, with significance dependent on reference databases used. Taken together, these findings demonstrate important differences in diversity results and prompt important considerations for future experiments and downstream analyses aiming to incorporate microbiome datasets from museum specimens.}, }
@article {pmid37725094, year = {2023}, author = {Rossetto Marcelino, V}, title = {The value of connections.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37725094}, issn = {2050-084X}, mesh = {*Gastrointestinal Microbiome ; }, abstract = {High proportions of gut bacteria that produce their own food can be an indicator for poor gut health.}, }
@article {pmid37724912, year = {2023}, author = {Metko, D and McMullen, E and Borovsky, D and Abu-Hilal, M}, title = {The Effects of Naturally Fermented Foods in Atopic Dermatitis: A Scoping Review.}, journal = {Journal of cutaneous medicine and surgery}, volume = {}, number = {}, pages = {12034754231199755}, doi = {10.1177/12034754231199755}, pmid = {37724912}, issn = {1615-7109}, }
@article {pmid37724888, year = {2023}, author = {Jiang, X and Liu, J and Xi, Y and Zhang, Q and Wang, Y and Zhao, M and Lu, X and Wu, H and Shan, T and Ni, B and Zhang, W and Ma, X}, title = {Virome of high-altitude canine digestive tract and genetic characterization of novel viruses potentially threatening human health.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0034523}, doi = {10.1128/msphere.00345-23}, pmid = {37724888}, issn = {2379-5042}, abstract = {The majority of currently emerging infectious illnesses are zoonotic infections, which have caused serious public health and economic implications. The development of viral metagenomics has helped us to explore unknown viruses. We collected 1,970 canine feces from Yushu and Guoluo in the plateau region of China for this study to do a metagenomics analysis of the viral community of the canine digestive tract. Our analysis identified 203 novel viruses, classified into 11 known families and 2 unclassified groups. These viruses include the hepatitis E virus, first identified in dogs, and the astrovirus, coronavirus, polyomavirus, and others. The relationship between the newly identified canine viruses and known viruses was investigated through the use of phylogenetic analysis. Furthermore, we demonstrated the cross-species transmission of viruses and predicted new viruses that may cause diseases in both humans and animals, providing technical support for the prevention and control of diseases caused by environmental pollution viruses. IMPORTANCE Most emerging infectious diseases are due to zoonotic disease agents. Because of their effects on the security of human or animal life, agriculture production, and food safety, zoonotic illnesses and livestock diseases are of worldwide significance. Because dogs are closely related to humans and domestic animals, they serve as one of the important links in the transmission of zoonotic and livestock diseases. Canines can contaminate the environment in which humans live such as water and soil through secretions, potentially altering the human gut microbiota or causing diseases. Our study enriched the viral community in the digestive tract microbiome of dogs and found types of viruses that threaten human health, providing technical support for the prevention and control of early warning of diseases caused by environmental contaminant viruses.}, }
@article {pmid37724869, year = {2023}, author = {Leroux, N and Sylvain, FE and Holland, A and Luis Val, A and Derome, N}, title = {Gut microbiota of an Amazonian fish in a heterogeneous riverscape: integrating genotype, environment, and parasitic infections.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0275522}, doi = {10.1128/spectrum.02755-22}, pmid = {37724869}, issn = {2165-0497}, abstract = {A number of key factors can structure the gut microbiota of fish such as environment, diet, health state, and genotype. Mesonauta festivus, an Amazonian cichlid, is a relevant model organism to study the relative contribution of these factors on the community structure of fish gut microbiota. M. festivus has well-studied genetic populations and thrives in rivers with drastically divergent physicochemical characteristics. Here, we collected 167 fish from 12 study sites and used 16S and 18S rRNA metabarcoding approaches to characterize the gut microbiome structure of M. festivus. These data sets were analyzed in light of the host fish genotypes (genotyping-by-sequencing) and an extensive characterization of environmental physico-chemical parameters. We explored the relative contribution of environmental dissimilarity, the presence of parasitic taxa, and phylogenetic relatedness on structuring the gut microbiota. We documented occurrences of Nyctotherus sp. infecting a fish and linked its presence to a dysbiosis of the host gut microbiota. Moreover, we detected the presence of helminths which had a minor impact on the gut microbiota of their host. In addition, our results support a higher impact of the phylogenetic relatedness between fish rather than environmental similarity between sites of study on structuring the gut microbiota for this Amazonian cichlid. Our study in a heterogeneous riverscape integrates a wide range of factors known to structure fish gut microbiomes. It significantly improves understanding of the complex relationship between fish, their parasites, their microbiota, and the environment. IMPORTANCE The gut microbiota is known to play important roles in its host immunity, metabolism, and comportment. Its taxonomic composition is modulated by a complex interplay of factors that are hard to study simultaneously in natural systems. Mesonauta festivus, an Amazonian cichlid, is an interesting model to simultaneously study the influence of multiple variables on the gut microbiota. In this study, we explored the relative contribution of the environmental conditions, the presence of parasitic infections, and the genotype of the host on structuring the gut microbiota of M. festivus in Amazonia. Our results highlighted infections by a parasitic ciliate that caused a disruption of the gut microbiota and by parasitic worms that had a low impact on the microbiota. Finally, our results support a higher impact of the genotype than the environment on structuring the microbiota for this fish. These findings significantly improve understanding of the complex relationship among fish, their parasites, their microbiota, and the environment.}, }
@article {pmid37724851, year = {2023}, author = {Marangon, E and Uthicke, S and Patel, F and Marzinelli, EM and Bourne, DG and Webster, NS and Laffy, PW}, title = {Life-stage specificity and cross-generational climate effects on the microbiome of a tropical sea urchin (Echinodermata: Echinoidea).}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.17124}, pmid = {37724851}, issn = {1365-294X}, support = {//Australian Institute of Marine Science/ ; }, abstract = {Microbes play a critical role in the development and health of marine invertebrates, though microbial dynamics across life stages and host generations remain poorly understood in most reef species, especially in the context of climate change. Here, we use a 4-year multigenerational experiment to explore microbe-host interactions under the Intergovernmental Panel on Climate Change (IPCC)-forecast climate scenarios in the rock-boring tropical urchin Echinometra sp. A. Adult urchins (F0) were exposed for 18 months to increased temperature and pCO2 levels predicted for years 2050 and 2100 under RCP 8.5, a period which encompassed spawning. After rearing F1 offspring for a further 2 years, spawning was induced, and F2 larvae were raised under current day and 2100 conditions. Cross-generational climate effects were also explored in the microbiome of F1 offspring through a transplant experiment. Using 16S rRNA gene sequence analysis, we determined that each life stage and generation was associated with a distinct microbiome, with higher microbial diversity observed in juveniles compared to larval stages. Although life-stage specificity was conserved under climate conditions projected for 2050 and 2100, we observed changes in the urchin microbial community structure within life stages. Furthermore, we detected a climate-mediated parental effect when juveniles were transplanted among climate treatments, with the parental climate treatment influencing the offspring microbiome. Our findings reveal a potential for cross-generational impacts of climate change on the microbiome of a tropical invertebrate species.}, }
@article {pmid37724759, year = {2023}, author = {Gill, SR and O'Connor, TG and Kopycka-Kedzierawski, DT}, title = {Early childhood caries prevention through a developmental origins model of the oral microbiome, host and oral environment, and sociodemographic influences.}, journal = {Quintessence international (Berlin, Germany : 1985)}, volume = {54}, number = {8}, pages = {610-611}, doi = {10.3290/j.qi.b4417923}, pmid = {37724759}, issn = {1936-7163}, }
@article {pmid37724467, year = {2023}, author = {Chew, RJJ and Goh, CE and Sriram, G and Preshaw, PM and Tan, KS}, title = {Microbial biomarkers as a predictor of periodontal treatment response: A systematic review.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.13188}, pmid = {37724467}, issn = {1600-0765}, support = {//Ministry of Education, Singapore/ ; }, abstract = {To evaluate the prognostic accuracy of microbial biomarkers and their associations with the response to active periodontal treatment (APT) and supportive periodontal therapy (SPT). Microbial dysbiosis plays a crucial role in the disease processes of periodontitis. Biomarkers based on microbial composition may offer additional prognostic value, supplementing the limitations of current clinical parameters. While these microbial biomarkers have been clinically evaluated, there is a lack of consensus regarding their prognostic accuracy. A structured search strategy was applied to MEDLINE (PubMed), Cochrane Library, and Embase on 1/11/2022 to identify relevant publications. Prospective clinical studies involving either APT or SPT, with at least 3-month follow-up were included. There were no restrictions on the type of microbial compositional analysis. 1918 unique records were retrieved, and 13 studies (comprising 943 adult patients) were included. Heterogeneity of the studies precluded a meta-analysis, and none of the included studies had performed the sequence analysis of the periodontal microbiome. Seven and six studies reported on response to APT and SPT, respectively. The prognostic accuracy of the microbial biomarkers for APT and SPT was examined in only two and four studies, respectively. Microbial biomarkers had limited predictive accuracy for APT and inconsistent associations for different species across studies. For SPT, elevated abundance of periodontal pathogens at the start of SPT was predictive of subsequent periodontal progression. Similarly, persistent high pathogen loads were consistently associated with progressive periodontitis, defined as an increased pocket probing depth or clinical attachment loss. While there was insufficient evidence to support the clinical use of microbial biomarkers as prognostic tools for active periodontal treatment outcomes, biomarkers that quantify periodontal pathogen loads may offer prognostic value for predicting progressive periodontitis in the subsequent supportive periodontal therapy phase. Additional research will be required to translate information regarding subgingival biofilm composition and phenotype into clinically relevant prognostic tools.}, }
@article {pmid37723566, year = {2023}, author = {Ruparell, A and Gibbs, M and Colyer, A and Wallis, C and Harris, S and Holcombe, LJ}, title = {Developing diagnostic tools for canine periodontitis: combining molecular techniques and machine learning models.}, journal = {BMC veterinary research}, volume = {19}, number = {1}, pages = {163}, pmid = {37723566}, issn = {1746-6148}, mesh = {Animals ; Dogs ; Prospective Studies ; *Periodontitis/diagnosis/veterinary ; *Periodontal Diseases/diagnosis/veterinary ; *Gingivitis/diagnosis/veterinary ; *Dog Diseases/diagnosis ; Machine Learning ; }, abstract = {BACKGROUND: Dental plaque microbes play a key role in the development of periodontal disease. Numerous high-throughput sequencing studies have generated understanding of the bacterial species associated with both canine periodontal health and disease. Opportunities therefore exist to utilise these bacterial biomarkers to improve disease diagnosis in conscious-based veterinary oral health checks. Here, we demonstrate that molecular techniques, specifically quantitative polymerase chain reaction (qPCR) can be utilised for the detection of microbial biomarkers associated with canine periodontal health and disease.<br><br>RESULTS: Over 40 qPCR assays targeting single microbial species associated with canine periodontal health, gingivitis and early periodontitis were developed and validated. These were used to quantify levels of the respective taxa in canine subgingival plaque samples collected across periodontal health (PD0), gingivitis (PD1) and early periodontitis (PD2). When qPCR outputs were compared to the corresponding high-throughput sequencing data there were strong correlations, including a periodontal health associated taxa, Capnocytophaga sp. COT-339 (rs =0.805), and two periodontal disease associated taxa, Peptostreptococcaceae XI [G-4] sp. COT-019 (rs=0.902) and Clostridiales sp. COT-028 (rs=0.802). The best performing models, from five machine learning approaches applied to the qPCR data for these taxa, estimated 85.7% sensitivity and 27.5% specificity for Capnocytophaga sp. COT-339, 74.3% sensitivity and 67.5% specificity for Peptostreptococcaceae XI [G-4] sp. COT-019, and 60.0% sensitivity and 80.0% specificity for Clostridiales sp. COT-028.<br><br>CONCLUSIONS: A qPCR-based approach is an accurate, sensitive, and cost-effective method for detection of microbial biomarkers associated with periodontal health and disease. Taken together, the correlation between qPCR and high-throughput sequencing outputs, and early accuracy insights, indicate the strategy offers a prospective route to the development of diagnostic tools for canine periodontal disease.}, }
@article {pmid37723422, year = {2023}, author = {Hess, MK and Hodgkinson, HE and Hess, AS and Zetouni, L and Budel, JCC and Henry, H and Donaldson, A and Bilton, TP and van Stijn, TC and Kirk, MR and Dodds, KG and Brauning, R and McCulloch, AF and Hickey, SM and Johnson, PL and Jonker, A and Morton, N and Hendy, S and Oddy, VH and Janssen, PH and McEwan, JC and Rowe, SJ}, title = {Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {551}, pmid = {37723422}, issn = {1471-2164}, support = {SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; Curiosity Fund//AgResearch/ ; Curiosity Fund//AgResearch/ ; 119400343//Meat and Livestock Australia and the Australian Commonwealth Government/ ; 119400343//Meat and Livestock Australia and the Australian Commonwealth Government/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; C10X1306//Ministry of Business, Innovation and Employment/ ; }, mesh = {Animals ; Sheep/genetics ; *Metagenome ; Rumen ; *Microbiota ; Livestock ; Methane ; }, abstract = {BACKGROUND: Producing animal protein while reducing the animal's impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to reduce the environmental impact of livestock production, but these traits are difficult and expensive to measure on many animals. The rumen microbiome may serve as a proxy for these traits due to its role in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible.<br><br>RESULTS: Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (New Zealand or Australia) at the time of sample collection. Systematic effects were found to have minimal influence on metagenome profiles. Diet was a major driver of differences between samples, followed by time off feed, then age of the sheep. The RF approach resulted in more reads being assigned per sample and afforded greater resolution when distinguishing between groups than the RB approach. Normalizing relative abundances within the sampling Cohort abolished structures related to age, diet, and time off feed, allowing a clear signal based on methane emissions to be elucidated. Genus-level abundances of rumen microbes showed low-to-moderate heritability and repeatability and were consistent between diets.<br><br>CONCLUSIONS: Variation in rumen metagenomic profiles was influenced by diet, age, time off feed and genetics. Not accounting for environmental factors may limit the ability to associate the profile with traits of interest. However, these differences can be accounted for by adjusting for Cohort effects, revealing robust biological signals. The abundances of some genera were consistently heritable and repeatable across different environments, suggesting that metagenomic profiles could be used to predict an individual's future performance, or performance of its offspring, in a range of environments. These results highlight the potential of using rumen metagenomic profiles for selection purposes in a practical, agricultural setting.}, }
@article {pmid37723150, year = {2023}, author = {Li, Y and Xing, S and Chen, F and Li, Q and Dou, S and Huang, Y and An, J and Liu, W and Zhang, G}, title = {Intracellular Fusobacterium nucleatum infection attenuates antitumor immunity in esophageal squamous cell carcinoma.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5788}, pmid = {37723150}, issn = {2041-1723}, support = {81972289//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2019A1515010500//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; }, mesh = {Animals ; Fusobacterium nucleatum ; *Esophageal Squamous Cell Carcinoma ; B7-H1 Antigen/genetics ; *Esophageal Neoplasms/therapy ; Activating Transcription Factor 3 ; }, abstract = {Currently, the influence of the tumor microbiome on the effectiveness of immunotherapy remains largely unknown. Intratumoural Fusobacterium nucleatum (Fn) functions as an oncogenic bacterium and can promote tumor progression in esophageal squamous cell carcinoma (ESCC). Our previous study revealed that Fn is a facultative intracellular bacterium and that its virulence factor Fn-Dps facilitates the intracellular survival of Fn. In this study, we find that Fn DNA is enriched in the nonresponder (NR) group among ESCC patients receiving PD-1 inhibitor and that the serum antibody level of Fn is significantly higher in the NR group than in the responder (R) group. In addition, Fn infection has an opposite impact on the efficacy of αPD-L1 treatment in animals. Mechanistically, we confirm that Fn can inhibit the proliferation and cytokine secretion of T cells and that Fn-Dps binds to the PD-L1 gene promoter activating transcription factor-3 (ATF3) to transcriptionally upregulate PD-L1 expression. Our results suggest that it may be an important therapeutic strategy to eradicate intratumoral Fn infection before initiating ESCC immunotherapies.}, }
@article {pmid37722688, year = {2023}, author = {Morrill, SR and Saha, S and Varki, AP and Lewis, WG and Ram, S and Lewis, AL}, title = {Gardnerella vaginolysin potentiates glycan molecular mimicry by Neisseria gonorrhoeae.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiad391}, pmid = {37722688}, issn = {1537-6613}, abstract = {Bacterial vaginosis (BV) is a dysbiotic condition of the vaginal microbiome associated with higher risk of infection by Neisseria gonorrhoeae - the cause of gonorrhea. Here we test if one known facet of BV - the presence of bacterial cytolysins - leads to mobilization of intracellular contents that enhance gonococcal virulence. We cloned and expressed recombinant vaginolysin (VLY), a cytolysin produced by the BV-associated bacterium Gardnerella, verifying that it liberates contents of cervical epithelial (HeLa) cells, while vector control preparations did not. We tested if VLY mediates a well-known gonococcal virulence mechanism - the molecular mimicry of host glycans. To evade host immunity, N. gonorrhoeae caps its lipooligosaccharide (LOS) with α2-3-linked sialic acid. For this, gonococci must scavenge a metabolite made inside host cells. Flow-cytometry based lectin-binding assays showed that gonococci exposed to vaginolysin-liberated contents of HeLa cells displayed greater sialic acid capping of their LOS. This higher level of bacterial sialylation was accompanied by increased binding of the complement regulatory protein Factor H, and greater resistance to complement attack. Together these results suggest that cytolytic activities present during BV may enhance the ability of N. gonorrhoeae to capture intracellular metabolites and evade host immunity via glycan molecular mimicry.}, }
@article {pmid37722584, year = {2023}, author = {Wang, S and Han, Y and Wu, X and Sun, H}, title = {Metagenomics reveals the effects of glyphosate on soil microbial communities and functional profiles of C and P cycling in the competitive vegetation control process of Chinese fir plantation.}, journal = {Environmental research}, volume = {}, number = {}, pages = {117162}, doi = {10.1016/j.envres.2023.117162}, pmid = {37722584}, issn = {1096-0953}, abstract = {Although considerable efforts have been devoted to investigate the behavior of glyphosate on microbiome in various environment, knowledge about the soil microbial community and functional profile in weeds control process of the Chinese fir plantation are limited. In this study, shotgun metagenomic sequencing was used to determine the abundance and diversity of microbial communities and functional genes after foliar application of glyphosate for 1, 2, 3 and 4 months in a Chinese fir plantation. The results showed that glyphosate increased the copy numbers (qPCR) of 16s rRNA gene for 16.9%, improved the bacterial diversity (Shannon index) and complexity of bacterial co-occurrence network, and changed the abundances of some bacterial and fungal taxa, but had no effects on ITS gene copy numbers, fungal Shannon index, and bacterial and fungal communities (PCoA). Glyphosate application significantly decreased the amount of microbial function potentials involved in organic P mineralization for 10.7%, chitin degradation for 13.1%, and CAZy gene families with an exception of PL for 11.5% at the first month, while did not affect the profile of microbial genes response to P and C cycling in longer term. In addition, glyphosate reduced the contents of soil TOC, DOC and NH4[+]-H for 17.6%, 52.3% and 44.6% respectively, and decreased the starch, soluble sugar, Zn and Fe of Chinese fir leaves for 20.6%, 19.8%, 32.8% and 48.4% respectively. Mantle test, Spearman's correlation, and PLS-PM model revealed the connections among soil properties, tree nutrients, bacterial and fungal communities, and microbial function potentials were influenced by glyphosate. While our findings need to be validated in other filed and mechanistic studies, they may indicate that the foliar application of glyphosate has a potential effect on Chinese fir seedlings, and this effect may contribute to the changes of the bacterial community and soil properties including AN, DON and NH4[+]-H.}, }
@article {pmid37722498, year = {2023}, author = {Harel, N and Shtern, NO and Reshef, L and Biran, D and Ron, EZ and Gophna, U}, title = {Skin microbiome bacteria enriched following long sun exposure can reduce oxidative damage.}, journal = {Research in microbiology}, volume = {}, number = {}, pages = {104138}, doi = {10.1016/j.resmic.2023.104138}, pmid = {37722498}, issn = {1769-7123}, abstract = {Sun exposure is harmful to the skin and increases the risk of skin aging and skin cancer. Here we examined the effects of daily exposure to sun radiation on the skin microbiome in order to determine whether skim microbiome bacteria can contribute to protection from solar damage. Skin swabs were collected from ten lifeguards before and after the summer to analyse the skin microbiome. The results indicates that specific skin microbiome bacteria were enriched following the seasonal sun exposure. Especially interesting were two bacterial families - Sphingomonas and Erythrobacteraceae - which may have the ability to protect against UV radiation as they produce potentially protective compounds. We concentrated on a Sphingomonas strain and could show that it was highly resistant to UV irradiation and was able to reduce reactive oxygen species levels in human keratinocytes. These results provide a proof-of-concept for the role of the skin microbiome in protection from solar radiation.}, }
@article {pmid37722475, year = {2023}, author = {Wardi, M and Slimani, N and Alla, AA and Belmouden, A}, title = {First study of the effect of wastewater treatment on microbial biodiversity at three wastewater treatment plants in Agadir, Morocco, using 16S rRNA sequencing.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {122528}, doi = {10.1016/j.envpol.2023.122528}, pmid = {37722475}, issn = {1873-6424}, abstract = {Wastewater treatment is a crucial step in preserving public health and the environment. The quality of treated wastewater depends on the efficiency of the treatment system, which necessitates the evaluation of effluent quality. This is the first study to evaluate the efficiency of three treatment processes used to treat wastewater in Agadir, Morocco. Microbial biodiversity was characterized at the inlet and outlet of three treatment plants based on sequencing of seven hypervariable regions of the 16 S rRNA gene. Based on the relative abundance of bacterial biodiversity between the inflow and effluent of AOURIR and ANZA WWTPs, activated sludge emerges as the more efficacious treatment in comparison to lamellar decantation. These two treatments reduced the relative abundances and even eliminated several bacteria, including pathogenic bacteria. However, the primary M'ZAR treatment increased bacterial biodiversity from the influent to the effluent, which requires secondary and tertiary treatments to eliminate pathogenic bacteria and prevent environmental pollution. This study demonstrates the importance of assessing effluent quality to protect public health and the health of systems that receive effluents.}, }
@article {pmid37721866, year = {2023}, author = {Jiang, Q and Sherlock, DN and Elolimy, AA and Vailati-Riboni, M and Yoon, I and Loor, JJ}, title = {Impact of a Saccharomyces cerevisiae fermentation product during an intestinal barrier challenge in lactating Holstein cows on ileal microbiota and markers of tissue structure and immunity.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skad309}, pmid = {37721866}, issn = {1525-3163}, abstract = {Feeding a Saccharomyces cerevisiae fermentation product (SCFP; NutriTek®, Diamond V, Cedar Rapids, IA) during periods of metabolic stress is beneficial to the health of dairy cows partially through its effect on the gut microbiota. Whether SCFP alters the ileal microbiota in lactating cows during intestinal challenges induced by feed restriction (FR) is not known. We used 16S rRNA sequencing to assess if feeding SCFP during FR to induce gut barrier dysfunction alters microbiota profiles in the ileum. The mRNA abundance of key genes associated with tissue structures and immunity was also detected. Multiparous cows (97.1 ± 7.6 DIM; n = 7 per treatment) fed a control diet or the control plus 19 g/d NutriTek for 9 wk were subjected to an FR challenge for 5 d, during which they were fed 40% of their ad libitum intake from the 7 d before feed restriction. All cows were slaughtered at the end of FR. DNA extracted from ileal digesta was subjected to PacBio Full-Length 16S rRNA gene sequencing. High-quality amplicon sequence analyses were performed with Targeted Amplicon Diversity Analysis (TADA) and MicrobiomeAnalyst. Functional analysis was performed and analyzed using PICRUSt and STAMP. Feeding SCFP did not (P > 0.05) alter DMI, milk yield, or milk components during FR. In addition, SCFP supplementation tended (P = 0.07) to increase the relative abundance of Proteobacteria and Bifidobacterium animalis. Compared with controls, feeding SCFP increased the relative abundance of Lactobacillales (P = 0.03). Gluconokinase, oligosaccharide reducing-end xylanase, and 3-hydroxy acid dehydrogenase were among the enzymes overrepresented (P < 0.05) in response to feeding SCFP. Cows fed SCFP had a lower representation of adenosylcobalamin biosynthesis I (early cobalt insertion) and pyrimidine deoxyribonucleotides de novo biosynthesis III (P < 0.05). Subsets of the Firmicutes genus, Bacteroidota phylum, and Treponema genus were correlated with the mRNA abundance of genes associated with ileal integrity (GCNT3, GALNT5, B3GNT3, FN1, ITGA2, LAMB2) and inflammation (AOX1, GPX8, CXCL12, CXCL14, CCL4, SAA3). Our data indicated that the moderate feed restriction induced dysfunction of the ileal microbiome, but feeding SCFP increased the abundance of some beneficial gut probiotic bacteria and other species related to tissue structures and immunity.}, }
@article {pmid37721699, year = {2023}, author = {Li, KT and Li, F and Jaspan, H and Nyemba, D and Myer, L and Aldrovandi, G and Joseph-Davey, D}, title = {Changes in the Vaginal Microbiome During Pregnancy and the Postpartum Period in South African Women: a Longitudinal Study.}, journal = {Reproductive sciences (Thousand Oaks, Calif.)}, volume = {}, number = {}, pages = {}, pmid = {37721699}, issn = {1933-7205}, support = {K01TW011187/TW/FIC NIH HHS/United States ; }, abstract = {Pregnant women in sub-Saharan Africa have high rates of maternal morbidity. There is interest in the impact of the vaginal microbiome on maternal health, including HIV and sexually transmitted infection (STI) acquisition. We characterized the vaginal microbiota of South African women ≥ 18 years with and without HIV in a longitudinal cohort over two visits during pregnancy and one visit postpartum. At each visit, we obtained HIV testing and self-collected vaginal swabs for point-of-care testing for STIs and microbiota sequencing. We categorized microbial communities and evaluated changes over pregnancy and associations with HIV status and STI diagnosis. Across 242 women (mean age 29, 44% living with HIV, 33% diagnosed with STIs), we identified four main community state types (CSTs): two lactobacillus-dominant CSTs (dominated by Lactobacillus crispatus and Lactobacillus iners respectively) and two diverse, non-lactobacillus-dominant CSTs (one dominated by Gardnerella vaginalis and one by diverse facultative anaerobes). From the first antenatal visit to the third trimester (24-36 weeks gestation), 60% of women in the Gardnerella-dominant CST shifted to lactobacillus-dominant CSTs. From the third trimester to postpartum (mean 17 days post-delivery), 80% of women in lactobacillus-dominant CSTs shifted to non-lactobacillus-dominant CSTs with a large proportion in the facultative anaerobe-dominant CST. Microbial composition differed by STI diagnosis (PERMANOVA R[2] = 0.002, p = 0.004), and women diagnosed with an STI were more likely to be categorized as L. iners-dominant or Gardnerella-dominant CSTs. Overall, we found a shift toward lactobacillus dominance during pregnancy and the emergence of a distinct, highly diverse anaerobe-dominant microbiota profile in the postpartum period.}, }
@article {pmid37721335, year = {2023}, author = {Mahajan, A and Bandaru, D and Parikh, K and Gupta, V and Patel, M}, title = {From the inside out: understanding the gut-heart connection.}, journal = {Future cardiology}, volume = {}, number = {}, pages = {}, doi = {10.2217/fca-2023-0068}, pmid = {37721335}, issn = {1744-8298}, abstract = {The gut microbiome was first termed as 'Animalcules' by Antonie van Leeuwenhoek in the 17th century. The diverse composition and complex interactions of gut microbes are essential for good human health. They play a crucial role in inflammation, which by itself leads to the development of cardiovascular diseases. Although the mechanisms are not fully understood, it has been studied that the gut microbiota produce several bioactive metabolites impacting cardiovascular health mainly through TMAO pathway, SCFA pathway and bile acid pathway. Moreover, studies have found that using dietary interventions like high fiber diet and probiotics to re-establish a healthy equilibrium show promising results on improving cardiovascular health and thus, could be potentially used for prevention and management of cardiovascular diseases.}, }
@article {pmid37721161, year = {2023}, author = {Guo, K and Figueroa-Romero, C and Noureldein, MH and Murdock, BJ and Savelieff, MG and Hur, J and Goutman, SA and Feldman, EL}, title = {Gut microbiome correlates with plasma lipids in amyotrophic lateral sclerosis.}, journal = {Brain : a journal of neurology}, volume = {}, number = {}, pages = {}, doi = {10.1093/brain/awad306}, pmid = {37721161}, issn = {1460-2156}, abstract = {Amyotrophic lateral sclerosis (ALS) is a complex, fatal neurodegenerative disease. Disease pathophysiology is incompletely understood, but evidence suggests gut dysbiosis occurs in ALS, linked to impaired gastrointestinal integrity, immune system dysregulation, and altered metabolism. Gut microbiome and plasma metabolome have been separately investigated in ALS, but little is known about gut microbe-plasma metabolite correlations, which could identify robust disease biomarkers and potentially shed mechanistic insight. Here, gut microbiome changes were longitudinally profiled in ALS, and correlated to plasma metabolome. Gut microbial structure at the phylum level differed in ALS versus control participants, with differential abundance of several distinct genera. Unsupervised clustering of microbe and metabolite levels identified modules, which differed significantly in ALS versus control participants. Network analysis found several prominent amplicon sequence variants strongly linked to a group of metabolites, primarily lipids. Similarly, identifying the features that contributed most to case versus control separation pinpointed several bacteria correlated to metabolites, predominantly lipids. Mendelian randomization indicated possible causality from specific lipids related to fatty acid and acylcarnitine metabolism. Overall, the results suggest ALS cases and controls differ in their gut microbiome, which correlates with plasma metabolites, particularly lipids, through specific genera. These findings have the potential to identify robust disease biomarkers and shed mechanistic insight into ALS.}, }
@article {pmid37721071, year = {2023}, author = {Singh, VK and Fatanmi, OO and Wise, SY and Carpenter, AD and Janocha, B and Seed, TM}, title = {Novel biomarkers for acute radiation injury and countermeasures using large and small animal models and multi-omics approach.}, journal = {Radiation protection dosimetry}, volume = {199}, number = {14}, pages = {1526-1532}, doi = {10.1093/rpd/ncad035}, pmid = {37721071}, issn = {1742-3406}, mesh = {United States ; Animals ; Mice ; Multiomics ; *Radiation Injuries/prevention &amp; control ; Biomarkers ; Models, Animal ; *Nuclear Medicine ; }, abstract = {Threats of radiological or nuclear disasters are of serious concern and a top priority for government agencies involved in domestic security and public health preparedness. There is a need for sensitive bioassays for biodosimetric assessments of radiation exposures originating from unanticipated nuclear/radiological events. The Food and Drug Administration Animal Rule approval pathway requires an in-depth understanding of the mechanisms of radiation injury, drug efficacy and biomarkers for radiation medical countermeasure approval. Biomarkers can be helpful for extrapolating the efficacious countermeasure dose in animals to humans. We summarised here our studies to identify candidate biomarkers for the acute radiation injury using various omic platforms (metabolomics/lipidomics, proteomics, microbiome and transcriptomics/microRNA) using murine and non-human primate models conducted in our laboratory. Multi-omic platforms appear to be highly useful in assessing radiation exposure levels and for identifying biomarkers of radiation injury and countermeasure efficacy, which can expedite the regulatory approval of countermeasures.}, }
@article {pmid37720529, year = {2023}, author = {Luo, K and Chen, Y and Fang, S and Wang, S and Wu, Z and Li, H}, title = {Study on inflammation and fibrogenesis in MAFLD from 2000 to 2022: a bibliometric analysis.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1231520}, pmid = {37720529}, issn = {1664-2392}, mesh = {Humans ; Bibliometrics ; Inflammation ; Adiponectin ; China ; *Metabolic Syndrome ; *Non-alcoholic Fatty Liver Disease ; }, abstract = {Chronic inflammation and fibrosis are significant factors in the pathogenesis of metabolic-associated fatty liver disease (MAFLD). In this study, we conducted a bibliometric analysis of publications on inflammation and fibrogenesis in MAFLD, with a focus on reporting publication trends. Our findings indicate that the USA and China are the most productive countries in the field, with the University of California San Diego being the most productive institution. Over the past 23 years, Prof. Diehl AM has published 25 articles that significantly contributed to the research community. Notably, the research focus of the field has shifted from morbid obesity and adiponectin to metabolic syndrome, genetics, and microbiome. Our study provides a comprehensive and objective summary of the historical characteristics of research on inflammation and fibrogenesis in MAFLD, which will be of interest to scientific researchers in this field.}, }
@article {pmid37720502, year = {2023}, author = {Suryani, IR and Ahmadzai, I and That, MT and Shujaat, S and Jacobs, R}, title = {Are medication-induced salivary changes the culprit of osteonecrosis of the jaw? A systematic review.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1164051}, pmid = {37720502}, issn = {2296-858X}, abstract = {PURPOSE: This systematic review was performed to assess the potential influence of medication-induced salivary changes on the development of medication-related osteonecrosis of the jaw (MRONJ).<br><br>METHODS: An electronic search was conducted using PubMed, Web of Science, Cochrane, and Embase databases for articles published up to June 2023. A risk of bias assessment was performed according to the modified Newcastle-Ottawa Scale (NOS). Due to the heterogeneity of the selected studies in relation to the type of medications and outcomes evaluated, a meta-analysis could not be performed.<br><br>RESULTS: The initial search revealed 765 studies. Only 10 articles were found to be eligible based on the inclusion criteria that reported on the impact of salivary changes on MRONJ following the administration of different medications. A total of 272 cases of MRONJ (35% women, 32% men, and 32% with no gender reported) with a mean age of 66 years at the time of diagnosis were included. Patients administered with bisphosphonates, steroids, chemotherapy, thalidomide, interferon, and hormone therapy had a significantly higher association between decreased salivary flow and MRONJ occurrence. In addition, bisphosphonates, denosumab, and other bone-modifying agents showed a significantly higher risk of developing MRONJ owing to the changes in salivary microbiome profiles, cytokine profiles, interleukins, hypotaurine, and binding proteins.<br><br>CONCLUSION: The reduction in salivary flow and changes in the concentration of salivary proteins were associated with the development of MRONJ. However, due to the availability of limited evidence, the findings of the review should be interpreted with caution.<br><br>PROSPERO REVIEW REGISTRATION: https://www.crd.york.ac.uk/PROSPERO/, identifier: CRD42022327645.}, }
@article {pmid37720467, year = {2023}, author = {Lerch, F and Yosi, F and Vötterl, JC and Koger, S and Ehmig, J and Sharma, S and Verhovsek, D and Metzler-Zebeli, BU}, title = {An insight into the temporal dynamics in the gut microbiome, metabolite signaling, immune response, and barrier function in suckling and weaned piglets under production conditions.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1184277}, pmid = {37720467}, issn = {2297-1769}, abstract = {Little information is available on age- and creep-feeding-related microbial and immune development in neonatal piglets. Therefore, we explored age- and gut-site-specific alterations in the microbiome, metabolites, histo-morphology, and expression of genes for microbial signaling, as well as immune and barrier function in suckling and newly weaned piglets that were receiving sow milk only or were additionally offered creep feed from day of life (DoL) 10. The experiment was conducted in two replicate batches. Creep feed intake was estimated at the litter level. Piglets were weaned on day 28 of life. Gastric and cecal digesta and jejunal and cecal tissue were collected on DoL 7, 14, 21, 28, 31, and 35 for microbial and metabolite composition, histomorphology, and gene expression. In total, results for 10 piglets (n = 5/sex) per dietary group (sow milk only versus additional creep feed) were obtained for each DoL. The creep feed intake was low at the beginning and only increased in the fourth week of life. Piglets that were fed creep feed had less lactate and acetate in gastric digesta on DoL 28 compared to piglets fed sow milk only (p < 0.05). Age mainly influenced the gastric and cecal bacteriome and cecal mycobiome composition during the suckling phase, whereas the effect of creep feeding was small. Weaning largely altered the microbial communities. For instance, it reduced gastric Lactobacillaceae and cecal Bacteroidaceae abundances and lowered lactate and short-chain fatty acid concentrations on DoL 31 (p < 0.05). Jejunal and cecal expression of genes related to microbial and metabolite signaling, and innate immunity showed age-related patterns that were highest on DoL 7 and declined until DoL 35 (p < 0.05). Weaning impaired barrier function and enhanced antimicrobial secretion by lowering the expression of tight junction proteins and stimulating goblet cell recruitment in the jejunum and cecum (p < 0.05). Results indicated that age-dependent alterations, programmed genetically and by the continuously changing gut microbiome, had a strong impact on the expression of genes for gut barrier function, integrity, innate immunity, and SCFA signaling, whereas creep feeding had little influence on the microbial and host response dynamics at the investigated gut sites.}, }
@article {pmid37724079, year = {2021}, author = {Cheng, CK and Huang, Y}, title = {The gut-cardiovascular connection: new era for cardiovascular therapy.}, journal = {Medical review (Berlin, Germany)}, volume = {1}, number = {1}, pages = {23-46}, pmid = {37724079}, issn = {2749-9642}, abstract = {Our gut microbiome is constituted by trillions of microorganisms including bacteria, archaea and eukaryotic microbes. Nowadays, gut microbiome has been gradually recognized as a new organ system that systemically and biochemically interact with the host. Accumulating evidence suggests that the imbalanced gut microbiome contributes to the dysregulation of immune system and the disruption of cardiovascular homeostasis. Specific microbiome profiles and altered intestinal permeability are often observed in the pathophysiology of cardiovascular diseases. Gut-derived metabolites, toxins, peptides and immune cell-derived cytokines play pivotal roles in the induction of inflammation and the pathogenesis of dysfunction of heart and vasculature. Impaired crosstalk between gut microbiome and multiple organ systems, such as gut-vascular, heart-gut, gut-liver and brain-gut axes, are associated with higher cardiovascular risks. Medications and strategies that restore healthy gut microbiome might therefore represent novel therapeutic options to lower the incidence of cardiovascular and metabolic disorders.}, }
@article {pmid37720222, year = {2023}, author = {Zhong, MM and Xie, JH and Feng, Y and Zhang, SH and Xia, JN and Tan, L and Chen, NX and Su, XL and Zhang, Q and Feng, YZ and Guo, Y}, title = {Causal effects of the gut microbiome on COVID-19 susceptibility and severity: a two-sample Mendelian randomization study.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1173974}, pmid = {37720222}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome ; Genome-Wide Association Study ; Mendelian Randomization Analysis ; *COVID-19/genetics ; Causality ; }, abstract = {BACKGROUND: The coronavirus disease 2019 (COVID-19) caused a global pandemic, with potential severity. We aimed to investigate whether genetically predicted gut microbiome is associated with susceptibility and severity of COVID-19 risk.<br><br>METHODS: Mendelian randomization (MR) analysis of two sets with different significance thresholds was carried out to infer the causal relationship between the gut microbiome and COVID-19. SNPs associated with the composition of the gut microbiome (n = 5,717,754) and with COVID-19 susceptibility (n = 14,328,058), COVID-19 severity (n = 11,707,239), and COVID-19 hospitalization (n = 12,018,444) from publicly available genome-wide association studies (GWAS). The random-effect inverse variance weighted (IVW) method was used to determine causality. Three more MR techniques-MR Egger, weighted median, and weighted mode-and a thorough sensitivity analysis were also used to confirm the findings.<br><br>RESULTS: IVW showed that 18 known microbial taxa were causally associated with COVID-19. Among them, six microbial taxa were causally associated with COVID-19 susceptibility; seven microbial taxa were causally associated with COVID-19 severity ; five microbial taxa were causally associated with COVID-19 hospitalization. Sensitivity analyses showed no evidence of pleiotropy or heterogeneity. Then, the predicted 37 species of the gut microbiome deserve further study.<br><br>CONCLUSION: This study found that some microbial taxa were protective factors or risky factors for COVID-19, which may provide helpful biomarkers for asymptomatic diagnosis and potential therapeutic targets for COVID-19.}, }
@article {pmid37720157, year = {2023}, author = {Fudjoe, SK and Li, L and Anwar, S and Shi, S and Xie, J and Wang, L and Xie, L and Yongjie, Z}, title = {Nitrogen fertilization promoted microbial growth and N2O emissions by increasing the abundance of nirS and nosZ denitrifiers in semiarid maize field.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1265562}, doi = {10.3389/fmicb.2023.1265562}, pmid = {37720157}, issn = {1664-302X}, abstract = {Nitrous oxide (N2O) emissions are a major source of gaseous nitrogen loss, causing environmental pollution. The low organic content in the Loess Plateau region, coupled with the high fertilizer demand of maize, further exacerbates these N losses. N fertilizers play a primary role in N2O emissions by influencing soil denitrifying bacteria, however, the underlying microbial mechanisms that contribute to N2O emissions have not been fully explored. Therefore, the research aimed to gain insights into the intricate relationships between N fertilization, soil denitrification, N2O emissions, potential denitrification activity (PDA), and maize nitrogen use efficiency (NUE) in semi-arid regions. Four nitrogen (N) fertilizer rates, namely N0, N1, N2, and N3 (representing 0, 100, 200, and 300 kg ha[-1] yr.[-1], respectively) were applied to maize field. The cumulative N2O emissions were 32 and 33% higher under N2 and 37 and 39% higher under N3 in the 2020 and 2021, respectively, than the N0 treatment. N fertilization rates impacted the abundance, composition, and network of soil denitrifying communities (nirS and nosZ) in the bulk and rhizosphere soil. Additionally, within the nirS community, the genera Cupriavidus and Rhodanobacter were associated with N2O emissions. Conversely, in the nosZ denitrifier, the genera Azospirillum, Mesorhizobium, and Microvirga in the bulk and rhizosphere soil reduced N2O emissions. Further analysis using both random forest and structural equation model (SEM) revealed that specific soil properties (pH, NO3[-]-N, SOC, SWC, and DON), and the presence of nirS-harboring denitrification, were positively associated with PDA activities, respectively, and exhibited a significant association to N2O emissions and PDA activities but expressed a negative effect on maize NUE. However, nosZ-harboring denitrification showed an opposite trend, suggesting different effects on these variables. Our findings suggest that N fertilization promoted microbial growth and N2O emissions by increasing the abundance of nirS and nosZ denitrifiers and altering the composition of their communities. This study provides new insights into the relationships among soil microbiome, maize productivity, NUE, and soil N2O emissions in semi-arid regions.}, }
@article {pmid37720155, year = {2023}, author = {Yelverton, CA and Killeen, SL and Feehily, C and Moore, RL and Callaghan, SL and Geraghty, AA and Byrne, DF and Walsh, CJ and Lawton, EM and Murphy, EF and Van Sinderen, D and Cotter, PD and McAuliffe, FM}, title = {Maternal breastfeeding is associated with offspring microbiome diversity; a secondary analysis of the MicrobeMom randomized control trial.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1154114}, doi = {10.3389/fmicb.2023.1154114}, pmid = {37720155}, issn = {1664-302X}, abstract = {BACKGROUND: Microbial dysbiosis in infancy can influence long-term health outcomes such as childhood obesity. The aim of this study is to explore relationships among maternal well-being during pregnancy, breastfeeding, and the infant gut microbiome.<br><br>METHODS: This is a secondary analysis of healthy pregnant women from the MicrobeMom study, a double-blind randomized control trial of maternal probiotic supplementation (Bifidobacterium breve 702258) versus placebo antenatally and up to 3&#x2009;months postpartum. Maternal well-being was assessed using the WHO-5 well-being index at 16&#x2009;weeks' and 34&#x2009;weeks' gestation. Breastfeeding practices were recorded at discharge from hospital and at 1&#x2009;month postpartum. Infant stool samples were obtained at 1&#x2009;month of age. Next generation shotgun sequencing determined infant microbial diversity. Independent sample t-tests and Mann-Whitney U tests informed adjusted regression analysis, which was adjusted for delivery mode, antibiotics during delivery, maternal age and body mass index (BMI), and probiotic vs. control study group.<br><br>RESULTS: Women (n&#x2009;=&#x2009;118) with at least one measure of well-being were on average 33&#x2009;years (SD 3.93) of age and 25.09&#x2009;kg/m[2] (SD 3.28) BMI. Exclusive breastfeeding was initiated by 65% (n&#x2009;=&#x2009;74). Any breastfeeding was continued by 69% (n&#x2009;=&#x2009;81) after 1&#x2009;month. In early and late pregnancy, 87% (n&#x2009;=&#x2009;97/111) and 94% (n&#x2009;=&#x2009;107/114) had high well-being scores. Well-being was not associated with infant microbial diversity at 1&#x2009;month. In adjusted analysis, exclusive breastfeeding at discharge from hospital was associated with infant microbial beta diversity (PC2; 0.254, 95% CI 0.006, 0.038). At 1&#x2009;month postpartum, any breastfeeding was associated with infant microbial alpha diversity (Shannon index; -0.241, 95% CI -0.498, -0.060) and observed species; (-0.325, 95% CI -0.307, -0.060), and infant microbial beta diversity (PC2; 0.319, 95% CI 0.013, 0.045). Exclusive breastfeeding at 1&#x2009;month postpartum was associated with infant alpha diversity (Shannon index -0.364, 95% CI -0.573, -0.194; Simpson index 0.339, 95% CI 0.027, 0.091), and infant's number of observed microbial species (-0.271, 95% CI -0.172, -0.037).<br><br>CONCLUSION: Breastfeeding practices at 1&#x2009;month postpartum were associated with lower microbial diversity and observed species in infants at 1&#x2009;month postpartum, which is potentially beneficial to allow greater abundance of Bifidobacterium.<br><br>CLINICAL TRIAL REGISTRATION: ISRCTN53023014.}, }
@article {pmid37720144, year = {2023}, author = {Yang, JZ and Zhang, KK and Shen, HW and Liu, Y and Li, XW and Chen, LJ and Liu, JL and Li, JH and Zhao, D and Wang, Q and Zhou, CS}, title = {Sigma-1 receptor knockout disturbs gut microbiota, remodels serum metabolome, and exacerbates isoprenaline-induced heart failure.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1255971}, doi = {10.3389/fmicb.2023.1255971}, pmid = {37720144}, issn = {1664-302X}, abstract = {INTRODUCTION: Heart failure (HF) is usually the end stage of the continuum of various cardiovascular diseases. However, the mechanism underlying the progression and development of HF remains poorly understood. The sigma-1 receptor (Sigmar1) is a non-opioid transmembrane receptor implicated in many diseases, including HF. However, the role of Sigmar1 in HF has not been fully elucidated.<br><br>METHODS: In this study, we used isoproterenol (ISO) to induce HF in wild-type (WT) and Sigmar1 knockout (Sigmar1[-/-]) mice. Multi-omic analysis, including microbiomics, metabolomics and transcriptomics, was employed to comprehensively evaluate the role of Sigmar1 in HF.<br><br>RESULTS: Compared with the WT-ISO group, Sigmar1[-/-] aggravated ISO-induced HF, including left ventricular systolic dysfunction and ventricular remodeling. Moreover, Sigmar1[-/-] exacerbated ISO-induced gut microbiota dysbiosis, which was demonstrated by the lower abundance of probiotics g_Akkermansia and g_norank_f_Muribaculaceae, and higher abundance of pathogenic g_norank_f_Oscillospiraceae and Allobaculum. Furthermore, differential metabolites among WT-Control, WT-ISO and Sigmar[-/-]-ISO groups were mainly enriched in bile secretion, tryptophan metabolism and phenylalanine metabolism, which presented a close association with microbial dysbiosis. Corresponding with the exacerbation of the microbiome, the inflammation-related NOD-like receptor signaling pathway, NF-kappa B signaling pathway and TNF signaling pathway were activated in the heart tissues.<br><br>CONCLUSION: Taken together, this study provides evidence that a Sigmar1 knockout disturbs the gut microbiota and remodels the serum metabolome, which may exacerbate HF by stimulating heart inflammation.}, }
@article {pmid37720092, year = {2023}, author = {Tripodi, L and Feola, S and Granata, I and Whalley, T and Passariello, M and Capasso, C and Coluccino, L and Vitale, M and Scalia, G and Gentile, L and De Lorenzo, C and Guarracino, MR and Castaldo, G and D'Argenio, V and Szomolay, B and Cerullo, V and Pastore, L}, title = {Bifidobacterium affects antitumor efficacy of oncolytic adenovirus in a mouse model of melanoma.}, journal = {iScience}, volume = {26}, number = {10}, pages = {107668}, pmid = {37720092}, issn = {2589-0042}, abstract = {Gut microbiota plays a key role in modulating responses to cancer immunotherapy in melanoma patients. Oncolytic viruses (OVs) represent emerging tools in cancer therapy, inducing a potent immunogenic cancer cell death (ICD) and recruiting immune cells in tumors, poorly infiltrated by T cells. We investigated whether the antitumoral activity of oncolytic adenovirus Ad5D24-CpG (Ad-CpG) was gut microbiota-mediated in a syngeneic mouse model of melanoma and observed that ICD was weakened by vancomycin-mediated perturbation of gut microbiota. Ad-CpG efficacy was increased by oral supplementation with Bifidobacterium, reducing melanoma progression and tumor-infiltrating regulatory T cells. Fecal microbiota was enriched in bacterial species belonging to the Firmicutes phylum in mice treated with both Bifidobacterium and Ad-CpG; furthermore, our data suggest that molecular mimicry between melanoma and Bifidobacterium-derived epitopes may favor activation of cross-reactive T cells and constitutes one of the mechanisms by which gut microbiota modulates OVs response.}, }
@article {pmid37720019, year = {2023}, author = {Martinelli, F and Heinken, A and Henning, AK and Wörheide, MA and Hensen, T and González, A and Arnold, M and Asthana, S and Budde, K and Engelman, CD and Estaki, M and Grabe, HJ and Heston, M and Johnson, S and Kastenmüller, G and Martino, C and McDonald, D and Rey, F and Kilimann, I and Peters, O and Wang, X and Spruth, EJ and Schneider, A and Fliessbach, K and Wiltfang, J and Hansen, N and Glanz, W and Buerger, K and Janowitz, D and Laske, C and Munk, MH and Spottke, A and Roy, N and Nauck, M and Teipel, S and Knight, R and Kaddurah-Daouk, R and Bendlin, BB and Hertel, J and Thiele, I}, title = {Whole-body modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37720019}, abstract = {In this study, we aimed to understand the potential role of the gut microbiome in the development of Alzheimer's disease (AD). We took a multi-faceted approach to investigate this relationship. Urine metabolomics were examined in individuals with AD and controls, revealing decreased formate and fumarate concentrations in AD. Additionally, we utilized whole-genome sequencing (WGS) data obtained from a separate group of individuals with AD and controls. This information allowed us to create and investigate host-microbiome personalized models. Notably, AD individuals displayed diminished formate microbial secretion in these models. Additionally, we identified specific reactions responsible for the production of formate in the host, and interestingly, these reactions were linked to genes that have correlations with AD. This study suggests formate as a possible early AD marker and highlights genetic and microbiome contributions to its production. The reduced formate secretion and its genetic associations point to a complex connection between gut microbiota and AD. This holistic understanding might pave the way for novel diagnostic and therapeutic avenues in AD management.}, }
@article {pmid37719750, year = {2023}, author = {Becker, CC and Weber, L and Zgliczynski, B and Sullivan, C and Sandin, S and Muller, E and Clark, AS and Kido Soule, MC and Longnecker, K and Kujawinski, EB and Apprill, A}, title = {Microorganisms and dissolved metabolites distinguish Florida's Coral Reef habitats.}, journal = {PNAS nexus}, volume = {2}, number = {9}, pages = {pgad287}, pmid = {37719750}, issn = {2752-6542}, abstract = {As coral reef ecosystems experience unprecedented change, effective monitoring of reef features supports management, conservation, and intervention efforts. Omic techniques show promise in quantifying key components of reef ecosystems including dissolved metabolites and microorganisms that may serve as invisible sensors for reef ecosystem dynamics. Dissolved metabolites are released by reef organisms and transferred among microorganisms, acting as chemical currencies and contributing to nutrient cycling and signaling on reefs. Here, we applied four omic techniques (taxonomic microbiome via amplicon sequencing, functional microbiome via shotgun metagenomics, targeted metabolomics, and untargeted metabolomics) to waters overlying Florida's Coral Reef, as well as microbiome profiling on individual coral colonies from these reefs to understand how microbes and dissolved metabolites reflect biogeographical, benthic, and nutrient properties of this 500-km barrier reef. We show that the microbial and metabolite omic approaches each differentiated reef habitats based on geographic zone. Further, seawater microbiome profiling and targeted metabolomics were significantly related to more reef habitat characteristics, such as amount of hard and soft coral, compared to metagenomic sequencing and untargeted metabolomics. Across five coral species, microbiomes were also significantly related to reef zone, followed by species and disease status, suggesting that the geographic water circulation patterns in Florida also impact the microbiomes of reef builders. A combination of differential abundance and indicator species analyses revealed metabolite and microbial signatures of specific reef zones, which demonstrates the utility of these techniques to provide new insights into reef microbial and metabolite features that reflect broader ecosystem processes.}, }
@article {pmid37719672, year = {2023}, author = {, }, title = {Erratum: Alterations of gut microbiome following gastrointestinal surgical procedures and their potential complications.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1281527}, doi = {10.3389/fcimb.2023.1281527}, pmid = {37719672}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2023.1191126.].}, }
@article {pmid37719278, year = {2023}, author = {Lee, YH and Hong, JY}, title = {Oral microbiome as a co-mediator of halitosis and periodontitis: a narrative review.}, journal = {Frontiers in oral health}, volume = {4}, number = {}, pages = {1229145}, pmid = {37719278}, issn = {2673-4842}, abstract = {OBJECTIVE: Halitosis or oral malodor is an unpleasant odor from the oral cavity. However, although patients with periodontitis often complain of halitosis, their relationship has not been fully elucidated. We reviewed previous literature based on the hypothesis that the relationship between halitosis and periodontitis is mediated by the oral microbiome.<br><br>MATERIALS AND METHODS: This narrative review sought to provide insight into the causative role of the oral microbiome in influencing halitosis and periodontitis. In addition, we tried to deepen knowledge related to the relationship between halitosis and periodontitis generated by the oral microbiome accumulated over the past 40 years.<br><br>RESULTS: From 1984 to 2023, a total of 106 papers that carefully and scientifically dealt with halitosis and periodontitis were included in this narrative review. Based on previous results, halitosis and periodontitis were closely related. For decades, researchers have taken an intriguing approach to the question of whether there is a relationship between halitosis and periodontitis. Central factors in the relationship between halitosis and periodontitis include volatile sulfur compounds (VSCs), the oral microbiota that produce VSCs, and the inflammatory response.<br><br>CONCLUSIONS: Taken together, the more severe periodontitis, the higher the level of VSC in halitosis, which may be mediated by oral microbiome. However, the relationship between the occurrence, maintenance, and exacerbation of periodontitis and halitosis is not a necessary and sufficient condition for each other because they are complex interplay even in one individual.}, }
@article {pmid37719271, year = {2023}, author = {Xu, L and Mo, K and Ran, D and Ma, J and Zhang, L and Sun, Y and Long, Q and Jiang, G and Zhao, X and Zou, X}, title = {An endolysin gene from Candidatus Liberibacter asiaticus confers dual resistance to huanglongbing and citrus canker.}, journal = {Horticulture research}, volume = {10}, number = {9}, pages = {uhad159}, pmid = {37719271}, issn = {2662-6810}, abstract = {The most damaging citrus diseases are Huanglongbing (HLB) and citrus canker, which are caused by Candidatus Liberibacter asiaticus (CaLas) and Xanthomonas citri pv. citri (Xcc), respectively. Endolysins from bacteriophages are a possible option for disease resistance in plant breeding. Here, we report improvement of citrus resistance to HLB and citrus canker using the LasLYS1 and LasLYS2 endolysins from CaLas. LasLYS2 demonstrated bactericidal efficacy against several Rhizobiaceae bacteria and Xcc, according to inhibition zone analyses. The two genes, driven by a strong promoter from Cauliflower mosaic virus, 35S, were integrated into Carrizo citrange via Agrobacterium-mediated transformation. More than 2 years of greenhouse testing indicated that LasLYS2 provided substantial and long-lasting resistance to HLB, allowing transgenic plants to retain low CaLas titers and no obvious symptoms while also clearing CaLas from infected plants in the long term. LasLYS2 transgenic plants with improved HLB resistance also showed resistance to Xcc, indicating that LasLYS2 had dual resistance to HLB and citrus canker. A microbiome study of transgenic plants revealed that the endolysins repressed Xanthomonadaceae and Rhizobiaceae populations in roots while increasing Burkholderiaceae and Rhodanobacteraceae populations, which might boost the citrus defense response, according to transcriptome analysis. We also found that Lyz domain 2 is the key bactericidal motif of LasLYS1 and LasLYS2. Four endolysins with potential resistance to HLB and citrus canker were found based on the structures of LasLYS1 and LasLYS2. Overall, the work shed light on the mechanisms of resistance of CaLas-derived endolysins, providing insights for designing endolysins to develop broad-spectrum disease resistance in citrus.}, }
@article {pmid37719209, year = {2023}, author = {Ahmed, B and Beneš, F and Hajšlová, J and Fišarová, L and Vosátka, M and Hijri, M}, title = {Enhanced production of select phytocannabinoids in medical Cannabis cultivars using microbial consortia.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1219836}, pmid = {37719209}, issn = {1664-462X}, abstract = {The root microbiome of medical cannabis plants has been largely unexplored due to past legal restrictions in many countries. Microbes that live on and within the tissue of Cannabis sativa L. similar to other plants, provide advantages such as stimulating plant growth, helping it absorb minerals, providing protection against pathogen attacks, and influencing the production of secondary metabolites. To gain insight into the microbial communities of C. sativa cultivars with different tetrahydrocannabinol (THC) and cannabidiol (CBD) profiles, a greenhouse trial was carried out with and without inoculants added to the growth substrate. Illumina MiSeq metabarcoding was used to analyze the root and rhizosphere microbiomes of the five cultivars. Plant biomass production showed higher levels in three of five cultivars inoculated with the arbuscular mycorrhizal fungus Rhizophagus irregularis and microbial suspension. The blossom dry weight of the cultivar THE was greater when inoculated with R. irregularis and microbial suspension than with no inoculation. Increasing plant biomass and blossom dry weight are two important parameters for producing cannabis for medical applications. In mature Cannabis, 12 phytocannabinoid compounds varied among cultivars and were affected by inoculants. Significant differences (p ≤ 0.01) in concentrations of cannabidivarinic acid (CBDVA), cannabidivarin (CBDV), cannabigerol (CBG), cannabidiol (CBD), and cannabigerolic acid (CBGA) were observed in all Cannabis cultivars when amended with F, K1, and K2 inoculants. We found microbes that were shared among cultivars. For example, Terrimicrobium sp., Actinoplanes sp., and Trichoderma reesei were shared by the cultivars ECC-EUS-THE, CCL-ECC, and EUS-THE, respectively. Actinoplanes sp. is a known species that produces phosphatase enzymes, while Trichoderma reesei is a fungal train that produces cellulase and contributes to organic matter mineralization. However, the role of Terrimicrobium sp. as an anaerobic bacterium remains unknown. This study demonstrated that the use of inoculants had an impact on the production of phytocannabinoids in five Cannabis cultivars. These inoculants could have useful applications for optimizing cannabis cultivation practices and increasing the production of phytocannabinoids.}, }
@article {pmid37719200, year = {2023}, author = {Zhang, Q and Chumanevich, AA and Nguyen, I and Chumanevich, AA and Sartawi, N and Hogan, J and Khazan, M and Harris, Q and Massey, B and Chatzistamou, I and Buckhaults, PJ and Banister, CE and Wirth, M and Hebert, JR and Murphy, EA and Hofseth, LJ}, title = {The synthetic food dye, Red 40, causes DNA damage, causes colonic inflammation, and impacts the microbiome in mice.}, journal = {Toxicology reports}, volume = {11}, number = {}, pages = {221-232}, pmid = {37719200}, issn = {2214-7500}, abstract = {The incidence of colorectal cancer (CRC) among young people has been on the rise for the past four decades and its underlying causes are only just starting to be uncovered. Recent studies suggest that consuming ultra-processed foods and pro-inflammatory diets may be contributing factors. The increase in the use of synthetic food colors in such foods over the past 40 years, including the common synthetic food dye Allura Red AC (Red 40), coincides with the rise of early-onset colorectal cancer (EOCRC). As these ultra-processed foods are particularly appealing to children, there is a growing concern about the impact of synthetic food dyes on the development of CRC. Our study aimed to investigate the effects of Red 40 on DNA damage, the microbiome, and colonic inflammation. Despite a lack of prior research, high levels of human exposure to pro-inflammatory foods containing Red 40 highlight the urgency of exploring this issue. Our results show that Red 40 damages DNA both in vitro and in vivo and that consumption of Red 40 in the presence of a high-fat diet for 10 months leads to dysbiosis and low-grade colonic inflammation in mice. This evidence supports the hypothesis that Red 40 is a dangerous compound that dysregulates key players involved in the development of EOCRC.}, }
@article {pmid37719171, year = {2023}, author = {Shadboorestan, A and Koual, M and Dairou, J and Coumoul, X}, title = {The Role of the Kynurenine/AhR Pathway in Diseases Related to Metabolism and Cancer.}, journal = {International journal of tryptophan research : IJTR}, volume = {16}, number = {}, pages = {11786469231185102}, doi = {10.1177/11786469231185102}, pmid = {37719171}, issn = {1178-6469}, abstract = {The Aryl hydrocarbon receptor (AhR) is a xenobiotic and endobiotic receptor, which regulates many cellular processes from contaminant metabolism to immunomodulation. Consequently, it is also involved in pathophysiological pathways and now represents a potential therapeutical target. In this review, we will highlight the ancestral function of the protein together with an illustration of its ligand's battery, emphasizing the different responses triggered by these high diverse molecules. Among them, several members of the kynurenine pathway (one key process of tryptophan catabolism) are AhR agonists and are subsequently involved in regulatory functions. We will finally display the interplay between Tryptophan (Trp) catabolism and dysregulation in metabolic pathways drawing hypothesis on the involvement of the AhR pathway in these cancer-related processes.}, }
@article {pmid37719127, year = {2023}, author = {Castañeda-Molina, Y and Marulanda-Moreno, SM and Saldamando-Benjumea, C and Junca, H and Moreno-Herrera, CX and Cadavid-Restrepo, G}, title = {Microbiome analysis of Spodoptera frugiperda (Lepidoptera, Noctuidae) larvae exposed to Bacillus thuringiensis (Bt) endotoxins.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15916}, pmid = {37719127}, issn = {2167-8359}, abstract = {BACKGROUND: Spodoptera frugiperda (or fall armyworm, FAW) is a polyphagous pest native to Western Hemisphere and recently discovered in the Eastern Hemisphere. In Colombia, S. frugiperda is recognized as a pest of economic importance in corn. The species has genetically differentiated into two host populations named "corn" and "rice" strains. In 2012, a study made in central Colombia demonstrated that the corn strain is less susceptible to Bacillus thuringiensis (Bt) endotoxins (Cry1Ac and Cry 1Ab) than the rice strain. In this country, Bt transgenic corn has been extensively produced over the last 15 years. Since gut microbiota plays a role in the physiology and immunity of insects, and has been implicated in promoting the insecticidal activity of Bt, in this study an analysis of the interaction between Bt endotoxins and FAW gut microbiota was made. Also, the detection of endosymbionts was performed here, as they might have important implications in the biological control of a pest.<br><br>METHODS: The composition and diversity of microbiomes associated with larval specimens of S. frugiperda(corn strain) was investigated in a bioassay based on six treatments in the presence/absence of Bt toxins and antibiotics (Ab) through bacterial isolate analyses and by high throughput sequencing of the bacterial 16S rRNA gene. Additionally, species specific primers were used, to detect endosymbionts from gonads in S. frugiperda corn strain.<br><br>RESULTS: Firmicutes, Proteobacteria and Bacteroidota were the most dominant bacterial phyla found in S. frugiperda corn strain. No significant differences in bacteria species diversity and richness among the six treatments were found. Two species of Enterococcus spp., E. mundtii and E. casseliflavus were detected in treatments with Bt and antibiotics, suggesting that they are less susceptible to both of them. Additionally, the endosymbiont Arsenophonus was also identified on treatments in presence of Bt and antibiotics. The results obtained here are important since little knowledge exists about the gut microbiota on this pest and its interaction with Bt endotoxins. Previous studies made in Lepidoptera suggest that alteration of gut microbiota can be used to improve the management of pest populations, demonstrating the relevance of the results obtained in this work.}, }
@article {pmid37719116, year = {2023}, author = {Yuan, N and Wang, Y and Pan, Q and Zhao, L and Qi, X and Sun, S and Suolang, Q and Ciren, L and Danzeng, L and Liu, Y and Zhang, L and Gao, T and Basang, Z and Lian, H and Sun, Y}, title = {From the perspective of rumen microbiome and host metabolome, revealing the effects of feeding strategies on Jersey Cows on the Tibetan Plateau.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16010}, pmid = {37719116}, issn = {2167-8359}, abstract = {BACKGROUND: Previous studies have discussed the effects of grazing and house feeding on yaks during the cold season when forage is in short supply, but there is limited information on the effects of these feeding strategies on Jersey cows introduced to the Tibetan Plateau. The objective of this study was to use genomics and metabolomics analyses to examine changes in rumen microbiology and organism metabolism of Jersey cows with different feeding strategies.<br><br>METHODS: We selected 12 Jersey cows with similar body conditions and kept them for 60 days under grazing (n&#xa0;=&#xa0;6) and house-feeding (n&#xa0;=&#xa0;6) conditions. At the end of the experiment, samples of rumen fluid and serum were collected from Jersey cows that had been fed using different feeding strategies. The samples were analyzed for rumen fermentation parameters, rumen bacterial communities, serum antioxidant and immunological indices, and serum metabolomics. The results of the study were examined to find appropriate feeding strategies for Jersey cows during the cold season on the Tibetan plateau.<br><br>RESULTS: The results of rumen fermentation parameters showed that concentrations of acetic acid, propionic acid, and ammonia nitrogen in the house-feeding group (Group B) were significantly higher than in the grazing group (Group G) (P&#xa0;<&#xa0;0.05). In terms of the rumen bacterial community 16S rRNA gene, the Chao1 index was significantly higher in Group G than in Group B (P&#xa0;=&#xa0;0.038), while observed species, Shannon and Simpson indices were not significantly different from the above-mentioned groups (P&#xa0;>&#xa0;0.05). Beta diversity analysis revealed no significant differences in the composition of the rumen microbiota between the two groups. Analysis of serum antioxidant and immune indices showed no significant differences in total antioxidant capacity between Group G and Group B (P&#xa0;>&#xa0;0.05), while IL-6, Ig-M , and TNF-&#x3b1; were significantly higher in Group G than in Group B (P&#xa0;<&#xa0;0.05). LC-MS metabolomics analysis of serum showed that a total of 149 major serum differential metabolites were found in Group G and Group B. The differential metabolites were enriched in the metabolic pathways of biosynthesis of amino acids, protein digestion and absorption, ABC transporters, aminoacyl-tRNA biosynthesis, mineral absorption, and biosynthesis of unsaturated fatty acids. These data suggest that the house-feeding strategy is more beneficial to improve the physiological state of Jersey cows on the Tibetan Plateau during the cold season when forages are in short supply.}, }
@article {pmid37719072, year = {2023}, author = {Sayin, S and Mitchell, A}, title = {Functional Assay for Measuring Bacterial Degradation of Gemcitabine Chemotherapy.}, journal = {Bio-protocol}, volume = {13}, number = {17}, pages = {e4797}, pmid = {37719072}, issn = {2331-8325}, abstract = {Drug biotransformation by the host microbiome can impact the therapeutic success of treatment. In the context of cancer, drug degradation can take place within the microenvironment of the targeted tumor by intratumor bacteria. In pancreatic cancer, increased chemo-resistance against the frontline chemotherapy gemcitabine is thought to arise from drug degradation by the tumor microbiome. This bacterial-drug interaction highlights the need for developing rapid assays for monitoring bacterial gemcitabine breakdown. While chemical approaches such as high-performance liquid chromatography are suitable for this task, they require specialized equipment and expertise and are limited in throughput. Functional cell-based assays represent an alternate approach for performing this task. We developed a functional assay to monitor the rate of bacterial gemcitabine breakdown using a highly sensitive bacterial reporter strain. Our method relies on standard laboratory equipment and can be implemented at high throughput to monitor drug breakdown by hundreds of strains simultaneously. This functional assay can be readily adapted to monitor degradation of other drugs. Key features Quantification of gemcitabine breakdown by incubating bacteria that degrades the drug and subsequently testing the growth of a reporter strain on filtered supernatant. Use of an optimized reporter strain that was genetically engineered to be a non-degrader strain and highly sensitive to gemcitabine. A high-throughput assay performed in microplates that can be adjusted for identifying bacteria with a fast or slow gemcitabine degradation rate. The assay results can be compared to results from a standard curve with known drug concentrations to quantify degradation rate.}, }
@article {pmid37718683, year = {2023}, author = {Balasubramanian, I and Bandyopadhyay, S and Flores, J and Bianchi-Smak, J and Lin, X and Liu, H and Sun, S and Golovchenko, NB and Liu, Y and Wang, D and Patel, R and Joseph, I and Suntornsaratoon, P and Vargas, J and Green, PH and Bhagat, G and Lagana, SM and Ying, W and Zhang, Y and Wang, Z and Li, WV and Singh, S and Zhou, Z and Kollias, G and Farr, LA and Moonah, SN and Yu, S and Wei, Z and Bonder, EM and Zhang, L and Kiela, PR and Edelblum, KL and Ferraris, R and Liu, TC and Gao, N}, title = {Infection and inflammation stimulate expansion of a CD74[+] Paneth cell subset to regulate disease progression.}, journal = {The EMBO journal}, volume = {}, number = {}, pages = {e113975}, doi = {10.15252/embj.2023113975}, pmid = {37718683}, issn = {1460-2075}, support = {F31 DK121428/DK/NIDDK NIH HHS/United States ; }, abstract = {Paneth cells (PCs), a specialized secretory cell type in the small intestine, are increasingly recognized as having an essential role in host responses to microbiome and environmental stresses. Whether and how commensal and pathogenic microbes modify PC composition to modulate inflammation remain unclear. Using newly developed PC-reporter mice under conventional and gnotobiotic conditions, we determined PC transcriptomic heterogeneity in response to commensal and invasive microbes at single cell level. Infection expands the pool of CD74[+] PCs, whose number correlates with auto or allogeneic inflammatory disease progressions in mice. Similar correlation was found in human inflammatory disease tissues. Infection-stimulated cytokines increase production of reactive oxygen species (ROS) and expression of a PC-specific mucosal pentraxin (Mptx2) in activated PCs. A PC-specific ablation of MyD88 reduced CD74[+] PC population, thus ameliorating pathogen-induced systemic disease. A similar phenotype was also observed in mice lacking Mptx2. Thus, infection stimulates expansion of a PC subset that influences disease progression.}, }
@article {pmid37718519, year = {2023}, author = {Pandey, SP and Bhaskar, R and Han, SS and Narayanan, KB}, title = {Autoimmune responses and therapeutic interventions for systemic lupus erythematosus: a comprehensive review.}, journal = {Endocrine, metabolic &amp; immune disorders drug targets}, volume = {}, number = {}, pages = {}, doi = {10.2174/1871530323666230915112642}, pmid = {37718519}, issn = {2212-3873}, abstract = {Systemic Lupus Erythematosus (SLE) or Lupus is a multifactorial autoimmune disease of multiorgan malfunctioning of extremely heterogeneous and unclear etiology that affects multiple organs and physiological systems. Some racial groups and women of childbearing age are more susceptible to SLE pathogenesis. Impressive progress has been made towards a better understanding of different immune components contributing to SLE pathogenesis. Recent investigations have uncovered the detailed mechanisms of inflammatory responses and organ damage. Various environmental factors, pathogens, and toxicants, including ultraviolet light, drugs, viral pathogens, gut microbiome metabolites, and sex hormones trigger the onset of SLE pathogenesis in genetically susceptible individuals and result in the disruption of immune homeostasis of cytokines, macrophages, T cells, and B cells. Diagnosis and clinical investigations of SLE remain challenging due to its clinical heterogeneity and hitherto only a few approved antimalarials, glucocorticoids, immunosuppressants, and some nonsteroidal anti-inflammatory drugs (NSAIDs) are available for treatment. However, the adverse effects of renal and neuropsychiatric lupus and late diagnosis make therapy challenging. Additionally, SLE is also linked to an increased risk of cardiovascular diseases due to inflammatory responses and the risk of infection from immunosuppressive treatment. Due to the diversity of symptoms and treatment-resistant diseases, SLE management remains a challenging issue. Nevertheless, the use of next-generation therapeutics with stem cell and gene therapy may bring better outcomes to SLE treatment in the future. This review highlights the autoimmune responses as well as potential therapeutic interventions for SLE particularly focusing on the recent therapeutic advancements and challenges.}, }
@article {pmid37718380, year = {2023}, author = {Joshi, A and Joshi, R and Koradiya, P and Vank, H}, title = {Changes of microbiome in response to supplements with silver nanoparticles in cotton rhizosphere.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jobm.202300275}, pmid = {37718380}, issn = {1521-4028}, abstract = {The current study focuses on analyzing the effects of supplements containing silver nanoparticles (AgNPs) on plant growth and rhizospheric bacterial communities. Specifically, the impact of AgNP supplements was assessed on both plant growth promoting traits and bacterial communities in the soil. To do this, a screening process was conducted to select bacteria capable of synthesizing AgNPs through extracellular biosynthesis. UV-Visible spectrophotometer, Fourier transform infrared, X-ray diffraction, scanning electron microscope, and field emission scanning electron microscopy all confirmed, produced AgNPs is in agglomerates form. The resulting AgNPs were introduced into soil along with various supplements and their effects were evaluated after 10 days using next generation sequencing (Illumina-16S rDNA V3-V4 region dependent) to analyze changes in bacterial communities. Seed germination, root-shoot biomass and chlorophyll content were used to assess the growth of the cotton plant, whereas the bacterial ability to promote growth was evaluated by measuring its culturable diversity including traits like phosphate solubilization and indole acetic acid production. The variance in Bray-Curtis β diversity among six selected combinations including control depends largely on the type of added supplements contributing to 95%-97% of it. Moreover, seed germination improves greatly between 63% and 100% at a concentration range of 1.4 to 2.8 mg/L with different types of supplements. Based on the results obtained through this study, it is evident that using AgNPs along with fructose could be an effective tool for promoting Gossypium hirsutum growth and enhancing plant growth traits like profiling rhizospheric bacteria. The results that have been obtained endorse the idea of boosting the growth of rhizospheric bacteria in a natural way when AgNPs are present. Using these supplements in fields that have been contaminated will lead to a better understanding of how ecological succession occurs among rhizospheric bacteria, and what effect it has on the growth of plants.}, }
@article {pmid37717779, year = {2023}, author = {Fang, W and Fan, T and Wang, S and Yu, X and Lu, A and Wang, X and Zhou, W and Yuan, H and Zhang, L}, title = {Seasonal changes driving shifts in microbial community assembly and species coexistence in an urban river.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167027}, doi = {10.1016/j.scitotenv.2023.167027}, pmid = {37717779}, issn = {1879-1026}, abstract = {Microbial communities play a vital role in urban river biogeochemical cycles. However, the seasonal variations in microbial community characteristics, particularly phylogenetic group-based community assembly and species coexistence, have not been extensively investigated. Here, we systematically explored the microbiome characteristics and assembly mechanisms of urban rivers in different seasons using 16S rRNA gene sequencing and multivariate statistical methods. The results indicated that the microbial community presented significant temporal heterogeneity in different seasons, and the diversity decreased from spring to winter. The phylogenetic group-based microbial community assembly was governed by dispersal limitation and drift in spring, summer, and autumn but was structured by homogeneous selection in winter. Moreover, the main functions of nitrification, denitrification, and methanol oxidation were susceptible to dispersal limitation and drift processes, whereas sulfate respiration and aromatic compound degradation were controlled by dispersal limitation and homogeneous selection. Network analyses indicated that network complexity decreased and then increased with seasonal changes, while network stability showed the opposite trend, suggesting that higher complexity and diversity reduced community stability. Temperature was determined to be the primary driver of microbial community structure and assembly processes in different seasons based on canonical correspondence analysis and linear regression analysis. In conclusion, seasonal variation drives the dynamics of microbial community assembly and species coexistence patterns in urban rivers. This study provides new insights into the generation and maintenance of microbial community diversity in urban rivers under seasonal change conditions.}, }
@article {pmid37717771, year = {2023}, author = {Gu, K and Wu, A and Yu, B and Zhang, T and Lai, X and Chen, J and Yan, H and Zheng, P and Luo, Y and Luo, J and Pu, J and Wang, Q and Wang, H and Chen, D}, title = {Iron overload induces colitis by modulating ferroptosis and interfering gut microbiota in mice.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167043}, doi = {10.1016/j.scitotenv.2023.167043}, pmid = {37717771}, issn = {1879-1026}, abstract = {BACKGROUND: Iron plays a pivotal role in various physiological processes, including intestinal inflammation, ferroptosis, and the modulation of the gut microbiome. However, the way these factors interact with each other is unclear.<br><br>METHODS: Mice models were fed with low, normal and high iron diets to assess their impacts on colitis, ferroptosis and gut microbiota. Untargeted fecal metabolomics analysis, 16S rRNA sequencing, histopathology analysis, real-time quantitative PCR and western blot were performed to analyze the differences in the intestinal inflammatory response and understanding its regulatory mechanisms between low, normal and high iron groups.<br><br>RESULTS: The iron overload changed the serum iron, colon iron and fecal iron. In addition, the iron overload induced the colitis, induced the ferroptosis and altered the microbiome composition in the fecal of mice. By using untargeted fecal metabolomics analysis to screen of metabolites in the fecal, we found that different metabolomics profiles in the fecal samples between iron deficiency, normal iron and iron overload groups. The correlation analysis showed that both of iron deficiency and overload were closely related to Dubosiella. The relationship between microbial communities (e.g., Akkermansia, Alistipes, and Dubosiella) and colitis-related parameters was highly significant. Additionally, Alistipes and Bacteroides microbial communities displayed a close association with ferroptosis-related parameters. Iron overload reduced the concentration of metabolites, which exert the anti-inflammatory effects (e.g., (+)-.alpha.-tocopherol) in mice. The nucleotide metabolism, enzyme metabolism and metabolic diseases were decreased and the lipid metabolism was increased in iron deficiency and iron overload groups compared with normal iron group.<br><br>CONCLUSION: Iron overload exacerbated colitis in mice by modulating ferroptosis and perturbing the gut microbiota. Iron overload-induced ferroptosis was associated with NRF2/GPX-4 signaling pathway. Specific microbial taxa and their associated metabolites were closely intertwined with both colitis and ferroptosis markers.}, }
@article {pmid37717754, year = {2023}, author = {Jain, R and Gaur, A and Suravajhala, R and Chauhan, U and Pant, M and Tripathi, V and Pant, G}, title = {Microplastic pollution: Understanding microbial degradation and strategies for pollutant reduction.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167098}, doi = {10.1016/j.scitotenv.2023.167098}, pmid = {37717754}, issn = {1879-1026}, abstract = {Microplastics are ubiquitous environmental pollutants with the potential for adverse impacts on ecosystems and human health. These particles originate from the fragmentation of larger plastic items, shedding from synthetic fibers, tire abrasions, and direct release from personal care products and industrial processes. Once released into the environment, microplastics can disrupt ecosystems, accumulate in organisms, cause physical harm, and carry chemical pollutants that pose risks to both wildlife and human health. There is an urgent need to comprehensively explore the multifaceted issue of microplastic pollution and understand microbial degradation to reduce environmental pollution caused by microplastics. This paper presents a comprehensive exploration of microplastics, including their types, composition, advantages, and disadvantages, as well as the journey and evolution of microplastic pollution. The impact of microplastics on the microbiome and microbial communities is elucidated, highlighting the intricate interactions between microplastics and microbial ecosystems. Furthermore, the microbial degradation of microplastics is discussed, including the identification, characterization, and culturing methods of microplastic-degrading microorganisms. Mechanisms of microplastic degradation and the involvement of microbial enzymes are elucidated to shed light on potential biotechnological applications. Strategies for reducing microplastic pollution are presented, encompassing policy recommendations and the importance of enhanced waste management practices. Finally, the paper addresses future challenges and prospects in the field, emphasizing the need for international collaboration, research advancements, and public engagement. Overall, this study underscores the urgent need for concerted efforts to mitigate microplastic pollution and offers valuable insights for researchers, policymakers, and stakeholders involved in environmental preservation.}, }
@article {pmid37717689, year = {2023}, author = {Borroni, D and de Lossada, CR and Mazzotta, C and Sánchez-González, JM and Papa, F and Gabrielli, F}, title = {Ocular microbiome evaluation in dry eye disease and meibomian gland dysfunction: Values of variables.}, journal = {Experimental eye research}, volume = {}, number = {}, pages = {109656}, doi = {10.1016/j.exer.2023.109656}, pmid = {37717689}, issn = {1096-0007}, }
@article {pmid37717629, year = {2023}, author = {Mokhtari, P and Holzhausen, EA and Chalifour, BN and Schmidt, KA and Babaei, M and Machle, CJ and Adise, S and Alderete, TL and Goran, MI}, title = {Associations Between Dietary Sugar and Fiber with Infant Gut Microbiome Colonization at 6 Months of Age.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tjnut.2023.09.009}, pmid = {37717629}, issn = {1541-6100}, abstract = {BACKGROUND: The taxonomic composition of the gut microbiome undergoes rapid development during the first 2-3 years of life. Poor diet during complementary feeding has been associated with alterations in infant growth and compromised bone, immune system, and neurodevelopment, but how it may affect gut microbial composition is unknown.<br><br>OBJECTIVE: This cross-sectional study aimed to examine the associations between early life nutrition and the developing infant gut microbiota at 6 months of age.<br><br>METHODS: Latino mother-infant pairs from the Mother's Milk Study (n=105) were included. Infant gut microbiota and dietary intake were analyzed at 6 months of age using 16S rRNA amplicon sequencing and 24-hour dietary recalls, respectively. Poisson Generalized Linear regression analysis was performed to examine associations between dietary nutrients and microbial community abundance while adjusting for infants' mode of delivery, antibiotics, infant feeding type, time of introduction of solid foods, energy intake, and body weight. A p-value < 0.05 was used to determine the statistical significance in the study.<br><br>RESULTS: Infants with higher consumption of total sugar exhibited a lower relative abundance of the genera Bacteroides (&#x3b2;=-0.01, 95%CI:-0.02,-0.00 P= 0.03) and genus Clostridium belonging to the Lachnospiraceae family (&#x3b2;= -0.02, 95%CI:- 0.03,-0.00, P= 0.01). In addition, a higher intake of free sugar (which excludes sugar from milk, dairy, and whole fruit) was associated with several bacteria at the genus level including Parabacteroides genus (&#x3b2;=0.03, 95%CI:0.01, 0.05, P= 0.001). Total insoluble fiber intake was associated with favorable bacteria at the genus level such as Faecalibacterium (&#x3b2;=0.28, 95% CI: 0.03,0.52, P= 0.02) and Coprococcus (&#x3b2;=0.28, 95%CI: 0.02, 0.52, P=0.03) CONCLUSION: These findings demonstrate that early-life dietary intake at 6 months impacts the developing gut microbiome associated with the presence of both unfavorable gut microbes and dietary fiber-associated commensal microbes.}, }
@article {pmid37717575, year = {2023}, author = {Morin, C and Bokobza, C and Fleiss, B and Hill-Yardin, EL and Van Steenwinckel, J and Gressens, P}, title = {Preterm birth by cesarean section: the gut-brain axis, a key regulator of brain development.}, journal = {Developmental neuroscience}, volume = {}, number = {}, pages = {}, doi = {10.1159/000534124}, pmid = {37717575}, issn = {1421-9859}, abstract = {Understanding the long-term functional implications of gut microbial communities during the perinatal period is a bourgeoning area of research. Numerous studies have revealed the existence of a "gut-brain axis" and the impact of an alteration of gut microbiota composition in brain diseases. Recent research has highlighted how gut microbiota could affect brain development and behavior. Many factors in early life such as the mode of delivery or preterm birth could lead to disturbance in the assembly and maturation of gut microbiota. Notably, global rates of cesarean sections (C-sections) have increased in recent decades and remain important when considering premature delivery. Both preterm birth and C-sections are associated with an increased risk of neurodevelopmental disorders such as autism spectrum disorders; with neuroinflammation a major risk factor. In this review, we explore links between preterm birth by C-sections, gut microbiota alteration, and neuroinflammation. We also highlight C-sections as a risk factor for developmental disorders due to alterations in the microbiome.}, }
@article {pmid37717558, year = {2023}, author = {Rajkumar, J and Chandan, N and Lio, P and Shi, V}, title = {The Skin Barrier and Moisturization: Function, Disruption, and Mechanisms of Repair.}, journal = {Skin pharmacology and physiology}, volume = {}, number = {}, pages = {}, doi = {10.1159/000534136}, pmid = {37717558}, issn = {1660-5535}, abstract = {BACKGROUND: The anatomic layers of the skin are well-described; recent research into the barrier capabilities of the skin has led to the development of a functional model of the skin barrier. Moisturization has been consistently recommended for use in conditions such as atopic dermatitis, in which barrier disruption plays a key role in disease. This review aims to analyze the skin barrier in the context of this function model, with a focus on the mechanisms by which moisturizers support each of the functional layers of the skin barrier to promote homeostasis and repair.<br><br>METHODS: A PubMed literature search was conducted using combinations of the search terms "skin barrier", "functional skin barrier", "acid mantle", "skin microbiome", "moisturizer", "emollient", "humectant", and "occlusive" to uncover relevant articles. Abstract review was conducted to determine relevance for inclusion; references of articles were also reviewed and included as needed. The article search was limited to articles published in English.<br><br>RESULTS: The skin barrier is comprised of four interdependent layers - physical, chemical, microbiologic, and immunologic - which maintain barrier structure and function. Skin barrier disruption affects each of these four layers; moisturizers target each of these layers to promote homeostasis and repair. Occlusives, humectants, and emollients occlude the surface of the stratum corneum, draw water from the dermis into the epidermis, and assimilate into the stratum corneum, respectively, in order to strengthen the physical skin barrier. Acidic moisturizers bolster the chemical skin barrier by supporting optimal enzymatic function, increasing ceramide production, and facilitating ideal conditions for commensal microorganisms. Regular moisturization may strengthen the immunologic skin barrier by reducing permeability, allergen penetration, and sensitization.<br><br>CONCLUSIONS: The physical, chemical, microbiologic, and immunologic layers of the skin barrier are each uniquely impacted in states of skin barrier disruption. Moisturizers target each of the layers of the skin barrier to maintain homeostasis and facilitate repair.}, }
@article {pmid37717556, year = {2023}, author = {Kadogami, D and Kimura, F and Hanada, T and Tsuji, S and Nakaoka, Y and Murakami, T and Morimoto, Y}, title = {Impact of Lactobacillus in the uterine microbiota on in vitro fertilization outcomes.}, journal = {Journal of reproductive immunology}, volume = {160}, number = {}, pages = {104138}, doi = {10.1016/j.jri.2023.104138}, pmid = {37717556}, issn = {1872-7603}, abstract = {Abundant intrauterine Lactobacillus is associated with good in vitro fertilization (IVF) outcomes; however, whether specific species of Lactobacillus have any benefit remains unclear. So we examine the effect of Lactobacillus on the clinical outcomes of IVF at the species level. Uterine microbiota were classified as either Lactobacillus-dominant (LD) or non-Lactobacillus-dominant. In the LD group, we further investigated the clinical results for each Lactobacillus species and evaluated them in relation to IVF outcomes. In Uterine microbiome analysis, Lactobacillus was the most abundant, with the four species of L. crispatus, L. iners, L. gasseri, and L. jensenii accounting for the great majority. We compared the clinical outcomes of single frozen-thawed embryo transfer conducted by Lactobacillus species and found that the implantation rate was lowest in those in whom L. iners was dominant. This study is the first to conduct a species-level analysis of the uterine microbiota and report on a detailed investigation of Lactobacillus, which was believed to be particularly helpful for pregnancy.}, }
@article {pmid37717547, year = {2023}, author = {Fang, X and Gao, C and Wu, W and Hu, X and Shao, M and Zhou, C and Cai, R and Fang, J and Li, Y and Xu, Y and Zhang, X}, title = {The role of the gut microbiome in weight-gain in schizophrenia patients treated with atypical antipsychotics: Evidence based on altered composition and function in a cross-sectional study.}, journal = {Psychiatry research}, volume = {328}, number = {}, pages = {115463}, doi = {10.1016/j.psychres.2023.115463}, pmid = {37717547}, issn = {1872-7123}, abstract = {OBJECTIVES: We aimed to explore the interconnection between the weight-gain in schizophrenia patients with atypical antipsychotic treatment and gut microbiome.<br><br>METHODS: This study employed a cross-sectional design, encompassing a total of 88 schizophrenia patients with long-term atypical antipsychotic treatment. The 16S rRNA gene sequencing was used to identify gut microbiome contents.<br><br>RESULTS: No significant differences in alpha diversity between normal-weight and overweight schizophrenia treated with atypical antipsychotics. The beta diversity analysis showed that overweight patients clustered tightly while normal-weight patients clustered widely. For taxonomic composition, overweight patients had a lower relative abundance in Porphyromonadaceae at family level and Butyrivibrio at genus level, but higher relative abundance in Ruminococcus2 and Clostridium_XIVa at genus level than normal-weight patients. Function prediction revelated that four pathways (including Cell cycle, Non-homologous end-joining, Vibrio cholerae infection and Meiosis-yeast) were significantly different between groups. Correlation analysis indicated that Klebsiella, Butyrivibrio, Unassigned, Methanosphaera, Holdemania, Anaerotruncus were negatively, while Veillonella was positively correlated with BMI in patients.<br><br>CONCLUSION: Our findings offer evidence that perturbations in the gut microbiome composition, encompassing taxa such as Porphyromonadaceae, Butyrivibrio, Ruminococcus2, and Clostridium_XIVa, in conjunction with distinct functional pathways including Cell cycle, Non-homologous end-joining, Vibrio cholerae infection, and Meiosis-yeast, might contribute to the weight-gain in schizophrenia treated with atypical antipsychotics.}, }
@article {pmid37717481, year = {2023}, author = {Arango, M and Forga, A and Liu, J and Zhang, G and Gray, L and Moore, R and Coles, M and Atencio, A and Trujillo, C and Latorre, JD and Tellez-Isaias, G and Hargis, B and Graham, D}, title = {Characterizing the impact of Enterococcus cecorum infection during late embryogenesis on disease progression, cecal microbiome composition, and early performance in broiler chickens.}, journal = {Poultry science}, volume = {102}, number = {11}, pages = {103059}, doi = {10.1016/j.psj.2023.103059}, pmid = {37717481}, issn = {1525-3171}, abstract = {Enterococcus cecorum (EC) has been associated with septicemia and early mortality in broiler chickens. There is limited research investigating the pathogenicity of EC field strains obtained from affected birds. The purpose of this study was to evaluate the effect of in-ovo administration into the amnion with different EC field isolates at d 18 of embryogenesis (DOE18). In Exp 1, 7 EC field isolates alone or in combination (EC1-EC3, EC4-EC5, EC6, and EC7) were selected based on phenotypic characteristics and evaluated at different concentrations (1 × 10[2], 1 × 10[4], and 1 × 10[6] CFU/200 µL/embryo) to assess the impact on early performance and macroscopic lesions. Three isolates (n = 3; EC2, EC5, EC7) were selected for additional evaluation based on the significant (P < 0.05) BWG reduction (d 0-21) compared to the negative control (NC) and the presence of macroscopic lesions observed during posting sessions at d 14 and d 21. An additional isolate associated with enterococcal spondylitis was included in Exp 2 (EC11B). Treatment groups for Exp 2 include: 1) NC, 2) EC2, 3) EC5, 4) EC7, and 5) EC11B (n = 90-120/embryos/group). Groups 2 to 5 were challenged at 1 × 10[2] CFU/200 µL/embryo by in-ovo injection into the amnion at DOE18. Chicks were placed in battery cages for the duration of the study (21 d), and pen weights were recorded at d 0, d 7, d 14, and d 21 to calculate average BW and BWG. At d 14 and d 21 posthatch, liver, spleen, free thoracic vertebrae (FTV), and femoral head (FH) were aseptically collected to enumerate Enterococcus spp. using Chromagar Orientation as the selective media. Cecal contents were collected at d 21 to evaluate the effect of EC challenge on the cecal microbiome composition. There was a significant (P < 0.05) reduction in BW at d 21, and BWG from d 14 to 21 and d 0 to 21, for EC7 and EC11B. Enterococcus cecorum was recovered from the FTV of all challenged groups at d 14 and d 21. The most representative lesions were pericarditis, hydropericardium, focal heart necrosis, and FH osteomyelitis. However, lesions were not uniform across challenged groups or ages (d 14 and d 21). Alpha diversity of the cecal contents was markedly lower in EC5 and EC11B compared to all treatment groups suggesting that EC exposure during late embryogenesis affect the cecal microbiome up to 21 d posthatch. Additionally, these results highlight the differences in pathogenicity of EC strains isolated from field cases and suggest that hatchery exposure to EC during late embryogenesis is a potential route of introduction into a flock.}, }
@article {pmid37716897, year = {2023}, author = {Hung, CCU and Costa, RC and Pereira, G and Abdo, VL and Noronha, MDS and Retamal-Valdes, B and Bertolini, M and Feres, M and Shibli, JA and Barão, VAR and Souza, JGS}, title = {Oral microbial colonization on titanium and polyetheretherketone dental implant healing abutments: An in vitro and in vivo study.}, journal = {The Journal of prosthetic dentistry}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.prosdent.2023.08.010}, pmid = {37716897}, issn = {1097-6841}, abstract = {STATEMENT OF PROBLEM: Although polyetheretherketone (PEEK) implant healing abutments have become popular because of their esthetic, mechanical, and chemical properties, studies analyzing oral polymicrobial adhesion to PEEK abutments are lacking.<br><br>PURPOSE: The purpose of this in vitro and in vivo study was to evaluate oral microbial adhesion and colonization on titanium (Ti) and PEEK healing abutments.<br><br>MATERIAL AND METHODS: Ti (N=35) and PEEK substrates (N=35) were evaluated in vitro in terms of the initial adhesion (1 hour) or biofilm accumulation (48 hours) of Candida albicans and a polymicrobial inoculum using stimulated human saliva to mimic a diverse oral microbiome. Surface decontamination ability was evaluated after 24 hours of in vitro biofilm formation after exposure to an erbium-doped yttrium aluminum garnet (Er:YAG) laser. Conventional and flowable composite resin veneering on PEEK was also tested for microbial adhesion. In addition, an in vivo model with 3 healthy volunteers was conducted by using a palatal appliance containing the tested materials (3 or 4 specimens of each material per appliance) for 2 days to evaluate the effect of substrate on the microbial profile. Biofilms were evaluated by live cell counts and scanning electron microscopy images, and the microbial profile by Checkerboard deoxyribonucleic acid (DNA)-DNA hybridization. The t test and Mann-Whitney test were used to compare the groups (&#x3b1;=.05).<br><br>RESULTS: PEEK and Ti materials showed similar fungal adhesion (P>.05). Although the PEEK surface limited the initial in vitro polymicrobial adhesion (approximately 2 times less) compared with Ti (P=.040), after 48 hours of biofilm accumulation, the microbial load was statistically similar (P=.209). Er:YAG laser decontamination was more effective on PEEK than on Ti surfaces, reducing approximately 11 times more microbial accumulation (P=.019). Both composite resins tested showed similar microbial adhesion (1 hour). In vivo, the PEEK material showed reduced levels of 6 bacterial species (P<.05), including the putative pathogen Treponema denticola.<br><br>CONCLUSIONS: Although PEEK and Ti had similar bacterial and fungus biofilm attachment and accumulation, PEEK promoted a host-compatible microbial profile with a significantly reduced T. denticola load.}, }
@article {pmid37716416, year = {2023}, author = {Wyżga, B and Skóra, M and Hąc-Wydro, K}, title = {The influence of Leucidal - eco-preservative from radish - on model lipid membranes and selected pathogenic bacteria.}, journal = {Chemistry and physics of lipids}, volume = {}, number = {}, pages = {105338}, doi = {10.1016/j.chemphyslip.2023.105338}, pmid = {37716416}, issn = {1873-2941}, abstract = {In this work the effect of Leucidal - a natural preservative from radish dedicated to be used in cosmetics - on bacteria cells and model bacteria membranes was investigated. To get insight into the mechanism of action of this formulation the lipid Langmuir monolayers imitating Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) membranes were prepared. Then, the influence of Leucidal on model systems was investigated by means of the surface pressure/area measurements, penetration studies and Brewster Angle Microscopy (BAM) visualization. Similar experiments were done also for one component monolayers formed from the model membrane lipids. The in vitro tests were done on five different bacteria species (E. coli, Enterococcus faecalis, S. aureus, Salmonella enterica, Pseudomonas aeruginosa). Leucidal was found to decrease packing of the monolayers, however, it was excluded from the films at higher concentrations. Model membrane experiments evidenced also a stronger affinity of the components of this eco-preservative to E. coli vs S. aureus membrane. Among one component films, those formed from phosphatidylglycerols and cardiolipins were more sensitive to the presence of Leucidal. However, in vitro tests evidenced that Leucidal exerts stronger inhibitory effect against S. aureus bacteria as compared to E. coli strain. These findings were discussed from the point of view of the role of Leucidal components and the lipid membrane properties in the membrane - based mechanism of action of this preservative. The results allow one to suggest that the membrane may not be the main site of action of Leucidal on bacteria. Moreover, since high concentration of the tested preparation exerted antibacterial activity in relation to all tested bacteria, a low selectivity of Leucidal can be postulated, which may be problematic from the point of view of its effect on the skin microbiome.}, }
@article {pmid37716364, year = {2023}, author = {Worby, CJ and Sridhar, S and Turbett, SE and Becker, MV and Kogut, L and Sanchez, V and Bronson, RA and Rao, SR and Oliver, E and Walker, AT and Walters, MS and Kelly, P and Leung, DT and Knouse, MC and Hagmann, SHF and Harris, JB and Ryan, ET and Earl, AM and LaRocque, RC}, title = {Gut microbiome perturbation, antibiotic resistance, and Escherichia coli strain dynamics associated with international travel: a metagenomic analysis.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2666-5247(23)00147-7}, pmid = {37716364}, issn = {2666-5247}, abstract = {BACKGROUND: Culture-based studies have shown that acquisition of extended-spectrum β-lactamase-producing Enterobacterales is common during international travel; however, little is known about the role of the gut microbiome before and during travel, nor about acquisition of other antimicrobial-resistant organisms. We aimed to identify (1) whether the gut microbiome provided colonisation resistance against antimicrobial-resistant organism acquisition, (2) the effect of travel and travel behaviours on the gut microbiome, and (3) the scale and global heterogeneity of antimicrobial-resistant organism acquisition.<br><br>METHODS: In this metagenomic analysis, participants were recruited at three US travel clinics (Boston, MA; New York, NY; and Salt Lake City, UT) before international travel. Participants had to travel internationally between Dec 8, 2017, and April 30, 2019, and have DNA extractions for stool samples both before and after travel for inclusion. Participants were excluded if they had at least one low coverage sample (<1 million read pairs). Stool samples were collected at home before and after travel, sent to a clinical microbiology laboratory to be screened for three target antimicrobial-resistant organisms (extended-spectrum &#x3b2;-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales, and mcr-mediated colistin-resistant Enterobacterales), and underwent DNA extraction and shotgun metagenomic sequencing. We profiled metagenomes for taxonomic composition, antibiotic-resistant gene content, and characterised the Escherichia coli population at the strain level. We analysed pre-travel samples to identify the gut microbiome risk factors associated with acquisition of the three targeted antimicrobial resistant organisms. Pre-travel and post-travel samples were compared to identify microbiome and resistome perturbation and E coli strain acquisition associated with travel.<br><br>FINDINGS: A total of 368 individuals travelled between the required dates, and 296 had DNA extractions available for both before and after travel. 29 travellers were excluded as they had at least one low coverage sample, leaving a final group of 267 participants. We observed a perturbation of the gut microbiota, characterised by a significant depletion of microbial diversity and enrichment of the Enterobacteriaceae family. Metagenomic strain tracking confirmed that 67% of travellers acquired new strains of E coli during travel that were phylogenetically distinct from their pre-travel strains. We observed widespread enrichment of antibiotic-resistant genes in the gut, with a median 15% (95% CI 10-20, p<1&#x2009;&#xd7;&#x2009;10[-10]) increase in burden (reads per kilobase per million reads). This increase included antibiotic-resistant genes previously classified as threats to public health, which were 56% (95% CI 36-91, p=2&#x2009;&#xd7;&#x2009;10[-11]) higher in abundance after travel than before. Fluoroquinolone antibiotic-resistant genes were aquired by 97 (54%) of 181 travellers with no detected pre-travel carriage. Although we found that visiting friends or relatives, travel to south Asia, and eating uncooked vegetables were risk factors for acquisition of the three targeted antimicrobial resistant organisms, we did not observe an association between the pre-travel microbiome structure and travel-related antimicrobial-resistant organism acquisition.<br><br>INTERPRETATION: This work highlights a scale of E coli and antimicrobial-resistant organism acquisition by US travellers not apparent from previous culture-based studies, and suggests that strategies to control antimicrobial-resistant organisms addressing international traveller behaviour, rather than modulating the gut microbiome, could be worthwhile.<br><br>FUNDING: US Centers for Disease Control and Prevention and National Institute of Allergy and Infectious Diseases.}, }
@article {pmid37716071, year = {2023}, author = {Sun, Z and Liu, Y and Hou, A and Han, A and Yan, C and Sun, J}, title = {Transcriptome and gut microbiota analyses reveal a possible mechanism underlying rifampin-mediated interruption of the larval development of chironomid Propsilocerus akamusi (Diptera: Chironomidae).}, journal = {Ecotoxicology and environmental safety}, volume = {264}, number = {}, pages = {115467}, doi = {10.1016/j.ecoenv.2023.115467}, pmid = {37716071}, issn = {1090-2414}, abstract = {Chironomids, the most abundant insect group found in freshwater habitats, are known to be pollution tolerate and serve as important bioindicators of contaminant stress. Gut microbiota has recently been shown to potentially provide a number of beneficial services to insect hosts. However, the antibiotic-mediated interruption of chironomid gut microbial community and its subsequent influence on host body are still unclear. In the present study, the effects of rifampin on chironomid larvae were investigated at both transcriptome and microbiome level to assess the relationship between gut bacteria and associated genes. Our data indicated that the rifampin-induced imbalance of gut ecosystem could inhibit the development of chironomid larvae via decreasing the body weight, body length and larval eclosion rate during 96-h treatment. Both the community structure and taxonomic composition were significantly altered due to the invasion of rifampin in digestive tracts. The relative abundance of phylum Deferribacterota and Bacteroidota were dramatically increased with rifampin exposure. A set of genes involved in amino acid synthesis as well as xenobiotic metabolism pathways were greatly changed and proved to have tight correlation with certain genus. Bacterial genus Tyzzerella was positively correlated with detoxifying PaCYP6GF1 and PaCYP9HL1 genes. This study provides a reference for understanding the environmental risks of antibiotic and aims to accelerate new biological insights into the effects of antibiotic on the fitness of chironomids and into the microbe mediated-regulatory mechanism of aquatic insects.}, }
@article {pmid37715531, year = {2023}, author = {Härer, A and Mauro, AA and Laurentino, TG and Rosenblum, EB and Rennison, DJ}, title = {Gut microbiota parallelism and divergence associated with colonisation of novel habitats.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.17135}, pmid = {37715531}, issn = {1365-294X}, support = {458274593//Deutsche Forschungsgemeinschaft/ ; 1754125//National Science Foundation/ ; P2BSP3_195698//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, abstract = {An organism's gut microbiota can change in response to novel environmental conditions, in particular when colonisation of new habitats is accompanied by shifts in the host species' ecology. Here, we investigated the gut microbiota of three lizard species (A. inornata, H. maculata and S. cowlesi) from their ancestral-like habitat in the Chihuahuan desert and two colonised habitats with contrasting geological and ecological compositions: the White Sands and Carrizozo lava flow. The host species and the lizards' environment both shape gut microbiota composition, but host effects were overall stronger. Further, we found evidence that colonisation of the same environment by independent host species led to parallel changes of the gut microbiota, whereas the colonisation of two distinct environments by the same host species led to gut microbiota divergence. Some of the gut microbiota changes that accompanied the colonisation of the White Sands were associated with shifts in diet (based on diet information from previous studies), which is congruent with the general observation that trophic ecology has a strong effect on gut microbiota composition. Our study provides insights into how shifts in host ecology accompanying colonisation of novel environments can affect gut microbiota composition and diversity.}, }
@article {pmid37715517, year = {2023}, author = {Thomas, SC and Guo, Y and Xu, F and Saxena, D and Li, X}, title = {A novel SUCNR1 inhibitor alleviates dysbiosis through inhibition of host responses without direct interaction with host microbiota.}, journal = {Molecular oral microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/omi.12431}, pmid = {37715517}, issn = {2041-1014}, support = {DE027074/GF/NIH HHS/United States ; DE028212/GF/NIH HHS/United States ; AG055787/GF/NIH HHS/United States ; }, abstract = {Type 2 diabetes (T2D) is a chronic metabolic disorder in which insulin resistance and impaired insulin secretion result in altered metabolite balance, specifically elevated levels of circulating glucose and succinate, which increases the risk of many pathologies, including periodontitis. Succinate, a tricarboxylic acid (TCA) cycle intermediate, can be produced and metabolized by both host cells and host microbiota, where elevated levels serve as an inflammation and pathogen threat signal through activating the succinate G protein-coupled receptor, SUCNR1. Modulating succinate-induced SUCNR1 signaling remains a promising therapeutic approach for pathologies resulting in elevated levels of succinate, such as T2D and periodontitis. Here, we demonstrate hyperglycemia and elevated intracellular succinate in a T2D mouse model and determine gut microbiome composition. Drawing on previous work demonstrating the ability of a novel SUCNR1 antagonist, compound 7a, to block inflammation and alleviate dysbiosis in a mouse model, we examined if compound 7a has an impact on the growth and virulence gene expression of bacterial and fungal human microbiota in vitro, and if 7a could reduce bone loss in a periodontitis-induced mouse model. T2D mice harbored a significantly different gut microbiome, suggesting the altered metabolite profile of T2D causes shifts in host-microbial community structure, with enrichment in succinate producers and consumers and mucin-degrading bacteria. Bacterial and fungal cultures showed that 7a did not influence growth or virulence gene expression, suggesting the therapeutic effects of 7a are a direct result of 7a interacting with host cells and that alterations in microbial community structure are driven by reduced host SUCNR1 signaling. This work further suggests that targeting SUCNR1 signaling is a promising therapeutic approach in metabolic, inflammatory, or immune disorders with elevated succinate levels.}, }
@article {pmid37715479, year = {2023}, author = {Zhao, B and Jia, X and Yu, N and Murray, JD and Yi, K and Wang, E}, title = {Microbe-dependent and independent nitrogen and phosphate acquisition and regulation in plants.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19263}, pmid = {37715479}, issn = {1469-8137}, support = {31870218//National Science Foundation/ ; 32050081//National Science Foundation/ ; 31825003//National Science Foundation/ ; 31730103//National Science Foundation/ ; 32001886//National Science Foundation/ ; 32088102//National Science Foundation/ ; YSBR-011//Chinese Academy of Sciences Project for Young Scientists in Basic Research/ ; //XPLORER PRIZE/ ; }, abstract = {Nitrogen (N) and phosphorus (P) are the most important macronutrients required for plant growth and development. To cope with the limited and uneven distribution of N and P in complicated soil environments, plants have evolved intricate molecular strategies to improve nutrient acquisition that involve adaptive root development, production of root exudates, and the assistance of microbes. Recently, great advances have been made in understanding the regulation of N and P uptake and utilization and how plants balance the direct uptake of nutrients from the soil with the nutrient acquisition from beneficial microbes such as arbuscular mycorrhiza. Here, we summarize the major advances in these areas and highlight plant responses to changes in nutrient availability in the external environment through local and systemic signals.}, }
@article {pmid37715326, year = {2023}, author = {Grozina, AA and Ilina, LA and Laptev, GY and Yildirim, EA and Ponomareva, ES and Filippova, VA and Tyurina, DG and Fisinin, VI and Kochish, II and Griffin, DK and Surai, PF and Romanov, MN}, title = {Probiotics as an alternative to antibiotics in modulating the intestinal microbiota and performance of broiler chickens.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxad213}, pmid = {37715326}, issn = {1365-2672}, abstract = {AIMS: Gut bacteria play an important role in poultry nutrition and the immune defense system. Changes in the intestinal microbiome affect the physiological state, metabolism and innate im-munity of poultry. The present study aimed to characterize age-related changes in the gastrointestinal tract microflora in broiler chickens, depending on supplementation of the diet with the in-feed antibiotic Stafac® 110 and a Bacillus subtilis strain-based probiotic.<br><br>METHODS AND RESULTS: In this regard, a comprehensive analysis of the taxonomic structure of the microbial community in the gastrointestinal tract (GIT) of broiler chickens was carried out using a molecular genetic technique of the Terminal-Restriction Fragment Length Polymorphism analysis and taking into account age dynamics and feeding treatment. A beneficial effect on the microbiological composition and body weight of broilers was observed when using the antibiotic and probiotic in compound feeds. Different bacterial communities were revealed in the duodenum and cecum and their positive impact on broiler growth was established. The results obtained shed light on the formation of GIT microflora of broiler chickens during the growing period and its changes in response to the use of the antibiotic and the probiotic.<br><br>CONCLUSIONS: We suggest that the implementation of the tested in-feed antibiotic and probiotic can be beneficial in regulating the intestinal microflora microbiological processes in the GIT and improving the feeding efficiency and productivity of broiler chickens.}, }
@article {pmid37715299, year = {2023}, author = {Shaw, CG and Pavloudi, C and Hudgell, MAB and Crow, RS and Saw, JH and Pyron, RA and Smith, LC}, title = {Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium.}, journal = {Pathogens and disease}, volume = {}, number = {}, pages = {}, doi = {10.1093/femspd/ftad025}, pmid = {37715299}, issn = {2049-632X}, abstract = {Bald sea urchin disease (BSUD) is most likely a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages. The disease has a variety of additional symptoms, which may be the result of the many bacteria that are associated with BSUD. Previous studies have investigated causative agents of BSUD, however, there are few reports on the surface microbiome associated with the infection. Here we report changes to the surface microbiome on purple sea urchins in a closed marine aquarium that contracted and then recovered from BSUD in addition to the microbiome of healthy sea urchins in a separate aquarium. 16S rRNA gene sequencing shows that microhabitats of different aquaria are characterized by different microbial compositions, and that diseased, recovered, and healthy sea urchins have distinct microbial compositions, which indicates that there is a correlation between microbial shifts and recovery from disease.}, }
@article {pmid37715296, year = {2023}, author = {Mills, M and Lee, S and Piperata, BA and Garabed, R and Choi, B and Lee, J}, title = {Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {207}, pmid = {37715296}, issn = {2049-2618}, mesh = {Animals ; Child ; Child, Preschool ; Dogs ; Female ; Humans ; Infant ; Anti-Bacterial Agents/pharmacology ; Breast Feeding ; Escherichia coli ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Nicaragua ; Male ; Infant, Newborn ; }, abstract = {BACKGROUND: Early life plays a vital role in the development of the gut microbiome and subsequent health. While many factors that shape the gut microbiome have been described, including delivery mode, breastfeeding, and antibiotic use, the role of household environments is still unclear. Furthermore, the development of the gut antimicrobial resistome and its role in health and disease is not well characterized, particularly in settings with water insecurity and less sanitation infrastructure.<br><br>RESULTS: This study investigated the gut microbiome and resistome of infants and young children (ages 4&#xa0;days-6&#xa0;years) in rural Nicaragua using Oxford Nanopore Technology's MinION long-read sequencing. Differences in gut microbiome diversity and antibiotic resistance gene (ARG) abundance were examined for associations with host factors (age, sex, height for age z-score, weight for height z-score, delivery mode, breastfeeding habits) and household environmental factors (animals inside the home, coliforms in drinking water, enteric pathogens in household floors, fecal microbial source tracking markers in household floors). We identified anticipated associations of higher gut microbiome diversity with participant age and vaginal delivery. However, novel to this study were the significant, positive associations between ruminant and dog fecal contamination of household floors and gut microbiome diversity. We also identified greater abundance of potential pathogens in the gut microbiomes of participants with higher fecal contamination on their household floors. Path analysis revealed that water quality and household floor contamination independently and significantly influenced gut microbiome diversity when controlling for age. These gut microbiome contained diverse resistome, dominated by multidrug, tetracycline, macrolide/lincosamide/streptogramin, and beta-lactam resistance. We found that the abundance of ARGs in the gut decreased with age. The bacterial hosts of ARGs were mainly from the family Enterobacteriaceae, particularly Escherichia coli.<br><br>CONCLUSIONS: This study identified the role of household environmental contamination in the developing gut microbiome and resistome of young children and infants with a One Health perspective. We found significant relationships between host age, gut microbiome diversity, and the resistome. Understanding the impact of the household environment on the development of the resistome and microbiome in early life is essential to optimize the relationship between environmental exposure and human health. Video Abstract.}, }
@article {pmid37715236, year = {2023}, author = {ElKraly, OA and Awad, M and El-Saadany, HM and Hassanein, SE and Elrahman, TA and Elnagdy, SM}, title = {Impact of gut microbiota composition on black cutworm, Agrotis ipsilon (hufnagel) metabolic indices and pesticide degradation.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {44}, pmid = {37715236}, issn = {2524-4671}, abstract = {Endosymbionts are known to have significant effects on their insect hosts, including nutrition, reproduction, and immunity. Insects gut microbiota is a critical component that affects their physiological and behavioral characteristics. The black cutworm (BCW), Agrotis ipsilon, is an economically important lepidopteran pest that has a diverse gut microbiome composed of nine species belonging to three phyla: Proteobacteria, Actinobacteria, and Firmicutes. This study was conducted to investigate the diversity of gut bacteria isolated from BCW larvae and moths and their effects on metabolism and pesticide degradation. The bacterial isolates were identified using the 16 S rRNA gene. The study showed that the gut microbiome composition significantly affected the metabolism of BCW larvae. Based on the screening results of synthesis of digestive enzymes and pesticide degradation, Brachybacterium conglomeratum and Glutamicibacter sp were selected to perform the remaining experiments as single isolates and consortium. The consortium-fed larvae showed high metabolic indices compared to antibiotic-fed larvae and the control. The gut bacteria were also shown to degrade three pesticide groups. Concerns regarding the health risk of chlorpyrifos have been raised due to its extensive use in agriculture. The isolated B. conglomeratum was more effective in chlorpyrifos degradation than the consortium. Furthermore, the study also examined the presence of sex related endosymbionts (Wolbachia, Spiroplasma, and Rickettsia) in the reproductive tissues of adults. The outcomes demonstrated that none of the examined endosymbionts existed. In conclusion, the study highlights the importance of the gut microbiome in insect physiology and behavior and its potential applications in biotechnology. It provides insights into developing eco-friendly pest control and bioremediation strategies using gut bacteria.}, }
@article {pmid37714908, year = {2023}, author = {Miyata, R and Miyabe, C and Oki, H and Motooka, D and Nakamura, S and Miyabe, Y and Takenaka, Y and Fukuya, Y and Yudo, K and Ishiguro, N}, title = {Alteration of microbial composition in the skin and blood in vasculitis.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15317}, pmid = {37714908}, issn = {2045-2322}, mesh = {Humans ; *Vasculitis ; Skin ; Leukocytes ; *Actinomycetales ; Discriminant Analysis ; }, abstract = {Vasculitis is a systemic autoimmune disease characterized by leukocyte infiltration into blood vessels. Various microorganisms have been associated with the pathogenesis of vasculitis; however, the causal microbial agents and underlying mechanisms are not fully understood, possibly because of the technical limitations of pathogen detection. In the present study, we characterized the microbiome profile of patients with cutaneous vasculitis using comprehensive metagenome shotgun sequencing. We found that the abundance of the SEN virus was increased in the affected skin and serum of patients with vasculitis compared to healthy donors. In particular, the abundance of SEN virus reads was increased in the sera of patients with cutaneous arteritis. Among the bacteria identified, Corynebacteriales was the most differentially associated with vasculitis. Linear discriminant analysis effect size also indicated differences in the microbial taxa between patients with vasculitis and healthy donors. These findings demonstrate that vasculitis is associated with considerable alteration of the microbiome in the blood and skin and suggest a role for the infectious trigger in vasculitis.}, }
@article {pmid37714772, year = {2023}, author = {Amat, M and Le Brech, S and Manteca, X}, title = {The Relationship Between Aggression and Physical Disease in Dogs.}, journal = {The Veterinary clinics of North America. Small animal practice}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cvsm.2023.08.008}, pmid = {37714772}, issn = {1878-1306}, abstract = {Aggression is a very common behavioral problem in dogs. Although aggression can be part of the normal behavior of dogs, medical conditions can either trigger aggression as in the case of intracranial tumors or aggravate an existing aggression problem as it happens with painful conditions. Therefore, it is essential to include an assessment of physical health in the diagnostic protocol of canine aggression.}, }
@article {pmid37714737, year = {2023}, author = {Guo, Z and Yiu, N and Hu, Z and Zhou, W and Long, X and Yang, M and Liao, J and Zhang, G and Lu, Q and Zhao, M}, title = {Alterations of fecal microbiome and metabolome in pemphigus patients.}, journal = {Journal of autoimmunity}, volume = {}, number = {}, pages = {103108}, doi = {10.1016/j.jaut.2023.103108}, pmid = {37714737}, issn = {1095-9157}, abstract = {The role of gut microbiome and metabolic substances in the development of autoimmune diseases has gradually been revealed. However, the relevant gut features in pemphigus have not been well clarified. We collected stool samples from pemphigus patients and healthy controls (HCs). Metagenomic sequencing and liquid chromatography-mass spectrometry (LC/MS) metabolome sequencing were performed to analyze the compositional and metabolic alternations of the gut microbiome in pemphigus patients and HCs. We observed the reduced richness and diversity and greater heterogeneity in pemphigus patients, which was characterized by a significant decrease in Firmicutes and an increase in Proteobacteria. At the species level, Intestinal pathogenic bacteria such as Escherichia coli and Bacteroides fragilis were significantly enriched, while anti-inflammatory bacteria and butyric acid-producing bacteria were significantly reduced, which were related to clinical indicators (Dsg1/3 and PDAI). 4 species were selected by the machine learning algorithm to better distinguish pemphigus patients from healthy people. Metabolomic analysis showed that the composition of pemphigus patients was different from that of HCs. PE (18:3 (6Z,9Z, 12Z)/14:1 (9Z)) was the main metabolic substance in pemphigus and involved in a variety of metabolic pathways. While Retinol, flavonoid compounds and various amino acids decreased significantly compared with HCs. Furthermore, we found that differences in the levels of these metabolites correlated with changes in the abundance of specific species. Our study provides a comprehensive picture of gut microbiota and metabolites in pemphigus patients and suggests a potential mechanism of the aberrant gut microbiota and metabolites in the pathogenesis of pemphigus.}, }
@article {pmid37714481, year = {2023}, author = {Zhao, Z and Sun, Y and Wang, H and Yu, Q}, title = {Regulation of cadmium-induced biofilm formation by artificial polysaccharide-binding proteins for enhanced phytoremediation.}, journal = {Chemosphere}, volume = {342}, number = {}, pages = {140156}, doi = {10.1016/j.chemosphere.2023.140156}, pmid = {37714481}, issn = {1879-1298}, abstract = {Phytoremediation is an economic way to attenuate soil heavy metal pollution, but is frequently limited by its low pollutant-removing efficiency. Recently, we revealed the close relation between polysaccharide-based biofilm formation and cadmium removal. In this study, for improving the phytoremediation efficiency, an artificial polysaccharide-binding protein was designed by synthetic biology techniques to regulate biofilm formation. The artificial protein Syn contained two polysaccharide-binding domains from the Ruminococcus flavefaciens CttA and the Clostridium cellulolyticum CipC, preferentially binding polysaccharides exposed on both cadmium-treated bacteria and plant roots. Under cadmium stress, Syn remarkably promoted bacterial polysaccharide production from 99 mg/L to 237 mg/L, leading to 1.23-fold higher biofilm biomass. During treatment of the remediation plants with exogenous cadmium-capturing bacteria, Syn improved root biofilm formation, with the root surface polysaccharide contents increasing by 79%, and the Log10 CFU/g root increasing from 7.01 to 7.80. Meanwhile, Syn remodeled the rhizosphere microbiome, especially increasing the abundance of the bacterial groups involved in biofilm formation and stress tolerance, e.g., Pseudomonas, Enterobacter, etc. Consequently, Syn promoted plant cadmium adsorption, with the cadmium-removing efficiency increasing from 17.2% to 33.8%. This study sheds light on synthetic biology-based regulation of biofilm formation for enhanced phytoremediation.}, }
@article {pmid37714436, year = {2023}, author = {Mahdavinia, M and Fyolek, JP and Jiang, J and Thivalapill, N and Bilaver, LA and Warren, C and Fox, S and Nimmagadda, SR and Newmark, PJ and Sharma, H and Assa'ad, A and Seed, PC and Gupta, RS}, title = {Gut microbiome is associated with asthma and race in children with food allergy.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaci.2023.07.024}, pmid = {37714436}, issn = {1097-6825}, abstract = {BACKGROUND: The composition of the gut microbiome has been associated with development of atopic conditions such as food allergy (FA) and asthma. African American or Black children with FA have higher rate of asthma compared to their white counterparts.<br><br>OBJECTIVE: We sought to investigate whether the diversity and relative abundance (RA) of gut microbiota is different between children with FA from different racial backgrounds living in the same cities. Furthermore, we aimed to understand whether the difference in the gut microbiota is associated with asthma in children with FA.<br><br>METHOS: We analyzed and compared the stool microbiome of a cohort of Black and White children with FA using shotgun genomic sequencing.<br><br>RESULTS: 152 children with IgE-mediated FA(s) enrolled into FORWARD (Food Allergy Outcomes Related to White and African American Racial Differences); including 30 Black and 122 White children were included. The relative abundance of several bacteria was associated with race and asthma. Most notably the RA of Bacteroides thetaiotaomicron, Chlamydia thrachomatis, Parabacteroides goldsteinii and Bacteroides Eggerthii were significantly higher, while the RA of Bifidobacterium sp. CAG:754, Parabacterium johnsonii, Bacteroides intestinalis and Bifidobacterium breve were significantly lower in stool samples of Black children compared to White children. Asthma was associated with lower RA of Bifidobacterium breve, Bifidobacteria catenulatum, Prevotella copri, Veilloella sp. CAG:933 and Bacteroides plebius, and higher RA of three Bacteroides species.<br><br>CONCLUSIONS: The observed variations in the gut microbiota of Black and white children such as differences in the Bacteroides and Bifidobacterium species along with their association to history of asthma in our cohort is indicative of their potential role in the higher rate of asthma observed among Black children with FA.}, }
@article {pmid37714338, year = {2023}, author = {Liu, D and Gao, X and Huang, X and Fan, Y and Wang, YE and Zhang, Y and Chen, X and Wen, J and He, H and Hong, Y and Liang, Y and Zhang, Y and Liu, Z and Chen, S and Li, X}, title = {Moderate altitude exposure impacts host fasting blood glucose and serum metabolome by regulation of the intestinal flora.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167016}, doi = {10.1016/j.scitotenv.2023.167016}, pmid = {37714338}, issn = {1879-1026}, abstract = {Moderate altitude exposure has shown beneficial effects on diabetes incidence but the underlying mechanisms are not understood. Our study aimed to investigate how the human gut microbiome impacted the serum metabolome and associated with glucose homeostasis in healthy Chinese individuals upon moderate-altitude exposure. Faecal microbiome composition was assessed using shotgun metagenomic sequencing. Serum metabolome was acquired by untargeted metabolomics technology, and amino acids (AAs) and propionic acid in serum were quantified by targeted metabolomics technology. The results indicated that the moderate-altitude exposed individuals presented lowered fasting blood glucose (FBG) and propionic acid, increased circulating l-Glutamine but decreased L-Glutamate and L-Valine, which correlated with enriched Bacteroidetes and decreased Proteobacteria. Additionally, the silico causality associations among gut microbiota, serum metabolome and host FBG were analyzed by mediation analysis. It showed that increased Bacteroides ovatus (B. ovatus) and decreased Escherichia coli (E. coli) were identified as the main antagonistic species driving the association between L-Glutamate and FBG in silico causality. Furthermore, the high-fat diet (HFD) fed mice subjected to faecal microbiota transplantation (FMT) were applied to validate the cause-in-fact effects of gut microbiota on the beneficial glucose response. We found that microbiome in the moderate-altitude exposed donor could predict the extent of the FBG response in recipient mice, which showed lowered FBG, L-Glutamate and Firmicutes/Bacteroidetes ratio. Our findings suggest that moderate-altitude exposure targeting gut microbiota and circulating metabolome, may pave novel avenues to counter dysglycemia.}, }
@article {pmid37714334, year = {2023}, author = {Kang, Y and Oba, PM and Gaulke, CA and Sánchez-Sánchez, L and Swanson, KS}, title = {Dietary inclusion of yellow mealworms (T. molitor) and lesser mealworms (A. diaperinus) modifies intestinal microbiota populations of diet-induced obesity mice.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tjnut.2023.09.007}, pmid = {37714334}, issn = {1541-6100}, abstract = {BACKGROUND: Insect-based proteins are high-quality alternatives to support the shift toward more sustainable and healthy diets. Additionally, insects contain chitin and have unique fatty acid profiles. Studies have shown that mealworms may beneficially affect metabolism, but limited information is known regarding their effects on gut microbiota.<br><br>OBJECTIVE: We determined the effects of defatted yellow mealworm (Tenebrio molitor)- and whole lesser mealworm (Alphitobius diaperinus)-meals on the intestinal microbiota of diet-induced obesity mice.<br><br>METHODS: Male C57BL/6J mice were fed a high-fat diet (HFD; 46% kcal) to induce obesity. Obese mice were then randomly assigned to treatments (n=10/group) and fed for 8 wk: HFD: HFD with casein protein; B50: HFD with 50% protein from whole lesser mealworm; B100: HFD with 100% protein from whole lesser mealworm; Y50: HFD with 50% protein from defatted yellow mealworm; Y100: HFD with 100% protein from defatted yellow mealworm. Lean mice (n=10) fed a low-fat-diet (10% kcal) were included. Fresh feces was collected at baseline and every 2 weeks, with cecal digesta collected at sacrifice. Fecal and cecal DNA was analyzed for microbiota using 16S rRNA MiSeq Illumina sequencing.<br><br>RESULTS: In feces and cecal digesta, mice fed mealworms had greater (P<0.05) bacterial alpha diversity, with changes occurring in a time-dependent manner (P<0.05). Beta diversity analyses of cecal samples showed a clear separation of treatments, with a time-based separation shown in fecal samples. Widespread microbial differences were observed, with over 45 genera altered (P<0.05) by diet in cecal digesta. In feces, over 50 genera and 40 genera were altered (P<0.05) by diet and time, respectively.<br><br>CONCLUSION: Mealworm consumption changed the intestinal microbiota of obese mice, increasing alpha diversity measures and shifting bacterial taxa. More investigation is required to determine what mealworm components are responsible and how they may be linked with the metabolic benefits observed in mealworm-fed mice.}, }
@article {pmid37714308, year = {2023}, author = {Craig, CF and Finkelstein, DI and McQuade, RM and Diwakarla, S}, title = {Understanding the potential causes of gastrointestinal dysfunctions in multiple system atrophy.}, journal = {Neurobiology of disease}, volume = {}, number = {}, pages = {106296}, doi = {10.1016/j.nbd.2023.106296}, pmid = {37714308}, issn = {1095-953X}, abstract = {Multiple system atrophy (MSA) is a rare, progressive neurodegenerative disorder characterised by autonomic, pyramidal, parkinsonian and/or cerebellar dysfunction. Autonomic symptoms of MSA include deficits associated with the gastrointestinal (GI) system, such as difficulty swallowing, abdominal pain and bloating, nausea, delayed gastric emptying, and constipation. To date, studies assessing GI dysfunctions in MSA have primarily focused on alterations of the gut microbiome, however growing evidence indicates other structural components of the GI tract, such as the enteric nervous system, the intestinal barrier, GI hormones, and the GI-driven immune response may contribute to MSA-related GI symptoms. Here, we provide an in-depth exploration of the physiological, structural, and immunological changes theorised to underpin GI dysfunction in MSA patients and highlight areas for future research in order to identify more suitable pharmaceutical treatments for GI symptoms in patients with MSA.}, }
@article {pmid37714180, year = {2023}, author = {Awujoola, A and Torga, AP and Abdul Ghayum, MA and Mousa, N and Olorunsogo, T and DeSilva, S and Avades, M and Prince, O and Ankola, P}, title = {Neonatal Ampicillin/Gentamicin Exposure and the Risk of Childhood Obesity in South Bronx Pediatric Population.}, journal = {American journal of perinatology}, volume = {}, number = {}, pages = {}, doi = {10.1055/s-0043-1774315}, pmid = {37714180}, issn = {1098-8785}, abstract = {OBJECTIVE: This study aimed to assess the association between neonatal antibiotic exposure and the risk of childhood obesity.<br><br>STUDY DESIGN: &#x2003;This retrospective cohort study enrolled neonates born between 2011 and 2015 and followed up until 5 years. The incidence of obesity at 5 years old, and other characteristics were compared between the antibiotic-exposed and unexposed groups. Chi-square test was conducted on categorical variables and Student's t-test for normally distributed continuous variable. Significant variables (p&#x2009;<&#x2009;0.05) in bivariate analysis were modelled in a stepwise multivariate logistic regression analysis to ascertain independent predictors of obesity at 5 years.<br><br>RESULTS: &#x2003;Of the 1,447 subjects, 749 (51.8%) received ampicillin and gentamicin, and 333 (23%) were obese. Neonates exposed to antibiotics were more likely to be obese compared with those unexposed (26 vs. 20%, p&#x2009;=&#x2009;0.01). In the adjusted model, this association persisted (adjusted odds ratio: 1.37, p&#x2009;=&#x2009;0.02).<br><br>CONCLUSION: &#x2003;Neonatal antibiotic exposure is associated with early childhood obesity and may play a significant role in the weight trajectories of these children. Hence, antibiotic stewardship in this period cannot be overemphasized.<br><br>KEY POINTS: &#xb7; Findings from our study showed that neonatal antibiotic exposure is associated with early childhood obesity.. &#xb7; The prevalence of childhood obesity at 5 years is high (23%).. &#xb7; Further exploration of the role of antibiotics on the gut microbiome and its effect on weight trajectories is needed..}, }
@article {pmid37714151, year = {2023}, author = {Raso, F and Liu, S and Simpson, MJ and Barton, GM and Mayer, CT and Acharya, M and Muppidi, JR and Marshak-Rothstein, A and Reboldi, A}, title = {Antigen receptor signaling and cell death resistance controls intestinal humoral response zonation.}, journal = {Immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.immuni.2023.08.018}, pmid = {37714151}, issn = {1097-4180}, abstract = {Immunoglobulin A (IgA) maintains commensal communities in the intestine while preventing dysbiosis. IgA generated against intestinal microbes assures the simultaneous binding to multiple, diverse commensal-derived antigens. However, the exact mechanisms by which B cells mount broadly reactive IgA to the gut microbiome remains elusive. Here, we have shown that IgA B cell receptor (BCR) is required for B cell fitness during the germinal center (GC) reaction in Peyer's patches (PPs) and for generation of gut-homing plasma cells (PCs). We demonstrate that IgA BCR drove heightened intracellular signaling in mouse and human B cells, and as a consequence, IgA[+] B cells received stronger positive selection cues. Mechanistically, IgA BCR signaling offset Fas-mediated death, possibly rescuing low-affinity B cells to promote a broad humoral response to commensals. Our findings reveal an additional mechanism linking BCR signaling, B cell fate, and antibody production location, which have implications for how intestinal antigen recognition shapes humoral immunity.}, }
@article {pmid37714035, year = {2023}, author = {Wu, B and Li, J and Wang, Y and Yang, J and Ye, Y and Sun, J and Sheng, L and Wu, M and Zhang, Y and Gong, Y and Zhou, J and Ji, J and Sun, X}, title = {Exploring the impact of fungal spores from agricultural environments on the mice lung microbiome and metabolic profile.}, journal = {Ecotoxicology and environmental safety}, volume = {264}, number = {}, pages = {115456}, doi = {10.1016/j.ecoenv.2023.115456}, pmid = {37714035}, issn = {1090-2414}, abstract = {Exposure to particulate matter (PM) from agricultural environments has been extensively reported to cause respiratory health concerns in both animals and agricultural workers. Furthermore, PM from agricultural environments, containing fungal spores, has emerged as a significant threat to public health and the environment. Despite its potential toxicity, the impact of fungal spores present in PM from agricultural environments on the lung microbiome and metabolic profile is not well understood. To address this gap in knowledge, we developed a mice model of immunodeficiency using cyclophosphamide and subsequently exposed the mice to fungal spores via the trachea. By utilizing metabolomics techniques and 16 S rRNA sequencing, we conducted a comprehensive investigation into the alterations in the lung microbiome and metabolic profile of mice exposed to fungal spores. Our study uncovered significant modifications in both the lung microbiome and metabolic profile post-exposure to fungal spores. Additionally, fungal spore exposure elicited noticeable changes in α and β diversity, with these microorganisms being closely associated with inflammatory factors. Employing non-targeted metabolomics analysis via GC-TOF-MS, a total of 215 metabolites were identified, among which 42 exhibited significant differences. These metabolites are linked to various metabolic pathways, with amino sugar and nucleotide sugar metabolism, as well as galactose metabolism, standing out as the most notable pathways. Cysteine and methionine metabolism, along with glycine, serine and threonine metabolism, emerged as particularly crucial pathways. Moreover, these metabolites demonstrated a strong correlation with inflammatory factors and exhibited significant associations with microbial production. Overall, our findings suggest that disruptions to the microbiome and metabolome may hold substantial relevance in the mechanism underlying fungal spore-induced lung damage in mice.}, }
@article {pmid37713568, year = {2023}, author = {Berk, M and Köhler-Forsberg, O and Turner, M and Penninx, BWJH and Wrobel, A and Firth, J and Loughman, A and Reavley, NJ and McGrath, JJ and Momen, NC and Plana-Ripoll, O and O'Neil, A and Siskind, D and Williams, LJ and Carvalho, AF and Schmaal, L and Walker, AJ and Dean, O and Walder, K and Berk, L and Dodd, S and Yung, AR and Marx, W}, title = {Comorbidity between major depressive disorder and physical diseases: a comprehensive review of epidemiology, mechanisms and management.}, journal = {World psychiatry : official journal of the World Psychiatric Association (WPA)}, volume = {22}, number = {3}, pages = {366-387}, pmid = {37713568}, issn = {1723-8617}, abstract = {Populations with common physical diseases - such as cardiovascular diseases, cancer and neurodegenerative disorders - experience substantially higher rates of major depressive disorder (MDD) than the general population. On the other hand, people living with MDD have a greater risk for many physical diseases. This high level of comorbidity is associated with worse outcomes, reduced adherence to treatment, increased mortality, and greater health care utilization and costs. Comorbidity can also result in a range of clinical challenges, such as a more complicated therapeutic alliance, issues pertaining to adaptive health behaviors, drug-drug interactions and adverse events induced by medications used for physical and mental disorders. Potential explanations for the high prevalence of the above comorbidity involve shared genetic and biological pathways. These latter include inflammation, the gut microbiome, mitochondrial function and energy metabolism, hypothalamic-pituitary-adrenal axis dysregulation, and brain structure and function. Furthermore, MDD and physical diseases have in common several antecedents related to social factors (e.g., socioeconomic status), lifestyle variables (e.g., physical activity, diet, sleep), and stressful live events (e.g., childhood trauma). Pharmacotherapies and psychotherapies are effective treatments for comorbid MDD, and the introduction of lifestyle interventions as well as collaborative care models and digital technologies provide promising strategies for improving management. This paper aims to provide a detailed overview of the epidemiology of the comorbidity of MDD and specific physical diseases, including prevalence and bidirectional risk; of shared biological pathways potentially implicated in the pathogenesis of MDD and common physical diseases; of socio-environmental factors that serve as both shared risk and protective factors; and of management of MDD and physical diseases, including prevention and treatment. We conclude with future directions and emerging research related to optimal care of people with comorbid MDD and physical diseases.}, }
@article {pmid37713453, year = {2023}, author = {Louw, NL and Lele, K and Ye, R and Edwards, CB and Wolfe, BE}, title = {Microbiome Assembly in Fermented Foods.}, journal = {Annual review of microbiology}, volume = {77}, number = {}, pages = {381-402}, doi = {10.1146/annurev-micro-032521-041956}, pmid = {37713453}, issn = {1545-3251}, abstract = {For thousands of years, humans have enjoyed the novel flavors, increased shelf-life, and nutritional benefits that microbes provide in fermented foods and beverages. Recent sequencing surveys of ferments have mapped patterns of microbial diversity across space, time, and production practices. But a mechanistic understanding of how fermented food microbiomes assemble has only recently begun to emerge. Using three foods as case studies (surface-ripened cheese, sourdough starters, and fermented vegetables), we use an ecological and evolutionary framework to identify how microbial communities assemble in ferments. By combining in situ sequencing surveys with in vitro models, we are beginning to understand how dispersal, selection, diversification, and drift generate the diversity of fermented food communities. Most food producers are unaware of the ecological processes occurring in their production environments, but the theory and models of ecology and evolution can provide new approaches for managing fermented food microbiomes, from farm to ferment.}, }
@article {pmid37712669, year = {2023}, author = {Choudhury, A and Ortiz, PS and Young, M and Mahmud, MT and Stoffel, RT and Greathouse, KL and Kearney, CM}, title = {Control of Helicobacter pylori with engineered probiotics secreting selective guided antimicrobial peptides.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0201423}, doi = {10.1128/spectrum.02014-23}, pmid = {37712669}, issn = {2165-0497}, abstract = {Helicobacter pylori is the primary cause of 78% of gastric cancer cases, providing an opportunity to prevent cancer by controlling a single bacterial pathogen within the complex gastric microbiota. We developed highly selective antimicrobial agents against H. pylori by fusing an H. pylori-binding guide peptide (MM1) to broad-spectrum antimicrobial peptides. The common dairy probiotic Lactococcus lactis was then engineered to secrete these guided antimicrobial peptides (gAMPs). When co-cultured in vitro with H. pylori, the gAMP probiotics lost no toxicity compared to unguided AMP probiotics against the target, H. pylori, while losing >90% of their toxicity against two tested off-target bacteria. To test binding to H. pylori, the MM1 guide was fused to green fluorescent protein (GFP), resulting in enhanced binding compared to unguided GFP as measured by flow cytometry. In contrast, MM1-GFP showed no increased binding over GFP against five different off-target bacteria. These highly selective gAMP probiotics were then tested by oral gavage in mice infected with H. pylori. As a therapy, the probiotics outperformed antibiotic treatment, effectively eliminating H. pylori in just 5 days, and also protected mice from challenge infection as a prophylactic. As expected, the gAMP probiotics were as toxic against H. pylori as the unguided AMP probiotics. However, a strong rebound in gastric species diversity was found with both the selective gAMP probiotics and the non-selective AMP probiotics. Eliminating the extreme microbial dysbiosis caused by H. pylori appeared to be the major factor in diversity recovery. IMPORTANCE Alternatives to antibiotics in the control of Helicobacter pylori and the prevention of gastric cancer are needed. The high prevalence of H. pylori in the human population, the induction of microbial dysbiosis by antibiotics, and increasing antibiotic resistance call for a more sustainable approach. By selectively eliminating the pathogen and retaining the commensal community, H. pylori control may be achieved without adverse health outcomes. Antibiotics are typically used as a therapeutic post-infection, but a more targeted, less disruptive approach could be used as a long-term prophylactic against H. pylori or, by extension, against other gastrointestinal pathogens. Furthermore, the modular nature of the guided antimicrobial peptide (gAMP) technology allows for the substitution of different guides for different pathogens and the use of a cocktail of gAMPs to avoid the development of pathogen resistance.}, }
@article {pmid37712562, year = {2023}, author = {van Schaik, J and Li, Z and Cheadle, J and Crook, N}, title = {Engineering the Maize Root Microbiome: A Rapid MoClo Toolkit and Identification of Potential Bacterial Chassis for Studying Plant-Microbe Interactions.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.3c00371}, pmid = {37712562}, issn = {2161-5063}, abstract = {Sustainably enhancing crop production is a global necessity to meet the escalating demand for staple crops while sustainably managing their associated carbon/nitrogen inputs. Leveraging plant-associated microbiomes is a promising avenue for addressing this demand. However, studying these communities and engineering them for sustainable enhancement of crop production have remained a challenge due to limited genetic tools and methods. In this work, we detail the development of the Maize Root Microbiome ToolKit (MRMTK), a rapid Modular Cloning (MoClo) toolkit that only takes 2.5 h to generate desired constructs (5400 potential plasmids) that replicate and express heterologous genes in Enterobacter ludwigii strain AA4 (Elu), Pseudomonas putida strain AA7 (Ppu), Herbaspirillum robiniae strain AA6 (Hro), Stenotrophomonas maltophilia strain AA1 (Sma), and Brucella pituitosa strain AA2 (Bpi), which comprise a model maize root synthetic community (SynCom). In addition to these genetic tools, we describe a highly efficient transformation protocol (10[7]-10[9] transformants/μg of DNA) 1 for each of these strains. Utilizing this highly efficient transformation protocol, we identified endogenous Expression Sequences (ES; promoter and ribosomal binding sites) for each strain via genomic promoter trapping. Overall, MRMTK is a scalable and adaptable platform that expands the genetic engineering toolbox while providing a standardized, high-efficiency transformation method across a diverse group of root commensals. These results unlock the ability to elucidate and engineer plant-microbe interactions promoting plant growth for each of the 5 bacterial strains in this study.}, }
@article {pmid37712213, year = {2023}, author = {Mahroum, N and Seida, R and Shoenfeld, Y}, title = {Triggers and regulation: the gut microbiome in rheumatoid arthritis.}, journal = {Expert review of clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1080/1744666X.2023.2260103}, pmid = {37712213}, issn = {1744-8409}, abstract = {INTRODUCTION: Rheumatoid arthritis is a chronic inflammatory disease marked by systemic symptoms and joint degeneration. Interestingly, the development and progression of rheumatoid arthritis have been linked to the microbiome, notably the gut microbiome. Dysbiosis, an alteration in the gut microbiome, has been connected to the etiology and pathogenesis of rheumatoid arthritis. For instance, dysbiosis increases intestinal permeability and promotes the movement of bacteria and its products, which in turn triggers and aggravates systemic inflammation.<br><br>AREAS COVERED: The correlation between the gut microbiome and RA. Triggers of RA including dysbiosis. The therapeutic potential of the gut microbiome in RA due to its critical function in influencing the immune response. The fecal microbiota transplantation (FMT), a therapeutic strategy that involves the transfer of healthy fecal microbiota from a donor to a recipient, has produced encouraging results in the treatment of several autoimmune illnesses, including rheumatoid arthritis.<br><br>EXPERT OPINION: The role of the gut microbiome in RA is critical, and serves as a basis for the etiology, pathogenesis, as well as having therapeutic implications. In our opinion, FMT is an excellent example for this correlation. Still, more investigations and well-designed studied are needed in order to make firm conclusions and recommendations.}, }
@article {pmid37712178, year = {2023}, author = {Sfanos, KS}, title = {Intratumoral Bacteria as Mediators of Cancer Immunotherapy Response.}, journal = {Cancer research}, volume = {83}, number = {18}, pages = {2985-2986}, doi = {10.1158/0008-5472.CAN-23-1857}, pmid = {37712178}, issn = {1538-7445}, abstract = {Multiple lines of evidence spanning from animal models to human clinical trials indicate that the microbiome influences cancer immunotherapy response. Whereas initial studies focused exclusively on the gastrointestinal (gut) microbiota-tumor axis, more recent studies have examined the possibility that bacteria located within tumor cells or within the tumor microenvironment mediate cancer treatment response. Strikingly, this phenomenon has been demonstrated in cancers that arise in anatomic locations that are traditionally thought to be devoid of resident microbiota. In this issue of Cancer Research, Wu and colleagues examine the effects of intratumoral bacterial signatures on treatment response in the setting of neoadjuvant chemotherapy combined with immunotherapy (NACI) in the treatment of esophageal squamous cell carcinoma (ESCC). The study reports that intratumoral Streptococcus, presumably due to bacterial translocation from the gut, predicts the treatment efficacy of NACI in murine models as well as individuals with ESCC. These new findings further highlight the possibility that the presence of intratumoral microbes as well as their associated metabolites influence both the tumor immune microenvironment and immunotherapy efficacy. These findings also raise the intriguing possibility of cross-reactivity between tumor and bacterial antigens. Given that the gut microbiome is potentially a modifiable factor via diet, prebiotics/probiotics, and fecal microbiota transplantation, among other strategies, further exploration into the mechanisms by which gut and/or intratumoral bacteria influence antitumor immunity is certainly warranted. See related article by Wu et al., p. 3131.}, }
@article {pmid37712143, year = {2023}, author = {Escalante, V and Nayak, RR and Noecker, C and Babdor, J and Spitzer, M and Deutschbauer, AM and Turnbaugh, PJ}, title = {Simvastatin induces human gut bacterial cell surface genes.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.15151}, pmid = {37712143}, issn = {1365-2958}, support = {R01AT011117/AT/NCCIH NIH HHS/United States ; R01HL122593/HL/NHLBI NIH HHS/United States ; R01AR074500/AR/NIAMS NIH HHS/United States ; R01DK114034/DK/NIDDK NIH HHS/United States ; F32GM140808/GM/NIGMS NIH HHS/United States ; R25GM056847/GM/NIGMS NIH HHS/United States ; RM1GM135102/GM/NIGMS NIH HHS/United States ; }, abstract = {Drugs intended to target mammalian cells can have broad off-target effects on the human gut microbiota with potential downstream consequences for drug efficacy and side effect profiles. Yet, despite a rich literature on antibiotic resistance, we still know very little about the mechanisms through which commensal bacteria evade non-antibiotic drugs. Here, we focus on statins, one of the most prescribed drug types in the world and an essential tool in the prevention and treatment of high circulating cholesterol levels. Prior work in humans, mice, and cell culture support an off-target effect of statins on human gut bacteria; however, the genetic determinants of statin sensitivity remain unknown. We confirmed that simvastatin inhibits the growth of diverse human gut bacterial strains grown in communities and in pure cultures. Drug sensitivity varied between phyla and was dose-dependent. We selected two representative simvastatin-sensitive species for more in-depth analysis: Eggerthella lenta (phylum: Actinobacteriota) and Bacteroides thetaiotaomicron (phylum: Bacteroidota). Transcriptomics revealed that both bacterial species upregulate genes in response to simvastatin that alter the cell membrane, including fatty acid biogenesis (E. lenta) and drug efflux systems (B. thetaiotaomicron). Transposon mutagenesis identified a key efflux system in B. thetaiotaomicron that enables growth in the presence of statins. Taken together, these results emphasize the importance of the bacterial cell membrane in countering the off-target effects of host-targeted drugs. Continued mechanistic dissection of the various mechanisms through which the human gut microbiota evades drugs will be essential to understand and predict the effects of drug administration in human cohorts and the potential downstream consequences for health and disease.}, }
@article {pmid37712058, year = {2023}, author = {Perry, EK and Tan, MW}, title = {Bacterial biofilms in the human body: prevalence and impacts on health and disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1237164}, pmid = {37712058}, issn = {2235-2988}, abstract = {Bacterial biofilms can be found in most environments on our planet, and the human body is no exception. Consisting of microbial cells encased in a matrix of extracellular polymers, biofilms enable bacteria to sequester themselves in favorable niches, while also increasing their ability to resist numerous stresses and survive under hostile circumstances. In recent decades, biofilms have increasingly been recognized as a major contributor to the pathogenesis of chronic infections. However, biofilms also occur in or on certain tissues in healthy individuals, and their constituent species are not restricted to canonical pathogens. In this review, we discuss the evidence for where, when, and what types of biofilms occur in the human body, as well as the diverse ways in which they can impact host health under homeostatic and dysbiotic states.}, }
@article {pmid37711696, year = {2023}, author = {Lefler, FW and Barbosa, M and Zimba, PV and Smyth, AR and Berthold, DE and Laughinghouse, HD}, title = {Spatiotemporal diversity and community structure of cyanobacteria and associated bacteria in the large shallow subtropical Lake Okeechobee (Florida, United States).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1219261}, pmid = {37711696}, issn = {1664-302X}, abstract = {Lake Okeechobee is a large eutrophic, shallow, subtropical lake in south Florida, United States. Due to decades of nutrient loading and phosphorus rich sediments, the lake is eutrophic and frequently experiences cyanobacterial harmful algal blooms (cyanoHABs). In the past, surveys of the phytoplankton community structure in the lake have been conducted by morphological studies, whereas molecular based studies have been seldom employed. With increased frequency of cyanoHABs in Lake Okeechobee (e.g., 2016 and 2018 Microcystis-dominated blooms), it is imperative to determine the diversity of cyanobacterial taxa that exist within the lake and the limnological parameters that drive bloom-forming genera. A spatiotemporal study of the lake was conducted over the course of 1 year to characterize the (cyano)bacterial community structure, using 16S rRNA metabarcoding, with coincident collection of limnological parameters (e.g., nutrients, water temperature, major ions), and cyanotoxins. The objectives of this study were to elucidate spatiotemporal trends of community structure, identify drivers of community structure, and examine cyanobacteria-bacterial relationships within the lake. Results indicated that cyanobacterial communities within the lake were significantly different between the wet and dry season, but not between periods of nitrogen limitation and co-nutrient limitation. Throughout the year, the lake was primarily dominated by the picocyanobacterium Cyanobium. The bloom-forming genera Cuspidothrix, Dolichospermum, Microcystis, and Raphidiopsis were highly abundant throughout the lake and had disparate nutrient requirements and niches within the lake. Anatoxin-a, microcystins, and nodularins were detected throughout the lake across both seasons. There were no correlated (cyano)bacteria shared between the common bloom-forming cyanobacteria Dolichospermum, Microcystis, and Raphidiopsis. This study is the first of its kind to use molecular based methods to assess the cyanobacterial community structure within the lake. These data greatly improve our understanding of the cyanobacterial community structure within the lake and the physiochemical parameters which may drive the bloom-forming taxa within Lake Okeechobee.}, }
@article {pmid37711691, year = {2023}, author = {Huang, B and Fang, W and Gu, Q and Tilocca, B}, title = {Editorial: Soil microbiome community and functional succession mechanism driven by different factors in agricultural ecology.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1276119}, pmid = {37711691}, issn = {1664-302X}, }
@article {pmid37711689, year = {2023}, author = {He, H and Xu, J and Zhou, T and Yang, Y and Yang, C and Xiao, C and Zhang, C and Li, L and Zhou, T}, title = {Metabolomic and microbiomic insights into color changes during the sweating process in Dipsacus asper.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1195088}, pmid = {37711689}, issn = {1664-302X}, abstract = {Sweating is one of the most important primary processing methods of Chinese medicinal materials. Dipsacus asper is a typical representative of sweating treatment that is recommended by the Chinese Pharmacopoeia. The color change of the fracture surface of the root is the prominent feature of sweating treatment. However, few studies have focused on the mechanism of color change during sweating treatment. In this study, widely targeted metabolomics and ITS high-throughput sequencing technologies were applied to detect metabolites and microbial structure and diversity in the root of D. asper during sweating treatment. A total of 667 metabolites, including 36 downregulated and 78 upregulated metabolites, were identified in D. asper following sweating treatment. The significantly differential metabolites were divided into 12 classes, including terpenoids and phenolic acids. Moreover, all the differential terpenoids were upregulated and 20 phenolic acids showed a significant change after sweating treatment. In addition, microbial community diversity and richness increased following sweating treatment. The composition of microbial communities revealed that the relative abundances of Ascomycota and Basidiomycota significantly changed after sweating treatment. Correlation analysis revealed that Ascomycota (Fusarium sp., Macrophomina sp., Ilyonectria sp., Memnoniella sp., Penicillium sp., Cyphellophora sp., Neocosmospora sp., unclassified_f_Nectriaceae, and unclassified_o_Saccharomycetales) and Basidiomycota (Armillaria sp.) were associated with the content of terpenoids (6-deoxycatalpol and laciniatoside III) and phenolic acids (3-(4-hydroxyphenyl)-propionic acid, ethyl caffeate, 4-O-glucosyl-4-hydroxybenzoic acid, 2-acetyl-3-hydroxyphenyl-1-O-glucoside, 4-O-glucosyl-3,4-dihydroxybenzyl alcohol, 3-O-feruloylquinic acid, 3,4-O-dicaffeoylquinic acid methyl ester, O-anisic acid, and coniferyl alcohol). We speculate that the Ascomycota and Basidiomycota affect the content of terpenoids and phenolic acids, resulting in color change during sweating treatment in D. asper. This study provides a foundation for analyzing the mechanism involved in the processing of Chinese medicinal materials.}, }
@article {pmid37711620, year = {2023}, author = {Rosel-Pech, C and Pinto-Cardoso, S and Chávez-Torres, M and Montufar, N and Osuna-Padilla, I and Ávila-Ríos, S and Reyes-Terán, G and Aguirre-Alvarado, C and Matías Juan, NA and Pérez-Lorenzana, H and Vázquez-Rosales, JG and Bekker-Méndez, VC}, title = {Distinct fecal microbial signatures are linked to sex and chronic immune activation in pediatric HIV infection.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1244473}, pmid = {37711620}, issn = {1664-3224}, abstract = {INTRODUCTION: Our understanding of HIV-associated gut microbial dysbiosis in children perinatally-infected with HIV (CLWH) lags behind that of adults living with HIV. Childhood represents a critical window for the gut microbiota. Any disturbances, including prolonged exposure to HIV, antiretroviral drugs, and antibiotics are likely to have a significant impact on long-term health, resulting in a less resilient gut microbiome. The objective of our study was to characterize the gut microbiota in CLWH, and compare it with HIV-unexposed and -uninfected children.<br><br>METHODS: We enrolled 31 children aged 3 to 15 years; 15 were CLWH and 16 were HUU. We assessed dietary patterns and quality; quantified soluble and cellular markers of HIV disease progression by flow cytometry, enzyme-linked immunosorbent and multiplex-bead assays, and profiled the gut microbiota by 16S rRNA sequencing. We explored relationships between the gut microbiota, antibiotic exposure, dietary habits, soluble and cellular markers and host metadata.<br><br>RESULTS: Children had a Western-type diet, their median health eating index score was 67.06 (interquartile range 58.76-74.66). We found no discernable impact of HIV on the gut microbiota. Alpha diversity metrics did not differ between CLWH and HUU. Sex impacted the gut microbiota (R-squared= 0.052, PERMANOVA p=0.024). Male children had higher microbial richness compared with female children. Two taxa were found to discriminate female from male children independently from HIV status: Firmicutes for males, and Bacteroides for females. Markers of HIV disease progression were comparable between CLWH and HUU, except for the frequency of exhausted CD4+ T cells (PD-1+) which was increased in CLWH (p=0.0024 after adjusting for confounders). Both the frequency of exhausted CD4+ and activated CD4+ T cells (CD38+ HLADR+) correlated positively with the relative abundance of Proteobacteria (rho=0.568. false discovery rate (FDR)-adjusted p= 0.029, and rho=0.62, FDR-adjusted p=0.0126, respectively).<br><br>CONCLUSION: The gut microbiota of CLWH appears similar to that of HUU, and most markers of HIV disease progression are normalized with long-term ART, suggesting a beneficial effect of the latter on the gut microbial ecology. The relationship between exhausted and activated CD4+ T cells and Proteobacteria suggests a connection between the gut microbiome, and premature aging in CLWH.}, }
@article {pmid37711554, year = {2023}, author = {Gualtero, DF and Lafaurie, GI and Buitrago, DM and Castillo, Y and Vargas-Sanchez, PK and Castillo, DM}, title = {Oral microbiome mediated inflammation, a potential inductor of vascular diseases: a comprehensive review.}, journal = {Frontiers in cardiovascular medicine}, volume = {10}, number = {}, pages = {1250263}, pmid = {37711554}, issn = {2297-055X}, abstract = {The dysbiosis of the oral microbiome and vascular translocation of the periodontopathic microorganism to peripheral blood can cause local and systemic extra-oral inflammation. Microorganisms associated with the subgingival biofilm are readily translocated to the peripheral circulation, generating bacteremia and endotoxemia, increasing the inflammation in the vascular endothelium and resulting in endothelial dysfunction. This review aimed to demonstrate how the dysbiosis of the oral microbiome and the translocation of oral pathogen-induced inflammation to peripheral blood may be linked to cardiovascular diseases (CVDs). The dysbiosis of the oral microbiome can regulate blood pressure and activate endothelial dysfunction. Similarly, the passage of periodontal microorganisms into the peripheral circulation and their virulence factors have been associated with a vascular compartment with a great capacity to activate endothelial cells, monocytes, macrophages, and plaquettes and increase interleukin and chemokine secretion, as well as oxidative stress. This inflammatory process is related to atherosclerosis, hypertension, thrombosis, and stroke. Therefore, oral diseases could be involved in CVDs via inflammation. The preclinic and clinical evidence suggests that periodontal disease increases the proinflammatory markers associated with endothelial dysfunction. Likewise, the evidence from clinical studies of periodontal treatment in the long term evidenced the reduction of these markers and improved overall health in patients with CVDs.}, }
@article {pmid37711366, year = {2023}, author = {Khairulmunir, M and Gani, M and Karuppannan, KV and Mohd-Ridwan, AR and Md-Zain, BM}, title = {High-throughput DNA metabarcoding for determining the gut microbiome of captive critically endangered Malayan tiger (Pantheratigrisjacksoni) during fasting.}, journal = {Biodiversity data journal}, volume = {11}, number = {}, pages = {e104757}, pmid = {37711366}, issn = {1314-2828}, abstract = {The Malayan tiger (Pantheratigrisjacksoni) is a critically endangered species native to the Malaysian Peninsula. To imitate wild conditions where tigers do not hunt every day, numerous wildlife sanctuaries do not feed their tigers daily. However, the effects of fasting on the gut microbiota of captive Malayan tigers remains unknown. This study aimed to characterise the gut microbiota of captive Malayan tigers by comparing their microbial communities during fasting versus normal feeding conditions. This study was conducted at the Melaka Zoo, Malaysian Peninsula and involved Malayan tigers fasted every Monday. In total, ten faecal samples of Malayan tiger, two of Bengal tiger (outgroup) and four of lion (outgroup) were collected and analysed for metabarcoding targeting the 16S rRNA V3-V4 region. In total, we determined 14 phyla, 87 families, 167 genera and 53 species of gut microbiome across Malayan tiger samples. The potentially harmful bacterial genera found in this study included Fusobacterium, Bacteroides, Clostridium sensu stricto 1, Solobacterium, Echerichiashigella, Ignatzschineria and Negativibacillus. The microbiome in the fasting phase had a higher composition and was more diverse than in the feeding phase. The present findings indicate a balanced ratio in the dominant phyla, reflecting a resetting of the imbalanced gut microbiota due to fasting. These findings can help authorities in how to best maintain and improve the husbandry and health of Malayan tigers in captivity and be used for monitoring in ex-situ veterinary care unit.}, }
@article {pmid37711026, year = {2023}, author = {Yoon, HJ and Kang, W and Jo, S and Hwang, YS and Lee, JH and Chung, SJ and Park, YK}, title = {Dietary quality and the gut microbiome in early-stage Parkinson's disease patients.}, journal = {Nutritional neuroscience}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/1028415X.2023.2253025}, pmid = {37711026}, issn = {1476-8305}, abstract = {BACKGROUND: The prevalence of Parkinson's disease (PD) has increased steadily with the increase of the elderly population. PD may influence dietary intake and quality, and the gut microbiome composition. The present study examined differences in dietary intake and quality between PD patients and controls according to sex. In addition, we assessed the gut microbiome composition.<br><br>METHODS: This cross-sectional study was conducted at A Medical Center, Seoul, South Korea. PD severity, swallowing function, olfactory function, and constipation status were examined by a skilled nurse. Dietary data were collected through a semi-quantitative food frequency questionnaire. Stool samples were subjected to microbiome analysis. To examine dietary quality, the Dietary Quality Index-International (DQI-I), Healthy Eating Index (HEI), Index of Nutritional Quality (INQ), Dietary Diversity Score (DDS), and Mediterranean Diet Score (MDS) were used. An independent t-test was used to determine differences between patients and controls. A chi-square test was used to examine frequency differences.<br><br>RESULTS: Dietary intake did not differ between the PD patient and control groups. Regarding dietary quality, the patients consumed more saturated fat compared to controls. Overall, the dietary differences between the groups were minor. The composition of the gut microbiome differed between PD patients and controls. Lactobacillus and Bifidobacterium genus were most abundant in PD patients. Prevotella VZCB and other Faecalibacterium were most abundant in controls.<br><br>CONCLUSIONS: Our results indicated that PD patients may experience gut microbiome change even in the early stage, while nutritional needs can be met when a balanced diet including various food groups are consumed.}, }
@article {pmid37710149, year = {2023}, author = {Aizi, T and Lijuan, L and Lihua, L and Wei, L and Jiamei, Q}, title = {Comparative analysis of microbial community structure in different times of Panax ginseng Rhizosphere microbiome and soil properties under larch forest.}, journal = {BMC genomic data}, volume = {24}, number = {1}, pages = {51}, pmid = {37710149}, issn = {2730-6844}, abstract = {BACKGROUND: Panax ginseng cultivated under the forest is popular because its shape and effective ingredients are similar to wild ginseng. The growth of P. ginseng in the larch forest is generally better than in the broad-leaved forest, and the incidence rate of diseases is low. Therefore, the selection of forest species is one of the basic factors in the successful cropping of P. ginseng.<br><br>METHODS: Illumina HiSeq high-throughput sequencing was used to analyze the 16S rRNA/ITS gene sequence of P. ginseng rhizosphere soil under larch forest to study the rhizosphere microbiome's diversity and community composition structure.<br><br>RESULTS: The species classification and richness of rhizosphere bacterial and fungal communities in the same-aged P. ginseng were similar. Consistent with the soil system of commonly cultivated crops, Proteobacteria, Actinobacteriota, Acidobacteriota, Verrucomicrobiota, Chloroflexi, and Basidiomycota, Ascomycota were the dominant phylum of bacteria and fungi, respectively. Compared with the soil without planting P. ginseng, the diversity of microorganisms and community structure of continuous planting for 2&#xa0;years, 5&#xa0;years, and 18&#xa0;years of P. ginseng rhizosphere soil had little change. The accumulation levels of Ilyonectria, Fusarium, Gibberella, and Cylindrocarpon were not significantly increased with planting P. ginseng and the increased age of cropping P. ginseng.<br><br>CONCLUSIONS: The results of this study showed that the soil function of the larch forest was good, which provided a theoretical basis for the land selection and soil improvement of cultivating P. ginseng under the larch forest.}, }
@article {pmid37709905, year = {2023}, author = {Chau, KD and Shamekh, M and Huisken, J and Rehan, SM}, title = {The effects of maternal care on the developmental transcriptome and metatranscriptome of a wild bee.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {904}, pmid = {37709905}, issn = {2399-3642}, abstract = {Maternal care acts as a strong environmental stimulus that can induce phenotypic plasticity in animals and may also alter their microbial communities through development. Here, we characterize the developmental metatranscriptome of the small carpenter bee, Ceratina calcarata, across developmental stages and in the presence or absence of mothers. Maternal care had the most influence during early development, with the greatest number and magnitude of differentially expressed genes between maternal care treatments, and enrichment for transcription factors regulating immune response in motherless early larvae. Metatranscriptomic data revealed fungi to be the most abundant group in the microbiome, with Aspergillus the most abundant in early larvae raised without mothers. Finally, integrative analysis between host transcriptome and metatranscriptome highlights several fungi correlating with developmental and immunity genes. Our results provide characterizations of the influence of maternal care on gene expression and the microbiome through development in a wild bee.}, }
@article {pmid37709803, year = {2023}, author = {Mukohda, M and Yano, T and Matsui, T and Nakamura, S and Miyamae, J and Toyama, K and Mitsui, R and Mizuno, R and Ozaki, H}, title = {Treatment with Ligilactobacillus murinus lowers blood pressure and intestinal permeability in spontaneously hypertensive rats.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15197}, pmid = {37709803}, issn = {2045-2322}, support = {22H02527//Japan Society for the Promotion of Science/ ; 22K08369//Japan Society for the Promotion of Science/ ; OUS-RP-21-1//Promotion of Okayama University of Science (OUS) Research Project/ ; }, abstract = {One feature of hypertension is a microbial imbalance with increased intestinal permeability. In this study, we examined whether an alteration in the microbiota affects blood pressure and intestinal permeability in spontaneously hypertensive rats (SHRs). We performed a 16S metagenome analysis of feces from 10- to 15-week-old SHRs using a synthetic long-read sequencing approach, and found a candidate for the microbiome treatment, Ligilactobacillus murinus (L. murinus), that was robustly decreased. Oral administration of L. murinus to SHRs for 2 weeks significantly inhibited blood pressure elevation and improved endothelium-dependent vasodilation but did not attenuate enhanced vascular contraction in SHR mesenteric arteries. The proximal colon of SHRs exhibited increased intestinal permeability with decreased levels of the tight junction protein claudin 4, morphological changes such as decreased intestinal crypts and elevated TNF-α levels, which was reversed by treatment with L. murinus. Consistent with these intestinal phenotypes, plasma lipopolysaccharides levels were elevated in SHR but decreased following L. murinus administration. We concluded that oral administration of L. murinus to SHRs exerts protective effects on intestinal permeability via restoration of claudin 4 expression and reversal of morphologic disorder, which may improve low-grade endotoxemia and thus reduce development of hypertension via recovery of endothelial vasodilating functions.}, }
@article {pmid37709733, year = {2023}, author = {Lim, JJ and Diener, C and Wilson, J and Valenzuela, JJ and Baliga, NS and Gibbons, SM}, title = {Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5682}, pmid = {37709733}, issn = {2041-1723}, support = {R01DK133468//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {Longitudinal sampling of the stool has yielded important insights into the ecological dynamics of the human gut microbiome. However, human stool samples are available approximately once per day, while commensal population doubling times are likely on the order of minutes-to-hours. Despite this mismatch in timescales, much of the prior work on human gut microbiome time series modeling has assumed that day-to-day fluctuations in taxon abundances are related to population growth or death rates, which is likely not the case. Here, we propose an alternative model of the human gut as a stationary system, where population dynamics occur internally and the bacterial population sizes measured in a bolus of stool represent a steady-state endpoint of these dynamics. We formalize this idea as stochastic logistic growth. We show how this model provides a path toward estimating the growth phases of gut bacterial populations in situ. We validate our model predictions using an in vitro Escherichia coli growth experiment. Finally, we show how this method can be applied to densely-sampled human stool metagenomic time series data. We discuss how these growth phase estimates may be used to better inform metabolic modeling in flow-through ecosystems, like animal guts or industrial bioreactors.}, }
@article {pmid37709342, year = {2023}, author = {Fenneman, AC and Rampanelli, E and van der Spek, AH and Fliers, E and Nieuwdorp, M}, title = {Protocol for a double-blinded randomised controlled trial to assess the effect of faecal microbiota transplantations on thyroid reserve in patients with subclinical autoimmune hypothyroidism in the Netherlands: the IMITHOT trial.}, journal = {BMJ open}, volume = {13}, number = {9}, pages = {e073971}, pmid = {37709342}, issn = {2044-6055}, abstract = {BACKGROUND: Hashimoto's thyroiditis (HT) is a common endocrine autoimmune disease affecting roughly 5% of the general population and involves life-long treatment with levothyroxine, as no curative treatment yet exists. Over the past decade, the crosstalk between gut microbiota and the host immune system has been well-recognised, identifying the gut microbiome as an important factor in host health and disease, including susceptibility to autoimmune diseases. Previous observational studies yielded a link between disruption of the gut microbiome composition and HT. This is the first study that investigates the potential of restoring a disrupted gut microbiome with faecal microbiota transplantations (FMTs) to halt disease progression and dampen autoimmunity.<br><br>METHODS AND ANALYSIS: The IMITHOT trial is a randomised, double-blinded, placebo-controlled study evaluating either autologous or allogenic FMTs in medication-na&#xef;ve patients with subclinical autoimmune hypothyroidism. In total, 34 patients will be enrolled to receive either three allogenic or autologous FMTs. FMT will be made of fresh stool and directly administered into the duodenum. Patients will be evaluated at baseline before the first FMT is administered and at 6, 12 and 24 months post-intervention to assess efficacy and adverse events. The primary outcome measure will be the net incremental increase (incremental area under the curve) on thyrotropin-stimulated free thyroxine and free triiodothyronine release at 6 and 12 months compared with baseline. Results will be disseminated via peer-reviewed journals and international conferences. The recruitment of the first patient and donor occurred on 18 December 2019.<br><br>ETHICS AND DISSEMINATION: Ethics approval was obtained from the hospital Ethics Committee (Medical Ethics Committee) at Amsterdam University Medical Center. The trial's outcomes offer high-quality evidence that aids in unveiling distinct patterns within the gut microbiota potentially associated with improved thyroid function. Consequently, this may open avenues for the future clinical applications of microbial-targeted therapy in individuals at risk of developing overt HT.<br><br>TRIAL REGISTRATION NUMBER: NL7931.}, }
@article {pmid37709337, year = {2023}, author = {Montenegro, J and L P Oliveira, C and Armet, AM and Berg, A and Sharma, AM and Mereu, L and Cominetti, C and Ghosh, S and Richard, C and Nguyen, NK and Cani, PD and Walter, J and Prado, CM}, title = {Impact of a Powdered Meal Replacement on Metabolism and Gut Microbiota (PREMIUM) in individuals with excessive body weight: a study protocol for a randomised controlled trial.}, journal = {BMJ open}, volume = {13}, number = {9}, pages = {e070027}, doi = {10.1136/bmjopen-2022-070027}, pmid = {37709337}, issn = {2044-6055}, abstract = {INTRODUCTION: Excess body weight is associated with a state of low-grade chronic inflammation and alterations of the gut microbiome. Powdered meal replacements (PMR) have been shown to be an effective strategy for weight management; however, their effect on inflammation and the gut microbiome remains unclear. The aim of this 12-week randomised control clinical trial is to investigate the effects of PMR consumption, here given as a soy-yoghurt-honey formula, on inflammation, gut microbiome and overall metabolism in individuals with excessive body weight.<br><br>METHODS AND ANALYSIS: Healthy adults with excess body weight (n=88) are being recruited and randomly assigned to one of the following groups: (1) Control group (CON): maintaining usual diet for 12 weeks, or (2) PMR group: replacing morning and afternoon snacks daily with a PMR for 12 weeks. Participants are asked to maintain body weight throughout the study and fill out a journal with information about PMR consumption, body weight, food intake, appetite sensations and medications. Three study visits are required: baseline, week 6 and week 12. Outcome measures include systemic inflammatory biomarkers, gut microbiome composition, metabolic blood markers, host energy metabolism, body composition, appetite sensations and host gene expression profile.<br><br>ETHICS AND DISSEMINATION: This research protocol was approved by the University of Alberta Ethics Board (Pro00070712) and adheres to the Canadian Tri-Council Policy statement on the use of human participants in research. Procedures and potential risks are fully discussed with participants. Study findings will be disseminated in peer-reviewed journals, conference presentations and social media.<br><br>TRIAL REGISTRATION NUMBER: NCT03235804.}, }
@article {pmid37709186, year = {2023}, author = {Yaghy, A and Porteny, JR}, title = {The ocular microbiome: More than meets the eye.}, journal = {Experimental eye research}, volume = {235}, number = {}, pages = {109649}, doi = {10.1016/j.exer.2023.109649}, pmid = {37709186}, issn = {1096-0007}, }
@article {pmid37709081, year = {2023}, author = {Buchenauer, L and Haange, SB and Bauer, M and Rolle-Kampczyk, UE and Wagner, M and Stucke, J and Elter, E and Fink, B and Vass, M and von Bergen, M and Schulz, A and Zenclussen, AC and Junge, KM and Stangl, GI and Polte, T}, title = {Maternal exposure of mice to glyphosate induces depression- and anxiety-like behavior in the offspring via alterations of the gut-brain axis.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167034}, doi = {10.1016/j.scitotenv.2023.167034}, pmid = {37709081}, issn = {1879-1026}, abstract = {The past decade has been characterized by increased awareness and de-stigmatization of mental health issues, in particular the most common neuropsychiatric disorders depression and anxiety. Further, with growing understanding of neurodevelopmental disorders such as attention deficit and hyperactivity disorder and autism spectrum disorder, the number of diagnosed patients has increased. The pathogenesis of these behavioral disorders is multifactorial and early-life exposure to environmental chemicals has been proposed to be a relevant risk factor that might mediate these effects by disturbances on the gut-brain-axis. However, for glyphosate, the most widely used pesticide worldwide, there are only limited and inconsistent findings that link chronic low-dose exposure in particular during early life to neurobehavioral disorders. Here, we explored the impact of maternal oral glyphosate exposure (0.5 and 50 mg/kg body weight/day) during pregnancy and the lactational period on offspring's behavior, brain gene expression and gut microbiota using a cross-generational mouse model. Behavioral analyses revealed a depression- and anxiety-like behavior as well as social deficits most notably in adult female offspring of glyphosate-exposed dams. Furthermore, the expression of tryptophan hydroxylase 2, an enzyme discussed to be linked to behavioral problems, was reduced in the hippocampus of female offspring and correlated to a glyphosate-induced DNA hypermethylation of the gene. Moreover, maternal glyphosate exposure significantly altered the gut microbiota in the female offspring including a decreased abundance of Akkermansia and increased abundance of Alistipes and Blautia, bacteria involved in tryptophan metabolism and associated with depression- and anxiety-like disorders. Our results suggest that glyphosate might influence the gut-brain axis crosstalk following in-utero and lactational exposure. This study underlines the importance of understanding the impact of exposure to pesticides on the gut-brain axis and further emphasizes the need for microbiome analyses to be compulsorily included in health risk assessments of pesticides.}, }
@article {pmid37708940, year = {2023}, author = {Hishiya, N and Uno, K and Nakano, A and Konishi, M and Higashi, S and Eguchi, S and Ariyoshi, T and Matsumoto, A and Oka, K and Takahashi, M and Suzuki, Y and Horiuchi, S and Hirai, N and Ogawa, Y and Ogawa, T and Nakano, R and Mikasa, K and Kasahara, K and Yano, H}, title = {Association between the gut microbiome and organic acid profiles in a Japanese population with HIV infection.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jiac.2023.09.013}, pmid = {37708940}, issn = {1437-7780}, abstract = {INTRODUCTION: An increased incidence of metabolic syndrome has been observed in human immunodeficiency virus (HIV)-infected individuals. In contrast, gut dysbiosis is involved in various pathogeneses, including vascular endothelial disorders. Organic acids, including short-chain fatty acids (SCFAs), are essential for maintaining gut homeostasis. Therefore, this study aimed to explore the gut microbiome profile and organic acids in a Japanese population infected with HIV.<br><br>METHODS: Forty-nine patients with HIV infection on combination antiretroviral therapy (cART) were enrolled and divided into the high and low CD4 groups based on a CD4 cutoff of 350&#xa0;cells/&#x3bc;L. Stool samples were analyzed by 16S ribosomal RNA next-generation sequencing and high-performance liquid chromatography. The association between the gut microbiome, including bacterial taxa and organic acids, was statistically analyzed.<br><br>RESULTS: The fecal microbial community composition was significantly different between HIV patients with CD4 counts above and below 350&#xa0;cells/&#x3bc;L. The relative abundance of Roseburia, Prevotella, Prevotella_9, and [Clostridium]_methylpentosum_group were significantly enriched in the high CD4 group. Fecal succinic acid tended to be more abundant in the low CD4 group, and acetic, propionic, and butyric acids tended to be more abundant in the high CD4 group. Roseburia was positively correlated with butyric acid levels. Prevotella_9 and Prevotella were negatively correlated with succinic acid levels and positively correlated with acetic and propionic acid levels.<br><br>CONCLUSIONS: This study showed intestinal dysbiosis bordering on a CD4 count of 350 in patients with HIV infection undergoing cART. These findings might help in understanding intestinal damage and systemic inflammation in HIV infection.}, }
@article {pmid37708704, year = {2023}, author = {Su, Y and Han, Y and Choi, HS and Lee, GY and Cho, HW and Choi, H and Jang, YS and Choi, JH and Seo, JW}, title = {Lipid mediators derived from DHA alleviate DNCB-induced atopic dermatitis and improve the gut microbiome in BALB/c mice.}, journal = {International immunopharmacology}, volume = {124}, number = {Pt A}, pages = {110900}, doi = {10.1016/j.intimp.2023.110900}, pmid = {37708704}, issn = {1878-1705}, abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin condition that primarily results from immune dysregulation. We determined the potential therapeutic benefits of lipid mediators (LM, 17S-monohydroxy DHA, resolvin D5, and protectin DX in a ratio of 3:47:50) produced by soybean lipoxygenase from DHA. The underlying molecular mechanisms involved in TNF-α/IFN-γ-stimulated HaCaT cells as well as its effect in an AD mouse model induced by DNCB in BALB/c mice were examined. The results indicated that LM effectively attenuates the production of inflammatory cytokines (IL-6 and IL-1β) and chemokines (IL-8 and MCP-1) by inhibiting the NF-κB signaling pathway in TNF-α/IFN-γ-stimulated HaCaT cells. The oral administration of LM at 5 or 10 μg/kg/day significantly reduced skin lesions, epidermal thickness, and mast cell infiltration in AD mice. Furthermore, LM reduced the production of IgE and inflammatory cytokines (TNF-α, IL-6, and IL-1β) in the serum, modulated gut microbiota diversity, and restored the microbial composition. Overall, our findings suggest that LM represents a potential therapeutic agent for improving AD symptoms through its ability to suppress inflammatory cytokines and alter the composition of gut microbiota.}, }
@article {pmid37708536, year = {2023}, author = {Le Roux, JJ and Leishman, MR and Geraghty, DM and Manea, A}, title = {Rewiring critical plant-soil microbial interactions to assist ecological restoration.}, journal = {American journal of botany}, volume = {}, number = {}, pages = {e16228}, doi = {10.1002/ajb2.16228}, pmid = {37708536}, issn = {1537-2197}, }
@article {pmid37707749, year = {2023}, author = {Mondal, P and Meeran, SM}, title = {The emerging role of the gut microbiome in cancer cell plasticity and therapeutic resistance.}, journal = {Cancer metastasis reviews}, volume = {}, number = {}, pages = {}, pmid = {37707749}, issn = {1573-7233}, support = {1106/UGC NET/JULY2016//University Grants Commission/ ; CSIR-FIRST [6/1/FIRST/2020-RPPBDD-TMD-SeMI] MLP-0299//Council of Scientific and Industrial Research, India/ ; MLP-250//Central Food Technological Research Institute, Council of Scientific and Industrial Research/ ; }, abstract = {Resistance to therapeutic agents is one of the major challenges in cancer therapy. Generally, the focus is given to the genetic driver, especially the genetic mutation behind the therapeutic resistance. However, non-mutational mechanisms, such as epigenetic modifications, and TME alteration, which is mainly driven by cancer cell plasticity, are also involved in therapeutic resistance. The concept of plasticity mainly relies on the conversion of non-cancer stem cells (CSCs) to CSCs or epithelial-to-mesenchymal transition via different mechanisms and various signaling pathways. Cancer plasticity plays a crucial role in therapeutic resistance as cancer cells are able to escape from therapeutics by shifting the phenotype and thereby enhancing tumor progression. New evidence suggests that gut microbiota can change cancer cell characteristics by impacting the mechanisms involved in cancer plasticity. Interestingly, gut microbiota can also influence the therapeutic efficacy of anticancer drugs by modulating the mechanisms involved in cancer cell plasticity. The gut microbiota has been shown to reduce the toxicity of certain clinical drugs. Here, we have documented the critical role of the gut microbiota on the therapeutic efficacy of existing anticancer drugs by altering the cancer plasticity. Hence, the extended knowledge of the emerging role of gut microbiota in cancer cell plasticity can help to develop gut microbiota-based novel therapeutics to overcome the resistance or reduce the toxicity of existing drugs. Furthermore, to improve the effectiveness of therapy, it is necessary to conduct more clinical and preclinical research to fully comprehend the mechanisms of gut microbiota.}, }
@article {pmid37707718, year = {2023}, author = {Rambia, A and Veluchamy, C and Rawat, JM and Jamdhade, MD and Purohit, S and Pawar, KD and Rajasekaran, C and Rawat, B and Sharma, A}, title = {Revealing bacterial and fungal communities of the untapped forest and alpine grassland zones of the Western-Himalayan region.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {37707718}, issn = {1618-1905}, abstract = {The Western Himalayas offer diverse environments for investigating the diversity and distribution of microbial communities and their response to both the abiotic and biotic factors across the entire altitudinal gradient. Such investigations contribute significantly to our understanding of the complex ecological processes that shape microbial diversity. The proposed study focuses on the investigation of the bacterial and fungal communities in the forest and alpine grasslands of the Western Himalayan region, as well as their relationship with the physicochemical parameters of soil. A total of 185 isolates were obtained using the culture-based technique belonging to Bacillus (37%), Micrococcus (16%), and Staphylococcus (7%). Targeted metagenomics revealed the abundance of bacterial phyla Pseudomonadota (23%) followed by Acidobacteriota (20.2%), Chloroflexota (15%), and Bacillota (11.3%). At the genera level, CandidatusUdaeobacter (6%), Subgroup_2 (5.5%) of phylum Acidobacteriota, and uncultured Ktedonobacterales HSB_OF53-F07 (5.2%) of Choloroflexota phylum were found to be preponderant. Mycobiome predominantly comprised of phyla Ascomycota (54.1%), Basidiomycota (24%), and Mortierellomycota (19.1%) with Archaeorhizomyces (19.1%), Mortierella (19.1%), and Russula (5.4%) being the most abundant genera. Spearman's correlation revealed that the bacterial community was most influenced by total nitrogen in the soil followed by soil organic carbon as compared to other soil physicochemical factors. The study establishes a fundamental relationship between microbial communities and the physicochemical properties of soil. Furthermore, the study provides valuable insights into the complex interplay between biotic and abiotic factors that influence the microbial community composition of this unique region across various elevations.}, }
@article {pmid37707523, year = {2023}, author = {Movassagh, M and Schiff, SJ and Paulson, JN}, title = {mbQTL: An R/Bioconductor Package for Microbial Quantitative Trait Loci (QTL) Estimation.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btad565}, pmid = {37707523}, issn = {1367-4811}, abstract = {MOTIVATION: In recent years, significant strides have been made in the field of genomics, with the commencement of large-scale studies aimed at collecting host mutational profiles and microbiome data. The amalgamation of host gene mutational profiles in both healthy and diseased subjects with microbial abundance data holds immense promise in providing insights into several crucial research questions, including the development and progression of diseases, as well as individual responses to therapeutic interventions. With the advent of sequencing methods such as 16 s ribosomal RNA (rRNA) sequencing and whole genome sequencing, there is increasing evidence of interplay of human genetics and microbial communities. Quantitative trait loci associated with microbial abundance (mbQTLs), are genetic variants that influence the abundance of microbial populations within the host.<br><br>RESULTS: Here we introduce mbQTL, the first R package integrating 16S ribosomal RNA (rRNA) sequencing and single nucleotide variation (SNV) and single cell polymorphysim (SNP) data. We describe various statistical methods implemented for the identification of microbe-SNV pairs, relevant statistical measures, and plot functionality for interpretation.<br><br>AVAILABILITY: mbQTL is available on bioconductor at https://bioconductor.org/packages/mbQTL/.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid37706437, year = {2023}, author = {Garg, S and Sharma, N and Bharmjeet,  and Das, A}, title = {Unraveling the intricate relationship: Influence of microbiome on the host immune system in carcinogenesis.}, journal = {Cancer reports (Hoboken, N.J.)}, volume = {}, number = {}, pages = {e1892}, doi = {10.1002/cnr2.1892}, pmid = {37706437}, issn = {2573-8348}, support = {//Delhi Technological University/ ; }, abstract = {BACKGROUND: Cancer is an outcome of various disrupted or dysregulated metabolic processes like apoptosis, growth, and self-cell transformation. Human anatomy harbors trillions of microbes, and these microbes actively influence all kinds of human metabolic activities, including the human immune response. The immune system which inherently acts as a sentinel against microbes, curiously tolerates and even maintains a distinct normal microflora in our body. This emphasizes the evolutionarily significant role of microbiota in shaping our adaptive immune system and even potentiating its function in chronic ailments like cancers. Microbes interact with the host immune cells and play a part in cancer progression or regression by modulating immune cells, producing immunosuppressants, virulence factors, and genotoxins.<br><br>RECENT FINDINGS: An expanding plethora of studies suggest and support the evidence of microbiome impacting cancer etiology. Several studies also indicate that the microbiome can supplement various cancer therapies, increasing their efficacy. The present review discusses the relationship between bacterial and viral microbiota with cancer, discussing different carcinogenic mechanisms influenced by prokaryotes with special emphasis on their immunomodulatory axis. It also elucidates the potential of the microbiome in transforming the efficacy of immunotherapeutic treatments.<br><br>CONCLUSION: This review offers a thorough overview of the complex interaction between the human immune system and the microbiome and its impact on the development of cancer. The microbiome affects the immune responses as well as progression of tumor transformation, hence microbiome-based therapies can vastly improve the effectiveness of cancer immunotherapies. Individual variations of the microbiome and its dynamic variability in every individual impacts the immune modulation and cancer progression. Therefore, further research is required to understand these underlying processes in detail, so as to design better microbiome-immune system axis in the treatment of cancer.}, }
@article {pmid37706189, year = {2023}, author = {Lichtenstein, GR}, title = {Exploring Clostridioides difficile Infection and Microbiome Therapeutics.}, journal = {Gastroenterology &amp; hepatology}, volume = {19}, number = {6}, pages = {309}, pmid = {37706189}, issn = {1554-7914}, }
@article {pmid37706187, year = {2023}, author = {Gawey, BJ and Khanna, S}, title = {Clostridioides difficile Infection: Landscape and Microbiome Therapeutics.}, journal = {Gastroenterology &amp; hepatology}, volume = {19}, number = {6}, pages = {319-328}, pmid = {37706187}, issn = {1554-7914}, abstract = {Clostridioides difficile infection (CDI) is the leading cause of hospital-acquired diarrhea and is common in the community. Both younger individuals who may be healthy otherwise and older individuals with comorbid conditions are at risk for developing CDI, with the predominant risk factor being antibiotic use. Unlike other gastrointestinal infections, CDI is not self-limited, requires antimicrobial therapy, and tends to recur at high rates even without additional risk factor exposure. The goals of CDI management include controlling active symptoms and using a recurrence prevention strategy such as a narrow-spectrum antibiotic, tapered and pulsed regimens, antibody- based therapies (directed against toxin B), or microbiome restoration. In recent years, fecal microbiota transplantation (FMT) has been the most used modality to prevent recurrent CDI with high cure rates. Heterogeneity, lack of scalability, and serious adverse events from FMT have led to development of standardized microbiota restoration therapies (MRTs). The US Food and Drug Administration has approved 2 stool-derived MRTs for prevention of recurrent CDI: fecal microbiota, live-jslm, an enema-based therapy; and fecal microbiota spores, live-brpk, an oral therapy. A phase 3 trial for a synthetic oral MRT is underway. This article outlines the pathophysiology and treatment of CDI, focusing primarily on the gut microbiome and standardized MRTs.}, }
@article {pmid37705999, year = {2023}, author = {Cavallaro, A and Rhoads, WJ and Sylvestre, &#xc9; and Marti, T and Walser, JC and Hammes, F}, title = {Legionella relative abundance in shower hose biofilms is associated with specific microbiome members.}, journal = {FEMS microbes}, volume = {4}, number = {}, pages = {xtad016}, pmid = {37705999}, issn = {2633-6685}, abstract = {Legionella are natural inhabitants of building plumbing biofilms, where interactions with other microorganisms influence their survival, proliferation, and death. Here, we investigated the associations of Legionella with bacterial and eukaryotic microbiomes in biofilm samples extracted from 85 shower hoses of a multiunit residential building. Legionella spp. relative abundance in the biofilms ranged between 0-7.8%, of which only 0-0.46% was L. pneumophila. Our data suggest that some microbiome members were associated with high (e.g. Chthonomonas, Vrihiamoeba) or low (e.g. Aquabacterium, Vannella) Legionella relative abundance. The correlations of the different Legionella variants (30 Zero-Radius OTUs detected) showed distinct patterns, suggesting separate ecological niches occupied by different Legionella species. This study provides insights into the ecology of Legionella with respect to: (i) the colonization of a high number of real shower hoses biofilm samples; (ii) the ecological meaning of associations between Legionella and co-occurring bacterial/eukaryotic organisms; (iii) critical points and future directions of microbial-interaction-based-ecological-investigations.}, }
@article {pmid37705980, year = {2023}, author = {Gorgulho, J and Roderburg, C and Beier, F and Bokemeyer, C and Brümmendorf, TH and Luedde, T and Loosen, SH}, title = {Peripheral blood CD3+HLADR+ cells and associated gut microbiome species predict response and overall survival to immune checkpoint blockade.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1206953}, pmid = {37705980}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome ; Immune Checkpoint Inhibitors ; *Microbiota ; Blood Cells ; }, abstract = {BACKGROUND: The search for biomarkers to identify ideal candidates for immune checkpoint inhibitor (ICI) therapy is fundamental. In this study, we analyze peripheral blood CD3+HLADR+ cells (activated T-cells) as a novel biomarker for ICI therapy and how its association to certain gut microbiome species can indicate individual treatment outcomes.<br><br>METHODS: Flow cytometry analysis of peripheral mononuclear blood cells (PBMCs) was performed on n=70 patients undergoing ICI therapy for solid malignancies to quantify HLA-DR on circulating CD3+ cells. 16s-rRNA sequencing of stool samples was performed on n=37 patients to assess relative abundance of gut microbiota.<br><br>RESULTS: Patients with a higher frequency of CD3+HLADR+ cells before treatment initiation showed a significantly reduced tumor response and overall survival (OS), a worst response and experienced less toxicities to ICI therapy. As such, patients with a frequency of CD3+HLADR+ cells above an ideal cut-off value of 18.55% had a median OS of only 132 days compared to 569 days for patients below. Patients with increasing CD3+HLADR+ cell counts during therapy had a significantly improved OS. An immune signature score comprising CD3+HLADR+ cells and the neutrophil-lymphocyte ratio (NLR) was highly significant for predicting OS before and during therapy. When allied to the relative abundance of microbiota from the Burkholderiales order and the species Bacteroides vulgatus, two immune-microbial scores revealed a promising predictive and prognostic power.<br><br>CONCLUSION: We identify the frequencies and dynamics of CD3+HLADR+ cells as an easily accessible prognostic marker to predict outcome to ICIs, and how these could be associated with immune modulating microbiome species. Two unprecedented immune-microbial scores comprising CD3+HLADR+, NLR and relative abundance of gut bacteria from the Burkhorderiales order or Bacteroides vulgatus species could accurately predict OS to immune checkpoint blockade.}, }
@article {pmid37705931, year = {2023}, author = {Hwang, IC and Vasquez, R and Song, JH and Engstrand, L and Valeriano, VD and Kang, DK}, title = {Alterations in the gut microbiome and its metabolites are associated with the immune response to mucosal immunization with Lactiplantibacillus plantarum-displaying recombinant SARS-CoV-2 spike epitopes in mice.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1242681}, pmid = {37705931}, issn = {2235-2988}, mesh = {Female ; Animals ; Mice ; Humans ; *Gastrointestinal Microbiome ; SARS-CoV-2 ; Epitopes ; COVID-19 Vaccines ; *COVID-19/prevention &amp; control ; Immunization ; Bacteroidetes ; Butyrates ; Clostridiales ; Immunity ; }, abstract = {Lactic acid bacteria (LAB) expressing foreign antigens have great potential as mucosal vaccines. Our previous study reported that recombinant Lactiplantibacillus plantarum SK156 displaying SARS-CoV-2 spike S1 epitopes elicited humoral and cell-mediated immune responses in mice. Here, we further examined the effect of the LAB-based mucosal vaccine on gut microbiome composition and function, and gut microbiota-derived metabolites. Forty-nine (49) female BALB/c mice were orally administered L. plantarum SK156-displaying SARS-CoV-2 spike S1 epitopes thrice (at 14-day intervals). Mucosal immunization considerably altered the gut microbiome of mice by enriching the abundance of beneficial gut bacteria, such as Muribaculaceae, Mucispirillum, Ruminococcaceae, Alistipes, Roseburia, and Clostridia vadinBB60. Moreover, the predicted function of the gut microbiome showed increased metabolic pathways for amino acids, energy, carbohydrates, cofactors, and vitamins. The fecal concentration of short-chain fatty acids, especially butyrate, was also altered by mucosal immunization. Notably, alterations in gut microbiome composition, function, and butyrate levels were positively associated with the immune response to the vaccine. Our results suggest that the gut microbiome and its metabolites may have influenced the immunogenicity of the LAB-based SARS-CoV-2 vaccine.}, }
@article {pmid37705730, year = {2023}, author = {Saglam, D and Colak, GA and Sahin, E and Ekren, BY and Sezerman, U and Bas, M}, title = {Effects of Ramadan intermittent fasting on gut microbiome: is the diet key?.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1203205}, pmid = {37705730}, issn = {1664-302X}, abstract = {Much research has been conducted regarding the impact of diet on the gut microbiota. However, the effects of dietary habits such as intermittent fasting are unclear. This study aimed to investigate the effect of intermittent fasting during Ramadan on the gut microbiota. The study was conducted on 12 healthy adult individuals who practiced fasting 17 h per day for 29 consecutive days during the month of Ramadan. To determine the dietary intake of individuals, a 3-day dietary record was kept at the beginning and end of the study. Reads that passed quality filtering were clustered, and custom-prepared 16S rRNA gene regions of bacteria associated with the human microbiome were used as a reference. Consensus sequences were created, and genus-level taxonomic annotations were determined using a sequence identity threshold of 95%. The correlations between the dietary intake measurements of the participants and the respective relative abundance of bacterial genera were investigated. The results showed that Firmicutes were higher in abundance in the gut microbiota before fasting among participants, while they were significantly lower in abundance at the end of Ramadan fasting (p < 0.05). Proteobacteria were significantly higher in abundance at the end of the month of Ramadan (p < 0.05). Fasting was associated with a significant decrease in levels of seven genera: Blautia, Coprococcus, Dorea, Faecalicatena, Fusicatenibacter, Lachnoclostridium, and Mediterraneibacter. Conversely, the abundances of two bacterial genera were enhanced at the end of the fasting month: Escherichia and Shigella. The results of the dietary intake analysis showed that a negative correlation was detected for three comparisons: Ihubacter and protein (rho = -0.54, p = 0.0068), Fusicatenibacter and vegetables (rho = -0.54, p = 0.0042), and Intestinibacter and nuts (rho = -0.54, p-value = 0.0065). The results suggest that even when the fasting period during Ramadan is consistent, the types of food consumed by individuals can affect the gut microbiota.}, }
@article {pmid37705353, year = {2023}, author = {Kobyliak, N and Khomenko, M and Falalyeyeva, T and Fedchenko, A and Savchuk, O and Tseyslyer, Y and Ostapchenko, L}, title = {Probiotics for pancreatic β-cell function: from possible mechanism of action to assessment of effectiveness.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-21}, doi = {10.1080/1040841X.2023.2257776}, pmid = {37705353}, issn = {1549-7828}, abstract = {Type 2 diabetes (T2D) is a metabolic disease characterized by chronic hyperglycemia because of insulin resistance (IR) and\or pancreatic β-cell dysfunction. Last century research showed that gut microbiota has a direct effect on metabolism and metabolic diseases. New studies into the human microbiome and its connection with the host is making it possible to develop new therapies for a wide variety of diseases. Inflammation is a well-known precursor to metabolic syndrome, which increases the risk of hypertension, visceral obesity, and dyslipidemia, which can lead to T2D through the damage of pancreatic β-cell and reduce insulin secretion. Current understanding for beneficial effects of probiotics in T2D strictly rely on both animal and clinical data, which mostly focused on their impact on IR, anthropometric parameters, glycemic control and markers of chronic systemic inflammation. From the other hand, there is a lack of evidence-based probiotic efficacy on pancreatic β-cell function in terms of T2D and related metabolic disorders. Therefore, current review will focus on the efficacy of probiotics for the protection of β-cells damage and it`s mechanism in patients with T2D.}, }
@article {pmid37705113, year = {2023}, author = {De Filippis, F and Bonelli, M and Bruno, D and Sequino, G and Montali, A and Reguzzoni, M and Pasolli, E and Savy, D and Cangemi, S and Cozzolino, V and Tettamanti, G and Ercolini, D and Casartelli, M and Caccia, S}, title = {Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {205}, pmid = {37705113}, issn = {2049-2618}, mesh = {Animals ; Larva ; *Gastrointestinal Microbiome/genetics ; Plastics ; RNA, Ribosomal, 16S/genetics ; *Diptera ; }, abstract = {BACKGROUND: In the last few years, considerable attention has been focused on the plastic-degrading capability of insects and their gut microbiota in order to develop novel, effective, and green strategies for plastic waste management. Although many analyses based on 16S rRNA gene sequencing are available, an in-depth analysis of the insect gut microbiome to identify genes with plastic-degrading potential is still lacking.<br><br>RESULTS: In the present work, we aim to fill this gap using Black Soldier Fly (BSF) as insect model. BSF larvae have proven capability to efficiently bioconvert a wide variety of organic wastes but, surprisingly, have never been considered for plastic degradation. BSF larvae were reared on two widely used plastic polymers and shotgun metagenomics was exploited to evaluate if and how plastic-containing diets affect composition and functions of the gut microbial community. The high-definition picture of the BSF gut microbiome gave access for the first time to the genomes of culturable and unculturable microorganisms in the gut of insects reared on plastics and revealed that (i) plastics significantly shaped bacterial composition at species and strain level, and (ii) functions that trigger the degradation of the polymer chains, i.e., DyP-type peroxidases, multicopper oxidases, and alkane monooxygenases, were highly enriched in the metagenomes upon exposure to plastics, consistently with the evidences obtained by scanning electron microscopy and [1]H nuclear magnetic resonance analyses&#xa0;on plastics.<br><br>CONCLUSIONS: In addition to highlighting that the astonishing plasticity of the microbiota composition of BSF larvae is associated with functional shifts in the insect microbiome, the present work sets the stage for exploiting BSF larvae as "bioincubators" to isolate microbial strains and enzymes for the development of innovative plastic biodegradation strategies. However, most importantly, the larvae constitute a source of enzymes to be evolved and valorized by pioneering synthetic biology approaches. Video Abstract.}, }
@article {pmid37704987, year = {2023}, author = {Zhang, C and Hu, L and Hao, J and Cai, W and Qin, M and Gao, Q and Nie, M and Qi, D and Ma, R}, title = {Effects of plant-derived protein and rapeseed oil on growth performance and gut microbiomes in rainbow trout.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {255}, pmid = {37704987}, issn = {1471-2180}, mesh = {Animals ; Rapeseed Oil ; *Gastrointestinal Microbiome ; *Oncorhynchus mykiss ; Body Weight ; Bacteroides ; }, abstract = {BACKGROUND: Rainbow trout (Oncorhynchus mykiss) is becoming popular with the increased demand for fish protein. However, the limited resources and expense of fish meal and oil have become restrictive factors for the development of the rainbow trout related industry. To solve this problem, plant-derived proteins and vegetable oils have been developed as alternative resources. The present study focuses on evaluating the effects of two experimental diets, FMR (fish meal replaced with plant-derived protein) and FOR (fish oil replaced with rapeseed oil), through the alteration of the gut microbiota in triploid rainbow trout. The commercial diet was used in the control group (FOM).<br><br>RESULTS: Amplicon sequencing of the 16S and 18S rRNA genes was used to assess the changes in gut bacteria and fungi. Our analysis suggested that the &#x3b1;-diversity of both bacteria and fungi decreased significantly in the FMR and FOR groups, and &#x3b2;-diversity was distinct between FOM/FMR and FOM/FOR based on principal coordinate analysis (PCoA). The abundance of the Planctomycetota phylum increased significantly in the FMR group, while that of Firmicutes and Bacteroidetes decreased. We also found that the fungal phylum Ascomycota was significantly increased in the FMR and FOR groups. At the genus level, we found that the abundance of Citrobacter was the lowest and that of pathogenic Schlesneria, Brevundimonas, and Mycoplasma was highest in the FMR and FOR groups. Meanwhile, the pathogenic fungal genera Verticillium and Aspergillus were highest in the FMR and FOR groups. Furthermore, canonical correspondence analysis (CCA) and network analysis suggested that the relatively low-abundance genera, including the beneficial bacteria Methylobacterium, Enterococcus, Clostridium, Exiguobacterium, Sphingomonas and Bacteroides and the fungi Papiliotrema, Preussia, and Stachybotrys, were positively correlated with plant protein or rapeseed oil. There were more modules that had the above beneficial genera as the hub nodes in the FMR and FOR groups.<br><br>CONCLUSIONS: Our study suggested that the FMR and FOR diets could affect the gut microbiome in rainbow trout, which might offset the effects of the dominant and pathogenic microbial genera. This could be the underlying mechanism of explaining why no significant difference was observed in body weight between the different groups.}, }
@article {pmid37704974, year = {2023}, author = {Bohn, B and Chalupova, M and Staley, C and Holtan, S and Maakaron, J and Bachanova, V and El Jurdi, N}, title = {Temporal variation in oral microbiome composition of patients undergoing autologous hematopoietic cell transplantation with keratinocyte growth factor.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {258}, pmid = {37704974}, issn = {1471-2180}, mesh = {Humans ; Fibroblast Growth Factor 7 ; Pilot Projects ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {INTRODUCTION: Autologous hematopoietic cell transplantation (AHCT) is a well-established treatment for lymphoma. Unintended effects of this therapy include oral mucositis (OM) and gastrointestinal toxicities, resulting in poor clinical outcomes. The gut microbiome has been previously linked to transplant toxicities among allogeneic recipients, but little is known about the effects of AHCT on the oral microbiome.<br><br>METHODS: Seven patients with non-Hodgkin or Hodgkin lymphoma undergoing AHCT with palifermin (keratinocyte growth factor) were included. Buccal swab samples were collected at baseline and 14- and 28-days post-treatment. Oral microbial communities were characterized with 16&#xa0;S rRNA amplicon sequencing. Temporal trends in community composition, alpha diversity, and beta diversity were investigated.<br><br>RESULTS: A significant reduction in the relative abundance of the genera Gemella and Actinomyces were observed from baseline. No significant temporal differences in alpha diversity were observed. Significant changes in beta diversity were recorded.<br><br>CONCLUSION: Results of this pilot study suggest treatment with AHCT and palifermin affects the oral microbiome, resulting in temporal shifts in oral microbial community composition. Future studies are warranted to confirm these trends and further investigate the effects of AHCT on the oral microbiome and how these shifts may affect health outcomes.}, }
@article {pmid37704738, year = {2023}, author = {Chang, YH and Yanckello, LM and Chlipala, GE and Green, SJ and Aware, C and Runge, A and Xing, X and Chen, A and Wenger, K and Flemister, A and Wan, C and Lin, AL}, title = {Prebiotic inulin enhances gut microbial metabolism and anti-inflammation in apolipoprotein E4 mice with sex-specific implications.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15116}, pmid = {37704738}, issn = {2045-2322}, support = {RF1AG062480/AG/NIA NIH HHS/United States ; }, mesh = {Female ; Male ; Animals ; Mice ; Apolipoprotein E4/genetics ; Apolipoprotein E3 ; Dysbiosis ; *Gastrointestinal Microbiome ; Inulin/pharmacology ; *Alzheimer Disease ; Anti-Inflammatory Agents ; Escherichia coli ; }, abstract = {Gut dysbiosis has been identified as a crucial factor of Alzheimer's disease (AD) development for apolipoprotein E4 (APOE4) carriers. Inulin has shown the potential to mitigate dysbiosis. However, it remains unclear whether the dietary response varies depending on sex. In the study, we fed 4-month-old APOE4 mice with inulin for 16 weeks and performed shotgun metagenomic sequencing to determine changes in microbiome diversity, taxonomy, and functional gene pathways. We also formed the same experiments with APOE3 mice to identify whether there are APOE-genotype dependent responses to inulin. We found that APOE4 female mice fed with inulin had restored alpha diversity, significantly reduced Escherichia coli and inflammation-associated pathway responses. However, compared with APOE4 male mice, they had less metabolic responses, including the levels of short-chain fatty acids-producing bacteria and the associated kinases, especially those related to acetate and Erysipelotrichaceae. These diet- and sex- effects were less pronounced in the APOE3 mice, indicating that different APOE variants also play a significant role. The findings provide insights into the higher susceptibility of APOE4 females to AD, potentially due to inefficient energy production, and imply the importance of considering precision nutrition for mitigating dysbiosis and AD risk in the future.}, }
@article {pmid37704649, year = {2023}, author = {Zhou, W and Zhang, X and Chen, X and Wu, X and Ye, A and Cao, J and Hu, X}, title = {Short-term triphenyltin exposure alters microbial homeostasis in the silkworm (Bombyx mori) midgut.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15183}, pmid = {37704649}, issn = {2045-2322}, support = {2021C02072-1//Key Scientific and Technological Grant of Zhejiang for Breeding New Agricultural Varieties/ ; CARS-18//the earmarked fund for CARS-18/ ; 2019C02044//Zhejiang Provincial Key R&amp;D Project/ ; 2020E10025//Zhejiang Provincial Silkworm and Bee Resources Utilization and Innovation Research Key Laboratory/ ; }, mesh = {Animals ; *Bombyx ; *Diabetes Mellitus, Type 2 ; Homeostasis ; *Organotin Compounds ; }, abstract = {Triphenyltin (TPT) is a widespread synthetic chemical used in many fields and its potential risk to organisms has been comprehensively investigated using different animal models and species. Currently, little is known about the effects of TPT exposure on microbial midgut diversity, therefore we explored these effects in the lepidopterous silkworm model using 16S rDNA sequencing. In total, 5273 and 5065 operational taxonomic units (OTUs) were identified in control and TPT-exposure group samples, ranging from 424 to 728 OTUs/sample. Alpha-diversity analyses revealed that TPT exposure induced the fluctuations of gut microbial diversity and abundance while beta-diversity analyses identified a distinct impact on major gut microbiota components. In our microbiome analyses, 23 phyla and 353 genera were recognized in the control group, while 20 phyla and 358 genera were recognized in the TPT exposure group. At the genus level, midgut microbiota were composed of several predominant bacterial genera, including Muribaculaceae, Lactobacillus, and UCG-010. In the TPT exposure group, o__Bacillales, f__Bacillaceae, and f__Caldicoprobacteraceae abundance was relatively high, while f__Oscillospiraceae, f__Fusobacteriaceae, and f__SC_I_84 abundance was relatively high in the control group. Gene function analyses in silkworm microbiota after TPT exposure showed that biosynthesis of ansamycins, fructose and mannose metabolism, glycerolipid metabolism, type II diabetes mellitus, glycolysis/gluconeogenesis, lipid metabolism, translation proteins, atrazine degradation, DNA repair and recombination proteins, nicotinate and nicotinamide metabolism were significantly increased. Collectively, our silkworm model identified gut microbial diversity risks and the adverse effects from TPT exposure, which were similar to other aquatic animals. Therefore, TPT levels in environmental samples must be monitored to prevent ecological harm.}, }
@article {pmid37339735, year = {2023}, author = {McCann, JR and Rawls, JF}, title = {Essential Amino Acid Metabolites as Chemical Mediators of Host-Microbe Interaction in the Gut.}, journal = {Annual review of microbiology}, volume = {77}, number = {}, pages = {479-497}, doi = {10.1146/annurev-micro-032421-111819}, pmid = {37339735}, issn = {1545-3251}, abstract = {Amino acids are indispensable substrates for protein synthesis in all organisms and incorporated into diverse aspects of metabolic physiology and signaling. However, animals lack the ability to synthesize several of them and must acquire these essential amino acids from their diet or perhaps their associated microbial communities. The essential amino acids therefore occupy a unique position in the health of animals and their relationships with microbes. Here we review recent work connecting microbial production and metabolism of essential amino acids to host biology, and the reciprocal impacts of host metabolism of essential amino acids on their associated microbes. We focus on the roles of the branched-chain amino acids (valine, leucine, and isoleucine) and tryptophan on host-microbe communication in the intestine of humans and other vertebrates. We then conclude by highlighting research questions surrounding the less-understood aspects of microbial essential amino acid synthesis in animal hosts.}, }
@article {pmid37100405, year = {2023}, author = {Jaffe, AL and Castelle, CJ and Banfield, JF}, title = {Habitat Transition in the Evolution of Bacteria and Archaea.}, journal = {Annual review of microbiology}, volume = {77}, number = {}, pages = {193-212}, doi = {10.1146/annurev-micro-041320-032304}, pmid = {37100405}, issn = {1545-3251}, abstract = {Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, relatively little is known about the characteristics and mechanisms of these habitat transitions, particularly for populations that reside in animal microbiomes. Here, we review the literature concerning habitat transitions among a variety of bacterial and archaeal lineages, considering the frequency of migration events, potential environmental barriers, and mechanisms of adaptation to new physicochemical conditions, including the modification of protein inventories and other genomic characteristics. Cells dependent on microbial hosts, particularly bacteria from the Candidate Phyla Radiation, have undergone repeated habitat transitions from environmental sources into animal microbiomes. We compare their trajectories to those of both free-living cells-including the Melainabacteria, Elusimicrobia, and methanogenic archaea-and cellular endosymbionts and bacteriophages, which have made similar transitions. We conclude by highlighting major related topics that may be worthy of future study.}, }
@article {pmid37704617, year = {2023}, author = {Xia, C and Zhao, Y and Zhang, L and Li, X and Cheng, Y and Wang, D and Xu, C and Qi, M and Wang, J and Guo, X and Ye, X and Huang, Y and Shen, D and Dou, D and Cao, H and Li, Z and Cui, Z}, title = {Myxobacteria restrain Phytophthora invasion by scavenging thiamine in soybean rhizosphere via outer membrane vesicle-secreted thiaminase I.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5646}, pmid = {37704617}, issn = {2041-1723}, support = {32170123//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32070027//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32270066//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Public metabolites such as vitamins play critical roles in maintaining the ecological functions of microbial community. However, the biochemical and physiological bases for fine-tuning of public metabolites in the microbiome remain poorly understood. Here, we examine the interactions between myxobacteria and Phytophthora sojae, an oomycete pathogen of soybean. We find that host plant and soil microbes complement P. sojae's auxotrophy for thiamine. Whereas, myxobacteria inhibits Phytophthora growth by a thiaminase I CcThi1 secreted into extracellular environment via outer membrane vesicles (OMVs). CcThi1 scavenges the required thiamine and thus arrests the thiamine sharing behavior of P. sojae from the supplier, which interferes with amino acid metabolism and expression of pathogenic effectors, probably leading to impairment of P. sojae growth and pathogenicity. Moreover, myxobacteria and CcThi1 are highly effective in regulating the thiamine levels in soil, which is correlated with the incidence of soybean Phytophthora root rot. Our findings unravel a novel ecological tactic employed by myxobacteria to maintain the interspecific equilibrium in soil microbial community.}, }
@article {pmid37704544, year = {2023}, author = {Hird, SM}, title = {Deciphering the ecoevolutionary recipe of milk microbiomes.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2023.09.004}, pmid = {37704544}, issn = {1872-8383}, abstract = {In a recent article, Keady et al. analyzed mammalian milk microbiomes across 47 species and found their assembly to be largely determined by stochastic (i.e., random) processes. In many ways, host-associated microbiomes are not random, but random events may have an underappreciated role in microbiome assembly, persistence, and ecology.}, }
@article {pmid37704493, year = {2023}, author = {Guillot, N and Roméo, B and Manesh, SS and Milano, G and Brest, P and Zitvogel, L and Hofman, P and Mograbi, B}, title = {Manipulating the gut and tumor microbiota for immune checkpoint inhibitor therapy: from dream to reality.}, journal = {Trends in molecular medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molmed.2023.08.004}, pmid = {37704493}, issn = {1471-499X}, abstract = {The past decade has witnessed a revolution in cancer treatment by shifting from conventional therapies to immune checkpoint inhibitors (ICIs). These immunotherapies unleash the host immune system against the tumor and have achieved unprecedented durable remission. However, 80% of patients do not respond. This review discusses how bacteria are unexpected drivers that reprogram tumor immunity. Manipulating the microbiota impacts on tumor development and reprograms the tumor microenvironment (TME) of mice on immunotherapy. We anticipate that harnessing commensals and the tumor microbiome holds promise to identify patients who will benefit from immunotherapy and guide the choice of new ICI combinations to advance treatment efficacy.}, }
@article {pmid37704146, year = {2023}, author = {Li, J and Yang, L and Yu, S and Ding, A and Zuo, R and Yang, J and Li, X and Wang, J}, title = {Environmental stressors altered the groundwater microbiome and nitrogen cycling: A focus on influencing mechanisms and pathways.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167004}, doi = {10.1016/j.scitotenv.2023.167004}, pmid = {37704146}, issn = {1879-1026}, abstract = {Nitrogen cycling, as an important biogeochemical process in groundwater, strongly impacts the energy and matter flow of groundwater ecology. Phthalate esters (PAEs) were screened as key environmental stressors in the groundwater of Beijing, contributing to the alteration of microbial community structure and functions; thus, it could be deduced that these stressors might influence nitrogen cycling that is almost exclusively mediated by microorganisms. Identification of the influences of PAEs on groundwater nitrogen cycling and exploration of the potential influence mechanisms and pathways are vital but still challenging. This study explored the influence mechanisms and pathways of the environmental stressor PAE on nitrogen cycling in groundwater collected from a typical monitoring station in Beijing based on high-throughput sequencing and bioinformatics analysis combined with mediation analysis methods. The results suggested that among the 5 detected PAEs, dimethyl phthalate and diethyl phthalate significantly negatively impacted nitrogen cycling processes, especially nitrogen fixation and denitrification processes (p < 0.05), in groundwater. Their influences were fully or partially mediated by functional microorganisms, particularly assigned keystone genera (such as Dechloromonas, Aeromonas and Noviherbaspirillum), whose abundance was significantly inhibited by these PAEs via dysregulation of carbohydrate metabolism and activation of defense mechanisms. These findings confirmed that the influences of environmental stressors PAEs on nitrogen cycling in groundwater might be mediated by the "PAE stress-groundwater microbiome-nitrogen cycling alteration" pathway. This study may advance the understanding of the consequences of environmental stressors on groundwater ecology and support the ecological hazard assessment of groundwater stressors.}, }
@article {pmid37704090, year = {2023}, author = {Ding, S and Jiang, L and Hu, J and Huang, W and Lou, L}, title = {Microbiome data analysis via machine learning models: Exploring vital players to optimize kitchen waste composting system.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {129731}, doi = {10.1016/j.biortech.2023.129731}, pmid = {37704090}, issn = {1873-2976}, abstract = {Composting, reliant on microorganisms, effectively treats kitchen waste. However, it is difficult to precisely understand the specific role of key microorganisms in the composting process by relying solely on experimental research. This study aims to employ machine learning models to explore key microbial genera and to optimize composting systems. After introducing a novel microbiome preprocessing approach, Stacking models were constructed (R[2] is about 0.8). The SHAP method (SHapley Additive exPlanations) identified Bacillus, Acinetobacter, Thermobacillus, Pseudomonas, Psychrobacter, and Thermobifida as prominent microbial genera (Shapley values ranging from 3.84 to 1.24). Additionally, microbial agents were prepared to target the identified key genera, and experiments demonstrated that the composting quality score was 76.06 for the treatment and 70.96 for the control. The exogenous agents enhanced decomposition and improved compost quality in later stages. In summary, this study opens up a new avenue to identifying key microorganisms and optimizing the biological treatment process.}, }
@article {pmid37703976, year = {2023}, author = {Candra, A and Darge, HF and Ahmed, YW and Saragi, IR and Kitaw, SL and Tsai, HC}, title = {Eco-benign synthesis of nano-gold chitosan-bacterial cellulose in spent ground coffee kombucha consortium: Characterization, microbiome community, and biological performance.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {126869}, doi = {10.1016/j.ijbiomac.2023.126869}, pmid = {37703976}, issn = {1879-0003}, abstract = {Biomaterials that are mediocre for cell adhesion have been a concern for medical purposes. In this study, we fabricated nano‑gold chitosan-bacterial cellulose (CBC-Au) via a facile in-situ method using spent ground coffee (SGC) in a kombucha consortium. The eco-benign synthesis of monodispersed gold nanoparticles (Au NPs) in modified bacterial cellulose (BC) was successfully achieved in the presence of chitosan (CHI) and a symbiotic culture of bacteria and yeast (SCOBY). The dominant microbiome community in SGC kombucha were Lactobacillaceae and Saccharomycetes. Chitosan-bacterial cellulose (CBC) and CBC-Au affected the microfibril networks in the nano cellulose structures and decreased the porosity. The modified BC maintained its crystallinity up to 80 % after incorporating CHI and Au NPs. Depth profiling using X-ray photoelectron spectroscopy (XPS) indicated that the Au NPs were distributed in the deeper layers of the scaffolds and a limited amount on the surface of the scaffold. Aspergillus niger fungal strains validated the biodegradability of each scaffold as a decomposer. Bacteriostatically CBC-Au showed better antimicrobial activity than BC, in line with the adhesion of NIH-3 T3 fibroblast cells and red blood cells (RBCs), which displayed good biocompatibility performance, indicating its potential use as a medical scaffold.}, }
@article {pmid37703811, year = {2023}, author = {Tuor, M and LeibundGut-Landmann, S}, title = {The skin mycobiome and intermicrobial interactions in the cutaneous niche.}, journal = {Current opinion in microbiology}, volume = {76}, number = {}, pages = {102381}, doi = {10.1016/j.mib.2023.102381}, pmid = {37703811}, issn = {1879-0364}, abstract = {Mammalian microbiomes have coevolved with their host to establish a stable homeostatic relationship. Multifaceted commensal-host and commensal-commensal interactions contribute to the maintenance of the equilibrium with an impact on diverse host physiological processes. Despite constant exposure to physical and chemical insults from the environment, the skin harbors a surprisingly stable microbiome. The fungal compartment of the skin microbiome, the skin mycobiome, is unique in that it is dominated by a single fungus, Malassezia. The lack in diversity suggests that the skin may provide a unique niche for this fungal genus and that Malassezia may efficiently outcompete other fungi from the skin. This opinion article examines aspects in support of this hypothesis, discusses how changes in niche conditions associate with skin mycobiome dysregulation, and highlights an emerging example of Malassezia being displaced from the skin by the emerging fungal pathogen C. auris, thereby generating a predisposing situation for fatal-invasive infection.}, }
@article {pmid37703423, year = {2023}, author = {Pragman, AA}, title = {Investigating a Causal Role for Lung Microbiome Dysbiosis in Early COPD Pathogenesis.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1164/rccm.202309-1599ED}, pmid = {37703423}, issn = {1535-4970}, }
@article {pmid37702886, year = {2023}, author = {Hong, BV and Agus, JK and Tang, X and Zheng, JJ and Romo, EZ and Lei, S and Zivkovic, AM}, title = {Precision Nutrition and Cardiovascular Disease Risk Reduction: the Promise of High-Density Lipoproteins.}, journal = {Current atherosclerosis reports}, volume = {}, number = {}, pages = {}, pmid = {37702886}, issn = {1534-6242}, support = {RO1 AG062240/AG/NIA NIH HHS/United States ; R01 GM147545/GM/NIGMS NIH HHS/United States ; }, abstract = {PURPOSE OF REVIEW: Emerging evidence supports the promise of precision nutritional approaches for cardiovascular disease (CVD) prevention. Here, we discuss current findings from precision nutrition trials and studies reporting substantial inter-individual variability in responses to diets and dietary components relevant to CVD outcomes. We highlight examples where early precision nutrition research already points to actionable intervention targets tailored to an individual's biology and lifestyle. Finally, we make the case for high-density lipoproteins (HDL) as a compelling next generation target for precision nutrition aimed at CVD prevention. HDL possesses complex structural features including diverse protein components, lipids, size distribution, extensive glycosylation, and interacts with the gut microbiome, all of which influence HDL's anti-inflammatory, antioxidant, and cholesterol efflux properties. Elucidating the nuances of HDL structure and function at an individual level may unlock personalized dietary and lifestyle strategies to optimize HDL-mediated atheroprotection and reduce CVD risk.<br><br>RECENT FINDINGS: Recent human studies have demonstrated that HDL particles are key players in the reduction of CVD risk. Our review highlights the role of HDL and the importance of personalized therapeutic approaches to improve their potential for reducing CVD risk. Factors such as diet, genetics, glycosylation, and gut microbiome interactions can modulate HDL structure and function at the individual level. We emphasize that fractionating HDL into size-based subclasses and measuring particle concentration are necessary to understand HDL biology and for developing the next generation of diagnostics and biomarkers. These discoveries underscore the need to move beyond a one-size-fits-all approach to HDL management. Precision nutrition strategies that account for personalized metabolic, genetic, and lifestyle data hold promise for optimizing HDL therapies and function to mitigate CVD risk more potently. While human studies show HDL play a key role in reducing CVD risk, recent findings indicate that factors such as diet, genetics, glycosylation, and gut microbes modulate HDL function at the individual level, underscoring the need for precision nutrition strategies that account for personalized variability to optimize HDL's potential for mitigating CVD risk.}, }
@article {pmid37702557, year = {2023}, author = {Grosicki, GJ and Langan, SP and Bagley, JR and Galpin, AJ and Garner, D and Hampton-Marcell, JT and Allen, JM and Robinson, AT}, title = {Gut check: Unveiling the influence of acute exercise on the gut microbiota.}, journal = {Experimental physiology}, volume = {}, number = {}, pages = {}, doi = {10.1113/EP091446}, pmid = {37702557}, issn = {1469-445X}, abstract = {The human gastrointestinal microbiota and its unique metabolites regulate a diverse array of physiological processes with substantial implications for human health and performance. Chronic exercise training positively modulates the gut microbiota and its metabolic output. The benefits of chronic exercise for the gut microbiota may be influenced by acute changes in microbial community structure and function that follow a single exercise bout (i.e., acute exercise). Thus, an improved understanding of changes in the gut microbiota that occur with acute exercise could aid in the development of evidence-based exercise training strategies to target the gut microbiota more effectively. In this review, we provide a comprehensive summary of the existing literature on the acute and very short-term (<3 weeks) exercise responses of the gut microbiota and faecal metabolites in humans. We conclude by highlighting gaps in the literature and providing recommendations for future research in this area. NEW FINDINGS: What is the topic of this review? The chronic benefits of exercise for the gut microbiota are likely influenced by acute changes in microbial community structure and function that follow a single exercise bout. This review provides a summary of the existing literature on acute exercise responses of the gut microbiota and its metabolic output in humans. What advances does it highlight? Acute aerobic exercise appears to have limited effects on diversity of the gut microbiota, variable effects on specific microbial taxa, and numerous effects on the metabolic activity of gut microbes with possible implications for host health and performance.}, }
@article {pmid37702510, year = {2023}, author = {Holman, JM and Colucci, L and Baudewyns, D and Balkan, J and Hunt, T and Hunt, B and Kinney, M and Holcomb, L and Stratigakis, A and Chen, G and Moses, PL and Mawe, GM and Zhang, T and Li, Y and Ishaq, SL}, title = {Steamed broccoli sprouts alleviate DSS-induced inflammation and retain gut microbial biogeography in mice.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0053223}, doi = {10.1128/msystems.00532-23}, pmid = {37702510}, issn = {2379-5077}, abstract = {Inflammatory bowel diseases (IBDs) are devastating conditions of the gastrointestinal tract with limited treatments, and dietary intervention may be effective and affordable for managing symptoms. Glucosinolate compounds are highly concentrated in broccoli sprouts, especially glucoraphanin (GLR), and can be metabolized by certain mammalian gut bacteria into anti-inflammatory isothiocyanates, such as sulforaphane. Gut microbiota exhibit biogeographic patterns, but it is unknown if colitis alters these or whether the location of glucoraphanin-metabolizing bacteria affects anti-inflammatory benefits. We fed specific pathogen-free C57BL/6 mice either a control diet or a 10% steamed broccoli sprout diet and gave a three-cycle regimen of 2.5% dextran sodium sulfate (DSS) in drinking water over a 34-day experiment to simulate chronic, relapsing ulcerative colitis (UC). We monitored body weight, fecal characteristics, lipocalin, serum cytokines, and bacterial communities from the luminal- and mucosal-associated populations in the jejunum, cecum, and colon. Mice fed the broccoli sprout diet with DSS treatment performed better than mice fed the control diet with DSS, and had significantly more weight gain, lower Disease Activity Index scores, lower plasma lipocalin and proinflammatory cytokines, and higher bacterial richness in all gut locations. Bacterial communities were assorted by gut location but were more homogenous across locations in the control diet + DSS mice. Importantly, our results showed that broccoli sprout feeding abrogated the effects of DSS on gut microbiota, as bacterial richness and biogeography were similar between mice receiving broccoli sprouts with and without DSS. Collectively, these results support the protective effect of steamed broccoli sprouts against dysbiosis and colitis induced by DSS. IMPORTANCE Evaluating bacterial communities across different locations in the gut provides a greater insight than fecal samples alone and provides an additional metric by which to evaluate beneficial host-microbe interactions. Here, we show that 10% steamed broccoli sprouts in the diet protects mice from the negative effects of dextran sodium sulfate-induced colitis, that colitis erases biogeographic patterns of bacterial communities in the gut, and that the cecum is not likely to be a significant contributor to colonic bacteria of interest in the DSS mouse model of ulcerative colitis. Mice fed the broccoli sprout diet during colitis performed better than mice fed the control diet while receiving DSS. The identification of accessible dietary components and concentrations that help maintain and correct the gut microbiome may provide universal and equitable approaches to IBD prevention and recovery, and broccoli sprouts represent a promising strategy.}, }
@article {pmid37702461, year = {2023}, author = {Hussan, H and Clinton, SK and Grainger, EM and Webb, M and Wang, C and Webb, A and Needleman, B and Noria, S and Zhu, J and Choueiry, F and Pietrzak, M and Bailey, MT}, title = {Distinctive patterns of sulfide- and butyrate-metabolizing bacteria after bariatric surgery: potential implications for colorectal cancer risk.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2255345}, doi = {10.1080/19490976.2023.2255345}, pmid = {37702461}, issn = {1949-0984}, mesh = {Humans ; Female ; Middle Aged ; Aged ; Male ; Butyrates ; Cross-Sectional Studies ; Escherichia coli ; *Gastrointestinal Microbiome ; *Bariatric Surgery ; Bacteria/genetics ; *Colorectal Neoplasms/surgery ; }, abstract = {Despite improved cardiometabolic outcomes following bariatric surgery, its long-term impact on colorectal cancer (CRC) risk remains uncertain. In parallel, the influence of bariatric surgery on the host microbiome and relationships with disease outcomes is beginning to be appreciated. Therefore, we investigated the impact of Roux-en-Y gastric bypass (RYGB) and vertical sleeve gastrectomy (VSG) on the patterns of sulfide-reducing and butyrate-producing bacteria, which are hypothesized to modulate CRC risk after bariatric surgery. In this single-center, cross-sectional study, we included 15 pre-surgery subjects with severe obesity and patients who are at a median (range) of 25.6 (9.9-46.5) months after RYGB (n = 16) or VSG (n = 10). The DNA abundance of fecal bacteria and enzymes involved in butyrate and sulfide metabolism were identified using metagenomic sequencing. Differences between pre-surgery and post-RYGB or post-VSG cohorts were quantified using the linear discriminant analysis (LDA) effect size (LEfSe) method. Our sample was predominantly female (87%) with a median (range) age of 46 (23-71) years. Post-RYGB and post-VSG patients had a higher DNA abundance of fecal sulfide-reducing bacteria than pre-surgery controls (LDA = 1.3-4.4, p < .05). The most significant enrichments were for fecal E. coli, Acidaminococcus and A. finegoldii after RYGB, and for A. finegoldii, S. vestibularis, V. parvula after VSG. As for butyrate-producing bacteria, R. faecis was more abundant, whereas B. dentium and A. hardus were lower post-RYGB vs. pre-surgery. B. dentium was also lower in post-VSG vs. pre-surgery. Consistent with these findings, our analysis showed a greater enrichment of sulfide-reducing enzymes after bariatric surgery, especially RYGB, vs. pre-surgery. The DNA abundance of butyrate-producing enzymes was lower post-RYGB. In conclusion, the two most used bariatric surgeries, RYGB and VSG, are associated with microbiome patterns that are potentially implicated in CRC risk. Future studies are needed to validate and understand the impact of these microbiome changes on CRC risk after bariatric surgery.}, }
@article {pmid37702381, year = {2023}, author = {Slead, TS and Callahan, BJ and Schreeg, ME and Seiler, GS and Stowe, DM and Azcarate-Peril, MA and Jacob, ME and Gookin, JL}, title = {Microbiome analysis of bile from apparently healthy cats and cats with suspected hepatobiliary disease.}, journal = {Journal of veterinary internal medicine}, volume = {}, number = {}, pages = {}, doi = {10.1111/jvim.16852}, pmid = {37702381}, issn = {1939-1676}, support = {771817//Purina Institute/ ; P30DK034987//National Institute of Diabetes and Digestive and Kidney Diseases, Center for Gastrointestinal Biology and Disease (CGIBD)/ ; }, abstract = {BACKGROUND: Bacterial infection of bile is a common cause of hepatobiliary disease in cats. Whether bile harbors a core microbiota in health or in cases of suspected hepatobiliary disease in cats is unknown.<br><br>OBJECTIVES: Establish if gallbladder bile in apparently healthy cats harbors a core microbiota composed of bacterial taxa common to many individuals. Compare results of bile cytology, bile culture, and 16S rRNA gene amplicon sequencing in apparently healthy cats and cats with suspected hepatobiliary disease.<br><br>ANIMALS: Forty-three client-owned cats with suspected hepatobiliary disease and 17 control cats.<br><br>METHODS: Bile was collected by ultrasound guided cholecystocentesis (cats with suspected hepatobiliary disease) or laparotomy after euthanasia (controls). Bile samples underwent cytologic examination, aerobic and anaerobic culture, and DNA was extracted for 16S rRNA gene amplification and sequencing.<br><br>RESULTS: Microbiome sequencing did not identify a core microbiota in control cats or cats having bile sampled because of clinical suspicion for hepatobiliary disease. Microbiome profiles from control cats were indistinguishable from profiles obtained from sampling instruments and reagents that were not exposed to bile (technical controls). Bacterial taxa that could not be explained by contamination or off-target amplification were identified only in samples from cats with bactibilia and positive bile culture results for Escherichia coli. In several E. coli positive samples, microbiome sequencing also identified a small number of potentially co-infecting bacterial genera not identified by culture.<br><br>Cat bile does not harbor a core microbiota. Uncultured bacteria may contribute to pathogenesis of hepatobiliary disease in cats with bile E. coli infection.}, }
@article {pmid37702134, year = {2023}, author = {Lee, JS and Lowell, JL and Whitewater, K and Roane, TM and Miller, CS and Chan, AP and Sylvester, AW and Jackson, D and Hunter, LE}, title = {Monitoring environmental microbiomes: Alignment of microbiology and computational biology competencies within a culturally integrated curriculum and research framework.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13867}, pmid = {37702134}, issn = {1755-0998}, support = {1027445//National Science Foundation/ ; T15LM009451-12S1//U.S. National Library of Medicine/ ; //University of Colorado Cancer Center/ ; }, abstract = {We have developed a flexible undergraduate curriculum that leverages the place-based research of environmental microbiomes to increase the number of Indigenous researchers in microbiology, data science and scientific computing. Monitoring Environmental Microbiomes (MEM) provides a curriculum and research framework designed to integrate an Indigenous approach when conducting authentic scientific research and to build interest and confidence at the undergraduate level. MEM has been successfully implemented as a short summer workshop to introduce computing practices in microbiome analysis. Based on self-assessed student knowledge of topics and skills, increased scientific confidence and interest in genomics careers were observed. We propose MEM be incorporated in a scalable course-based research experience for undergraduate institutions, including tribal colleges and universities, community colleges and other minority serving institutions. This coupled curricular and research framework explicitly considers cultural perspectives, access and equity to train a diverse future workforce that is more informed to engage in microbiome research and to translate microbiome science to benefit community and environmental health.}, }
@article {pmid37702045, year = {2023}, author = {Song, J and Lu, X and Liu, D and Zhang, Y and Zhai, X and Zhou, L and Gao, J}, title = {Fucogalactan Sulfate (FS) from Laminaria japonica Regulates Lipid Metabolism in Diet-Induced Humanized Dyslipidemia Mice via an Intestinal FXR-FGF19-CYP7A1/CYP8B1 Pathway.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.3c04683}, pmid = {37702045}, issn = {1520-5118}, abstract = {Our previous study found that fucogalactan sulfate (FS) from Laminaria japonica exhibited significant hypolipidemic effects. To further elucidate the mechanism, we first constructed a dyslipidemia mouse model with humanized gut microbiota and proved the main differential metabolic pathway involved bile acid metabolism. Then, we evaluated the beneficial effects of FS on dyslipidemia in this model mice, which revealed that oral FS administration reduced serum cholesterol levels and mitigated liver fat accumulation. Gut microbiota and microbiome analysis showed FS increased the abundance of Ruminococcaceae_NK4A214_group, GCA-900066755, and Eubacterium, which were positively associated with the fecal DCA, β-MCA, and HDCA. Further investigation demonstrated that FS inhibited the hepatic farnesoid X receptor (FXR), while activating the intestinal FXR-FGF19 pathway, leading to suppression of CYP7A1 and CYP8B1, as well as potentially reduced bile acid synthesis and lipid absorption. Overall, FS regulated lipid metabolism in diet-induced humanized dyslipidemia mice via the bile acid-mediated intestinal FXR-FGF19-CYP7A1/CYP8B1 pathway.}, }
@article {pmid37701958, year = {2023}, author = {Zhang, X and Xu, W and Zhong, W and Zhang, W and Yang, C and Duan, L and Niu, H and Dong, Y and Liu, T and Xia, S and Wang, B}, title = {Exploring the links between gut microbiome changes and irritable bowel syndrome in Han populations in the Tibetan Plateau.}, journal = {Journal of Zhejiang University. Science. B}, volume = {24}, number = {9}, pages = {823-838}, pmid = {37701958}, issn = {1862-1783}, support = {KYCXTD0503//the Research and Innovation Team Topics of Characteristic Medical Center of Chinese People's Armed Police Force/ ; 82170558//the National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Irritable Bowel Syndrome ; Tibet ; Environment ; Feces ; }, abstract = {The gut microbiome shows changes under a plateau environment, while the disbalance of intestinal microbiota plays an important role in the pathogenesis of irritable bowel syndrome (IBS); however, the relationship between the two remains unexplored. In this work, we followed up a healthy cohort for up to a year before and after living in a plateau environment and performed 16S ribosomal RNA (rRNA) sequencing analysis of their fecal samples. Through evaluating the participants' clinical symptoms, combined with an IBS questionnaire, we screened the IBS sub-population in our cohort. The sequencing results showed that a high-altitude environment could lead to changes in the diversity and composition of gut flora. In addition, we found that the longer the time volunteers spent in the plateau environment, the more similar their gut microbiota composition and abundance became compared to those before entering the plateau, and IBS symptoms were significantly alleviated. Therefore, we speculated that the plateau may be a special environment that induces IBS. The taxonomic units g_Alistipes, g_Oscillospira, and s_Ruminococcus_torques, which had been proved to play important roles in IBS pathogenesis, were also abundant in the IBS cohort at high altitudes. Overall, the disbalance of gut microbiota induced by the plateau environment contributed to the high frequency of IBS and the psychosocial abnormalities associated with IBS. Our results prompt further research to elucidate the relevant mechanism.}, }
@article {pmid37701837, year = {2023}, author = {Bulygin, I and Shatov, V and Rykachevskiy, A and Raiko, A and Bernstein, A and Burnaev, E and Gelfand, MS}, title = {Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15838}, pmid = {37701837}, issn = {2167-8359}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Metagenome ; Algorithms ; }, abstract = {Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets of variable 16S rRNA regions, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.}, }
@article {pmid37701792, year = {2023}, author = {Zhou, F and Zhang, GD and Tan, Y and Hu, SA and Tang, Q and Pei, G}, title = {NOD-like receptors mediate homeostatic intestinal epithelial barrier function: promising therapeutic targets for inflammatory bowel disease.}, journal = {Therapeutic advances in gastroenterology}, volume = {16}, number = {}, pages = {17562848231176889}, pmid = {37701792}, issn = {1756-283X}, abstract = {Inflammatory bowel disease (IBD) is a chronic gastrointestinal inflammatory disease that involves host genetics, the microbiome, and inflammatory responses. The current consensus is that the disruption of the intestinal mucosal barrier is the core pathogenesis of IBD, including intestinal microbial factors, abnormal immune responses, and impaired intestinal mucosal barrier. Cumulative data show that nucleotide-binding and oligomerization domain (NOD)-like receptors (NLRs) are dominant mediators in maintaining the homeostasis of the intestinal mucosal barrier, which play critical roles in sensing the commensal microbiota, maintaining homeostasis, and regulating intestinal inflammation. Blocking NLRs inflammasome activation by botanicals may be a promising way to prevent IBD progression. In this review, we systematically introduce the multiple roles of NLRs in regulating intestinal mucosal barrier homeostasis and focus on summarizing the activities and potential mechanisms of natural products against IBD. Aiming to propose new directions on the pathogenesis and precise treatment of IBD.}, }
@article {pmid37701742, year = {2023}, author = {Lee, C and Lee, J and Eor, JY and Kwak, MJ and Huh, CS and Kim, Y}, title = {Effect of Consumption of Animal Products on the Gut Microbiome Composition and Gut Health.}, journal = {Food science of animal resources}, volume = {43}, number = {5}, pages = {723-750}, pmid = {37701742}, issn = {2636-0780}, abstract = {The gut microbiome is critical in human health, and various dietary factors influence its composition and function. Among these factors, animal products, such as meat, dairy, and eggs, represent crucial sources of essential nutrients for the gut microbiome. However, the correlation and characteristics of livestock consumption with the gut microbiome remain poorly understood. This review aimed to delineate the distinct effects of meat, dairy, and egg products on gut microbiome composition and function. Based on the previous reports, the impact of red meat, white meat, and processed meat consumption on the gut microbiome differs from that of milk, yogurt, cheese, or egg products. In particular, we have focused on animal-originated proteins, a significant nutrient in each livestock product, and revealed that the major proteins in each food elicit diverse effects on the gut microbiome. Collectively, this review highlights the need for further insights into the interactions and mechanisms underlying the impact of animal products on the gut microbiome. A deeper understanding of these interactions would be beneficial in elucidating the development of dietary interventions to prevent and treat diseases linked to the gut microbiome.}, }
@article {pmid37701609, year = {2023}, author = {Finn, PW and Perkins, DL}, title = {BORN TO WHEEZE OR LEARNED WHEN WE WERE YOUNG: MATERNAL AND ENVIRONMENTAL FACTORS INFLUENCE ATOPIC RISK.}, journal = {Transactions of the American Clinical and Climatological Association}, volume = {133}, number = {}, pages = {181-192}, pmid = {37701609}, issn = {0065-7778}, mesh = {Child ; Humans ; Learning ; *Asthma/etiology/genetics ; *Microbiota ; }, abstract = {The prevalence of atopic diseases is increasing globally, particularly in children. Heritable genetics can partially explain risk of disease. Evidence also points to acquired genetic material, in the form of the microbiome, as an important factor in disease pathogenesis. The acquisition of the microbiome dynamically changes in response to differences in lifestyle and environmental factors. Also, in utero, maternal and environmental factors influence atopic risk for allergic rhinitis, eczema, asthma, and food allergy. Combining the analytical power of omics, we focus on how the microbiota mediates effects between mother, environment, immunity, and risk of atopic disease. In parallel, we stress that health care disparities impact asthma morbidity and mortality. Efforts to improve asthma outcomes must include multidisciplinary strategies.}, }
@article {pmid37701571, year = {2023}, author = {Devi, P and Kumari, P and Yadav, A and Tarai, B and Budhiraja, S and Shamim, U and Pandey, R}, title = {Longitudinal study across SARS-CoV-2 variants identifies transcriptionally active microbes (TAMs) associated with Delta severity.}, journal = {iScience}, volume = {26}, number = {10}, pages = {107779}, pmid = {37701571}, issn = {2589-0042}, abstract = {Emergence of new SARS-CoV-2 VOCs jeopardize global vaccine and herd immunity safeguards. VOCs interactions with host microbiota might affect clinical course and outcome. This longitudinal investigation involving Pre-VOC and VOCs (Delta &amp; Omicron) holo-transcriptome based nasopharyngeal microbiome at taxonomic levels followed by metabolic pathway analysis and integrative host-microbiome interaction. VOCs showed enrichment of Proteobacteria with dominance of Pseudomonas. Interestingly, Proteobacteria with superiority of Pseudomonas and Acinetobacter, were highlights of Delta VOC rather than Omicron. Common species comprising the core microbiome across all variants, reiterated the significance of Klebsiella pneumoniae in Delta, and its association with metabolic pathways enhancing inflammation in patients. Microbe-host gene correlation network revealed Acinetobacter baumannii, Pseudomonas stutzeri, and Pseudomonas aeuroginosa modulating immune pathways, which might augment clinical severity in Delta. Importantly, opportunistic species of Acinetobacter, Enterococcus, Prevotella, and Streptococcus were abundant in Delta-mortality. The study establishes a functional association between elevated nasal pathobionts and dysregulated host response, particularly for Delta.}, }
@article {pmid37701514, year = {2022}, author = {Luis, JV and Andréeacute S, VS and Levano, KS and Pedro, NB and Marco, MR and Ruth, GD and Rony, CC and Diana, PL and Sharma, AK and Samuel, D and Pedro O, FV and Raul J, C and A, G and Ruth, SS and Heinner, G}, title = {Analysis of microbiome diversity in coprolites from Caral, Peru.}, journal = {Bioinformation}, volume = {18}, number = {12}, pages = {1159-1165}, pmid = {37701514}, issn = {0973-2063}, abstract = {We analyzed human coprolites from the Sacred City of Caral, the oldest civilization in America (3000- and 1800-years BC). Our objective was to know the microbial diversity of the Caral Civilization through the use of a mobile ancient laboratory. DNA extraction conducted in a mobile laboratory placed near the collection site to reduce exposure of samples to contaminants and favor a rapid molecular processing. Using 16S rRNA and ITS 1 amplicon sequencing, we have elaborated the first list of the microbiomes of Caral, based on the bacterial and fungal community fingerprints detected in the coprolites recovered in six sectors of that ancient urban center. Among the most abundant sequences were those associated with Firmicutes for bacteria, Ascomycota and Basidiomycota for fungi. Bacillus was the most abundant bacterial genera in all samples analyzed, compromising up to 24.81% of the total bacterial abundance; while Aspergillus (11.43%) was the most abundant genera among fungal communities.}, }
@article {pmid37701435, year = {2023}, author = {Yu, J and Mao, Z and Zhou, Z and Yuan, B and Wang, X}, title = {Microbiome dysbiosis occurred in hypertrophic scars is dominated by S. aureus colonization.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1227024}, doi = {10.3389/fimmu.2023.1227024}, pmid = {37701435}, issn = {1664-3224}, abstract = {BACKGROUND: The mechanisms of hypertrophic scar formation and its tissue inflammation remain unknown.<br><br>METHODS: We collected 33 hypertrophic scar (HS) and 36 normal skin (NS) tissues, and detected the tissue inflammation and bacteria using HE staining, Gram staining, and transmission electronic microscopy (TEM), in situ hybridization and immunohistochemistry for MCP-1, TNF-&#x3b1;, IL-6 and IL-8. In addition, the samples were assayed by 16S rRNA sequencing to investigate the microbiota diversity in HS, and the correlation between the microbiota and the indices of Vancouver Scar Scale(VSS)score.<br><br>RESULTS: HE staining showed that a dramatically increased number of inflammatory cells accumulated in HS compared with NS, and an enhanced number of bacteria colonies was found in HS by Gram staining, even individual bacteria could be clearly observed by TEM. In situ hybridization demonstrated that the bacteria and inflammation cells co-localized in the HS tissues, and immunohistochemistry indicated the expression of MCP-1, TNF-&#x3b1;, IL-6, and IL-8 were significantly upregulated in HS than that in NS. In addition, there was a significantly different microbiota composition between HS and NS. At the phylum level, Firmicutes was significantly higher in HS than NS. At the genus level, S. aureus was the dominant species, which was significantly higher in HS than NS, and was strongly correlated with VSS indices.<br><br>CONCLUSION: Microbiome dysbiosis, dominated by S. aureus, occurred in HS formation, which is correlated with chronic inflammation and scar formation, targeting the microbiome dysbiosis is perhaps a supplementary way for future scar management.}, }
@article {pmid37700908, year = {2023}, author = {Dahlen, CR and Amat, S and Caton, JS and Crouse, MS and Diniz, WJDS and Reynolds, LP}, title = {Paternal effects on fetal programming.}, journal = {Animal reproduction}, volume = {20}, number = {2}, pages = {e20230076}, doi = {10.1590/1984-3143-AR2023-0076}, pmid = {37700908}, issn = {1984-3143}, abstract = {Paternal programming is the concept that the environmental signals from the sire's experiences leading up to mating can alter semen and ultimately affect the phenotype of resulting offspring. Potential mechanisms carrying the paternal effects to offspring can be associated with epigenetic signatures (DNA methylation, histone modification and non-coding RNAs), oxidative stress, cytokines, and the seminal microbiome. Several opportunities exist for sperm/semen to be influenced during development; these opportunities are within the testicle, the epididymis, or accessory sex glands. Epigenetic signatures of sperm can be impacted during the pre-natal and pre-pubertal periods, during sexual maturity and with advancing sire age. Sperm are susceptible to alterations as dictated by their developmental stage at the time of the perturbation, and sperm and seminal plasma likely have both dependent and independent effects on offspring. Research using rodent models has revealed that many factors including over/under nutrition, dietary fat, protein, and ingredient composition (e.g., macro- or micronutrients), stress, exercise, and exposure to drugs, alcohol, and endocrine disruptors all elicit paternal programming responses that are evident in offspring phenotype. Research using livestock species has also revealed that sire age, fertility level, plane of nutrition, and heat stress can induce alterations in the epigenetic, oxidative stress, cytokine, and microbiome profiles of sperm and/or seminal plasma. In addition, recent findings in pigs, sheep, and cattle have indicated programming effects in blastocysts post-fertilization with some continuing into post-natal life of the offspring. Our research group is focused on understanding the effects of common management scenarios of plane of nutrition and growth rates in bulls and rams on mechanisms resulting in paternal programming and subsequent offspring outcomes. Understanding the implication of paternal programming is imperative as short-term feeding and management decisions have the potential to impact productivity and profitability of our herds for generations to come.}, }
@article {pmid37700874, year = {2023}, author = {Wan, J and Song, J and Lv, Q and Zhang, H and Xiang, Q and Dai, H and Zheng, H and Lin, X and Zhang, W}, title = {Alterations in the Gut Microbiome of Young Children with Airway Allergic Disease Revealed by Next-Generation Sequencing.}, journal = {Journal of asthma and allergy}, volume = {16}, number = {}, pages = {961-972}, doi = {10.2147/JAA.S422537}, pmid = {37700874}, issn = {1178-6965}, abstract = {PURPOSE: Recent studies had shown that gut microbiota played a significant role in the development of the immune system and may affect the course of airway allergic disease. We conducted this study to determine unique gut microbial associated with allergic disease in children by shotgun gene sequencing.<br><br>METHODS: We collected fecal samples from children with allergic asthma (n = 23) and allergic rhinitis (n = 18), and healthy control (n = 19). The gut microbiota of specimens was analyzed by high-throughput metagenomic shotgun gene sequencing.<br><br>RESULTS: The intestinal microbiota of children with allergic asthma and allergic rhinitis was characterized by increased microbial richness and diversity. Simpson and Shannon were significantly elevated in children with allergic asthma. Principal coordinates analysis (PCoA) showed that the gut microbial communities cluster patterns of children with asthma or rhinitis were significantly different from those of healthy controls. However, no significant difference was found between asthma group and rhinitis group At the phylum level, higher relative abundance of Firmicutes was found in the allergic rhinitis group and allergic asthma group, while the level of Bacteroidetes was significantly lower. At the genus level, Corynebacterium, Streptococcus, Dorea, Actinomyces, Bifidobacterium, Blautia, and Rothia were significantly enriched in the allergic asthma group. Finally, a random forest classifier model selected 16 general signatures to discriminate the allergic asthma group from the healthy control group.<br><br>CONCLUSION: In conclusion, children in the allergic rhinitis group and allergic asthma group had altered gut microbiomes in comparison with the healthy control group. Compared to healthy children, the gut microbiome in children with allergic diseases has higher pro-inflammatory potential and increased production of pro-inflammatory molecules.}, }
@article {pmid37700351, year = {2023}, author = {Hares, MF and Griffiths, BE and Johnson, F and Nelson, C and Haldenby, S and Stewart, CJ and Duncan, JS and Oikonomou, G and Coombes, JL}, title = {Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: a metagenomic analysis.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {43}, pmid = {37700351}, issn = {2524-4671}, support = {BB/M011186/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Cryptosporidium parvum is the main cause of calf scour worldwide. With limited therapeutic options and research compared to other Apicomplexa, it is important to understand the parasites' biology and interactions with the host and microbiome in order to develop novel strategies against this infection. The age-dependent nature of symptomatic cryptosporidiosis suggests a link to the undeveloped immune response, the immature intestinal epithelium, and its associated microbiota. This led us to hypothesise that specific features of the early life microbiome could predict calf susceptibility to C. parvum infection.<br><br>RESULTS: In this study, a single faecal swab sample was collected from each calf within the first week of life in a cohort of 346 animals. All 346 calves were subsequently monitored for clinical signs of cryptosporidiosis, and calves that developed diarrhoea were tested for Rotavirus, Coronavirus, E. coli F5 (K99) and C. parvum by lateral flow test (LFT). A retrospective case-control approach was taken whereby a subset of healthy calves (Control group; n&#x2009;=&#x2009;33) and calves that went on to develop clinical signs of infectious diarrhoea and test positive for C. parvum infection via LFT (Cryptosporidium-positive group; n&#x2009;=&#x2009;32) were selected from this cohort, five of which were excluded due to low DNA quality. A metagenomic analysis was conducted on the faecal microbiomes of the control group (n&#x2009;=&#x2009;30) and the Cryptosporidium-positive group (n&#x2009;=&#x2009;30) prior to infection, to determine features predictive of cryptosporidiosis. Taxonomic analysis showed no significant differences in alpha diversity, beta diversity, and taxa relative abundance between controls and Cryptosporidium-positive groups. Analysis of functional potential showed pathways related to isoprenoid precursor, haem and purine biosynthesis were significantly higher in abundance in calves that later tested positive for C. parvum (q&#x2009;&#x2264;&#x2009;0.25). These pathways are either absent or streamlined in the C. parvum parasites. Though the de novo production of isoprenoid precursors, haem and purines are absent, C. parvum has been shown to encode enzymes that catalyse the downstream reactions of these pathway metabolites, indicating that C. parvum may scavenge those products from an external source.<br><br>CONCLUSIONS: The host has previously been put forward as the source of essential metabolites, but our study suggests that C. parvum may also be able to harness specific metabolic pathways of the microbiota in order to survive and replicate. This finding is important as components of these microbial pathways could be exploited as potential therapeutic targets for the prevention or mitigation of cryptosporidiosis in bovine neonates.}, }
@article {pmid37700317, year = {2023}, author = {Zhang, JY and Whalley, JP and Knight, JC and Wicker, LS and Todd, JA and Ferreira, RC}, title = {SARS-CoV-2 infection induces a long-lived pro-inflammatory transcriptional profile.}, journal = {Genome medicine}, volume = {15}, number = {1}, pages = {69}, pmid = {37700317}, issn = {1756-994X}, support = {203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, abstract = {BACKGROUND: The immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in COVID-19 patients has been extensively investigated. However, much less is known about the long-term effects of infection in patients and how it could affect the immune system and its capacity to respond to future perturbations.<br><br>METHODS: Using a targeted single-cell multiomics approach, we have recently identified a prolonged anti-inflammatory gene expression signature in T and NK cells in type 1 diabetes patients treated with low-dose IL-2. Here, we investigated the dynamics of this signature in three independent cohorts of COVID-19 patients: (i) the Oxford COVID-19 Multi-omics Blood Atlas (COMBAT) dataset, a cross-sectional cohort including 77 COVID-19 patients and ten healthy donors; (ii) the INCOV dataset, consisting of 525 samples taken from 209 COVID-19 patients during and after infection; and (iii) a longitudinal dataset consisting of 269 whole-blood samples taken from 139 COVID-19 patients followed for a period of up to 7&#xa0;months after the onset of symptoms using a bulk transcriptomic approach.<br><br>RESULTS: We discovered that SARS-CoV-2 infection leads to a prolonged alteration of the gene expression profile of circulating T, B and NK cells and monocytes. Some of the genes affected were the same as those present in the IL-2-induced anti-inflammatory gene expression signature but were regulated in the opposite direction, implying a pro-inflammatory status. The altered transcriptional profile was detected in COVID-19 patients for at least 2 months after the onset of the disease symptoms but was not observed in response to influenza infection or sepsis. Gene network analysis suggested a central role for the transcriptional factor NF-&#x3ba;B in the regulation of the observed transcriptional alterations.<br><br>CONCLUSIONS: SARS-CoV-2 infection causes a prolonged increase in the pro-inflammatory transcriptional status that could predispose post-acute patients to the development of long-term health consequences, including autoimmune disease, reactivation of other viruses and disruption of the host immune system-microbiome ecosystem.}, }
@article {pmid37700054, year = {2023}, author = {Maier, L}, title = {Pioneering microbiome engineering.}, journal = {Nature reviews. Microbiology}, volume = {21}, number = {10}, pages = {630}, pmid = {37700054}, issn = {1740-1534}, }
@article {pmid37700035, year = {2023}, author = {Lin, X and Zhang, C and Han, R and Li, S and Peng, H and Zhou, X and Huang, L and Xu, Y}, title = {Oxytetracycline and heavy metals promote the migration of resistance genes in the intestinal microbiome by plasmid transfer.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37700035}, issn = {1751-7370}, support = {42277260//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41977340//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Horizontal gene transfer (HGT) has been considered the most important pathway to introduce antibiotic resistance genes (ARGs), which seriously threatens human health and biological security. The presence of ARGs in the aquatic environment and their effect on the intestinal micro-ecosystem of aquatic animals can occur easily. To investigate the HGT potential and rule of exogenous ARGs in the intestinal flora, a visual conjugative model was developed, including the donor of dual-fluorescent bacterium and the recipient of Xenopus tropicalis intestinal microbiome. Some common pollutants of oxytetracycline (OTC) and three heavy metals (Zn, Cu and Pb) were selected as the stressor. The multi-techniques of flow cytometry (FCM), scanning electron microscopy (SEM), atomic force microscopy (AFM), single-cell Raman spectroscopy with sorting (SCRSS) and indicator analysis were used in this study. The results showed that ARG transfer could occur more easily under stressors. Moreover, the conjugation efficiency mainly depended on the viability of the intestinal bacteria. The mechanisms of OTC and heavy metal stressing conjugation included the upregulation of ompC, traJ, traG and the downregulation of korA gene. Moreover, the enzymatic activities of SOD, CAT, GSH-PX increased and the bacterial surface appearance also changed. The predominant recipient was identified as Citrobacter freundi by SCRSS, in which the abundance and quantity of ARG after conjugation were higher than those before. Therefore, since the diversity of potential recipients in the intestine are very high, the migration of invasive ARGs in the microbiome should be given more attention to prevent its potential risks to public health.}, }
@article {pmid37700024, year = {2023}, author = {Baker, JL and Mark Welch, JL and Kauffman, KM and McLean, JS and He, X}, title = {The oral microbiome: diversity, biogeography and human health.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {37700024}, issn = {1740-1534}, abstract = {The human oral microbiota is highly diverse and has a complex ecology, comprising bacteria, microeukaryotes, archaea and viruses. These communities have elaborate and highly structured biogeography that shapes metabolic exchange on a local scale and results from the diverse microenvironments present in the oral cavity. The oral microbiota also interfaces with the immune system of the human host and has an important role in not only the health of the oral cavity but also systemic health. In this Review, we highlight recent advances including novel insights into the biogeography of several oral niches at the species level, as well as the ecological role of candidate phyla radiation bacteria and non-bacterial members of the oral microbiome. In addition, we summarize the relationship between the oral microbiota and the pathology of oral diseases and systemic diseases. Together, these advances move the field towards a more holistic understanding of the oral microbiota and its role in health, which in turn opens the door to the study of novel preventive and therapeutic strategies.}, }
@article {pmid37699793, year = {2023}, author = {Chakraborty, M and Acharya, D and Dutta, TK}, title = {Diversity analysis of hilsa (Tenualosa ilisha) gut microbiota using culture-dependent and culture-independent approaches.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxad208}, pmid = {37699793}, issn = {1365-2672}, abstract = {AIMS: The bacterial communities associated with the gastrointestinal tract are primarily involved in digestion, physiology and immune response against pathogenic bacteria for the overall development and health of the host. Hilsa shad (Tenualosa ilisha), a tropical anadromous fish, found predominantly in Bangladesh and India, has so far been poorly investigated for its gut bacterial communities. In this study, both culture-based and metagenomic approaches were used to detect intestinal isolates of hilsa, captured from both freshwater and seawater to investigate the community structure of intestinal microbiota.<br><br>METHODS AND RESULTS: Culture-dependent approach allowed to isolate a total of 23 distinct bacterial species comprising sixteen Gram-negative, and seven Gram-positive isolates, where Proteobacteria and Firmicutes were identified as the two most dominant phyla. While metagenomic approach explored a wide range of important gastrointestinal bacteria, primarily dominated by Proteobacteria, Firmicutes and Bacteroidetes, with Proteobacteria and Firmicutes, being the most abundant in freshwater and seawater samples, respectively.<br><br>CONCLUSIONS: A combination of these approaches provided the differential gastrointestinal-associated bacterial diversity in freshwater and seawater hilsa with the prediction of overall functional potential.}, }
@article {pmid37699776, year = {2023}, author = {Lin, W and Qin, Y and Wang, X and Du, M and Wang, Y and Chen, X and Ren, Y}, title = {Flunitrazepam and its metabolites exposure disturb the zebrafish gut-liver axis: Combined microbiome and metabolomic analysis.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {}, number = {}, pages = {106688}, doi = {10.1016/j.aquatox.2023.106688}, pmid = {37699776}, issn = {1879-1514}, abstract = {Due to clinical treatment and illegal use, psychoactive substances have been widely detected in the aquatic environment. In this study, we investigated the effects of the benzodiazepine drug flunitrazepam (FLZ) and its metabolite 7-aminoflunitrazepam (7-FLZ) on the gut-liver axis of zebrafish. Zebrafish were exposed to two concentrations of FLZ and 7-FLZ (0.05 and 1 μg/L) for 30 days. Results showed that both FLZ and 7-FLZ exposure altered the relative abundance of Proteobacteria at the phylum level, with significant differences observed at the genus level for pathogenic bacteria such as Paracoccus, Shewanella, and Aeromonas. Metabolomics results showed both exposures significantly interfered with nucleotide and amino acid metabolism. The imbalance of gut microbiota and metabolic disorder increased the level of malondialdehyde, which in turn heightened the permeability of the gut mucosal barrier. FLZ and 7-FLZ induced oxidative stress in the liver via the gut-liver axis, leading to decreased levels of glucose, total cholesterol, and triglyceride, as well as the down-regulation of glycolipid metabolism-related genes (PPARα, PPARγ, FABP2, Fabp11, PFKFB3, and LDHA). Metabolomics results revealed that FLZ and 7-FLZ significantly affected the biosynthesis of amino acids and arginine, and other metabolic pathways such as nucleotide, nicotinate and nicotinamide, and purine in the liver. Our results unveiled the mechanisms behind the toxicological effects of psychoactive substances on the gut-liver axis, providing valuable data for ecological and environmental risk assessments.}, }
@article {pmid37699488, year = {2023}, author = {Erban, T and Parizkova, K and Sopko, B and Talacko, P and Markovic, M and Jarosova, J and Votypka, J}, title = {Imidacloprid increases the prevalence of the intestinal parasite Lotmaria passim in honey bee workers.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {166973}, doi = {10.1016/j.scitotenv.2023.166973}, pmid = {37699488}, issn = {1879-1026}, abstract = {A challenge in bee protection is to assess the risks of pesticide-pathogen interactions. Lotmaria passim, a ubiquitous unicellular parasite in honey bees, is considered harmful under specific conditions. Imidacloprid causes unpredictable side effects. Research indicates that both L. passim and imidacloprid may affect the physiology, behavior, immunity, microbiome and lifespan of honey bees. We designed cage experiments to test whether the infection of L. passim is affected by a sublethal dose of imidacloprid. Workers collected at the time of emergence were exposed to L. passim and 2.5 μg/L imidacloprid in the coexposure treatment group. First, samples of bees were taken from cages since they were 5 days old and 3 days postinfection, i.e., after finishing an artificial 24 h L. passim infection. Additional bees were collected every two additional days. In addition, bees frozen at the time of emergence and collected from the unexposed group were analyzed. Abdomens were analyzed using qPCR to determine parasite load, while corresponding selected heads were subjected to a label-free proteomic analysis. Our results show that bees are free of L. passim at the time of emergence. Furthermore, imidacloprid considerably increased the prevalence as well as parasite loads in individual bees. This means that imidacloprid facilitates infection, enabling faster parasite spread in a colony and potentially to surrounding colonies. The proteomic analysis of bee heads showed that imidacloprid neutralized the increased transferrin 1 expression by L. passim. Importantly, this promising marker has been previously observed to be upregulated by infections, including gut parasites. This study contributes to understanding the side effects of imidacloprid and demonstrates that a single xenobiotic/pesticide compound can interact with the gut parasite. Our methodology can be used to assess the effects of different compounds on L. passim.}, }
@article {pmid37699408, year = {2023}, author = {Carvalho, MR and Yan, LP and Li, B and Zhang, CH and He, YL and Reis, RL and Oliveira, JM}, title = {Gastrointestinal organs and organoids-on-a-chip: advances and translation into the clinics.}, journal = {Biofabrication}, volume = {}, number = {}, pages = {}, doi = {10.1088/1758-5090/acf8fb}, pmid = {37699408}, issn = {1758-5090}, abstract = {Microfluidic organoids-on-a-chip models of human gastrointestinal systems have been established to recreate adequate microenvironments to study physiology and pathophysiology. In the effort to find more emulating systems and less costly models for drug screening or fundamental studies, gastrointestinal system organoids-on-a-chip (GOoC) have arisen as promising pre-clinical in vitro model. This progress has been built on the latest developments of several technologies such as bioprinting, microfluidics, and organoid research. In this review we will focus on healthy and disease models of: Human Microbiome-on-a-chip and its rising correlation with gastro pathophysiology; Stomach-on-a-chip; Liver-on-a-chip; Pancreas-on-a-chip; Small Intestine, Colon and Colorectal cancer organoids-on-a-chip and Multi-Organoids-on-a-chip. The current developments related to the design, ability to hold one or more "organs" and its challenges, microfluidic features, cell sources and whether they are used to test drugs are overviewed herein. Importantly, their contribution in terms of drug development and eminent clinical translation in precision medicine field, FDA approved models, and the impact of organoid-on-chip technology in terms of pharmaceutical research and development costs are also discussed by the authors.}, }
@article {pmid37699401, year = {2023}, author = {Nogal, A and Tettamanzi, F and Dong, Q and Louca, P and Visconti, A and Christiansen, C and Breuninger, T and Linseisen, J and Grallert, H and Wawro, N and Asnicar, F and Wong, K and Baleanu, AF and Michelotti, GA and Segata, N and Falchi, M and Peters, A and Franks, PW and Bagnardi, V and Spector, TD and Bell, JT and Gieger, C and Valdes, AM and Menni, C}, title = {A faecal metabolite signature of impaired fasting glucose: results from two independent population-based cohorts.}, journal = {Diabetes}, volume = {}, number = {}, pages = {}, doi = {10.2337/db23-0170}, pmid = {37699401}, issn = {1939-327X}, abstract = {Prediabetes is a metabolic condition associated with gut microbiome composition, though mechanisms remain elusive. We searched for faecal metabolites, a readout of gut microbiome function, associated with impaired fasting glucose (IFG) in 142 individuals with IFG and 1105 healthy individuals from TwinsUK. We used the KORA cohort (318 IFG individuals, 689 healthy individuals) to replicate our findings. We linearly combined 8 IFG-positively associated metabolites (1-methylxantine, nicotinate, glucuronate, uridine, cholesterol, serine, caffeine and protoporphyrin IX) into an IFG-metabolite score, which was significantly associated with higher odds ratios for IFG (TwinsUK: OR[95%CI]=3.9[3.02-5.02], p<0.0001, KORA: OR[95%CI]=1.3[1.16-1.52], p<0.0001) and incident type-2 diabetes (T2D) (TwinsUK: HR[95%CI]=4[1.97-8], p=0.0002). Although these are host-produced metabolites, we found that the gut microbiome is strongly associated with their faecal levels (AUC>70%). Abundances of Faecalibacillus intestinalis, Dorea formicigenerans, Ruminococcus torques and Dorea sp. AF24_7LB were positively associated with IFG, and such associations were partially mediated by 1-methylxanthine and nicotinate (VAF mean(SD)=14.4%(5.1), p<0.05). Our results suggest that gut microbiome is linked to prediabetes not only via the production of microbial metabolites but also by affecting intestinal absorption/excretion of host-produced metabolites and xenobiotics, which are correlated with the risk of IFG. Faecal metabolites enable modelling of another mechanism of gut microbiome effect on prediabetes and T2D onset.}, }
@article {pmid37699259, year = {2023}, author = {Maghboli Balasjin, N and Maki, J and Schlappi, M}, title = {Pseudomonas mosselii improves cold tolerance of Asian rice (Oryza sativa L.) in a genotype-dependent manner by increasing proline in japonica and reduced glutathione in indica varieties.}, journal = {Canadian journal of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1139/cjm-2023-0030}, pmid = {37699259}, issn = {1480-3275}, abstract = {Cold stress is an important factor limiting rice production and distribution. Identifying factors that contribute to cold tolerance in rice is of primary importance. While some plant specific genetic factors involved in cold tolerance have been identified, the role of the rice microbiome remains unexplored. In this study, we evaluated the influence of plant growth promoting bacteria (PGPB) with the ability of phosphate solubilization on rice cold tolerance and survival. To reach this goal, inoculated and uninoculated two-week old seedlings were cold stressed and evaluated for survival and other phenotypes such as electrolyte leakage (EL) and necessary elements for cold tolerance. The results of this study showed that of the five bacteria, Pseudomonas mosselii, improved both indica and japonica varietal plants' survival and decreased EL, indicating increased membrane integrity. We observed different possible cold tolerance mechanisms in japonica and indica plants such as increases in proline and reduced glutathione levels, respectively. This bacterium also improved the shoot growth of cold exposed indica plants during the recovery period. This study confirmed the host genotype dependent activity of P. mosselii and indicated that there is an interaction between specific plant genes and bacterial genes that causes different plant responses to cold stress.}, }
@article {pmid37699034, year = {2023}, author = {Sheng, H and Wu, S and Xue, Y and Zhao, W and Caplan, AB and Hovde, CJ and Minnich, SA}, title = {Engineering conjugative CRISPR-Cas9 systems for the targeted control of enteric pathogens and antibiotic resistance.}, journal = {PloS one}, volume = {18}, number = {9}, pages = {e0291520}, pmid = {37699034}, issn = {1932-6203}, abstract = {Pathogenic Escherichia coli and Salmonella enterica pose serious public health threats due to their ability to cause severe gastroenteritis and life-threatening sequela, particularly in young children. Moreover, the emergence and dissemination of antibiotic resistance in these bacteria have complicated control of infections. Alternative strategies that effectively target these enteric pathogens and negate or reduce the need of antibiotics are urgently needed. Such an alternative is the CRISPR-Cas9 system because it can generate sequence-specific lethal double stranded DNA breaks. In this study, two self-transmissible broad host range conjugative plasmids, pRK24 and pBP136, were engineered to deliver multiplexed CRSIPR-Cas9 systems that specifically target Enterohemorrhagic and Enteropathogenic strains of E. coli (EHEC and EPEC), S. enterica, and blaCMY-2 antibiotic resistance plasmids. Using in vitro mating assays, we show that the conjugative delivery of pRK24-CRISPR-Cas9 carrying guide RNAs to the EPEC/EHEC eae (intimin) gene can selectively kill enterohemorrhagic E. coli O157 eae+ cells (3 log kill at 6 h) but does not kill the isogenic Δeae mutant (P<0.001). Similar results were also obtained with a pBP136 derivative, pTF16, carrying multiplexed guide RNAs targeting E. coli eae and the S. enterica ssaN gene coding for the type III secretion ATPase. Another pBP136 derivative, TF18, carries guide RNAs targeting S. enterica ssaN and the antibiotic resistance gene, blaCMY-2, carried on the multi-drug resistant pAR06302. Introduction of pTF18 into bacteria harboring pAR06302 showed plasmids were cured at an efficiency of 53% (P<0.05). Using a murine neonate EPEC infection model, pTF16 was delivered by a murine derived E. coli strain to EPEC infected mice and showed significant reductions of intestinal EPEC (P<0.05). These results suggest that establishing conjugative CRISPR-Cas9 antimicrobials in the intestinal microbiome may provide protection from enteric pathogens and reduce antibiotic resistance without disrupting the normal microbiota.}, }
@article {pmid37699019, year = {2023}, author = {Sherwin, A and Shaw, IC}, title = {Sixty years of conjecture over a urinary biomarker: a step closer to understanding the proposed link between anxiety and urinary pyrroles.}, journal = {Laboratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/labmed/lmad086}, pmid = {37699019}, issn = {1943-7730}, abstract = {OBJECTIVE: For over 60 years there has been conjecture about the identity of an Ehrlich's test positive pyrrole (Mauve Factor) reputed to be a biomarker for psychological disorders, including anxiety. We reviewed studies that attempt to identify Mauve Factor and subjected authentic standards of the 2 main candidates, kryptopyrrole and hydroxypyrrole, to the Ehrlich's reaction.<br><br>METHODS: Modified Ehrlich's test for kryptopyrrole and hydroxypyrrole were applied to urine samples from 10 volunteers, anxious and nonanxious.<br><br>RESULTS: Based on the mechanistic chemistry of Ehrlich's reaction and reactions of the 2 compounds, Mauve Factor cannot be hydroxypyrrole. Analyses of urine samples from volunteers, identified by the Generalized Anxiety Disorder - 7 item scale (GAD-7 &#x2265;10; n = 5) and control urine samples (GAD-7 <10; n = 5) using a kryptopyrrole calibration graph, show that concentrations are similar in both groups.<br><br>CONCLUSION: Kryptopyrrole may be the elusive Mauve Factor. Its possible origin from stercobilin via gut microbiome-mediated metabolism, its link to gut-mediated neurological effects via &#x3b3;-aminobutyric acid (GABA) receptors, and its predicted interaction with Zn2+ and consequent impact on zinc homeostasis are discussed. The GAD-7 scale does not differentiate between state and trait anxiety and as such, the minimal difference in pyrrole levels between volunteer groups requires further study.}, }
@article {pmid37699008, year = {2023}, author = {Sohail, S and Burns, MB}, title = {Integrating current analyses of the breast cancer microbiome.}, journal = {PloS one}, volume = {18}, number = {9}, pages = {e0291320}, pmid = {37699008}, issn = {1932-6203}, abstract = {Many cancer types have significant associations with their resident microbial communities-emerging evidence suggests that breast cancers also interact with the local tissue-associated microbiota. Microbiome research advances rapidly and analysis pipelines and databases are updated frequently. This dynamic environment makes comparative evaluations challenging. Here, we have integrated all publicly available studies related to breast cancer and the mammary microbiome in light of advances in this rapidly progressing field. Based on alpha diversity, beta diversity, proportional abundance, and statistical analyses, we observed differences between our modern analytical approaches and the original findings. We were able to classify and identify additional taxa across samples through abundance analyses and identify previously unidentified statistically significant taxa. In our updated analyses there were more taxa identified as statistically significant in comparison to the original studies' results. In the re-analysis for The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease by Hieken et al., there were twelve statistically significant differentially abundant taxa identified in breast tissue microbiota in benign and invasive cancer disease states. In the re-analysis for The Microbiota of Breast Tissue and Its Association with Breast Cancer by Urbaniak et al., there were 18 taxa identified as statistically significant. In the re-analysis for Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors by Chan et al., there were three genera identified as statistically significant in the skin and fluid samples. Our work has discovered that reanalyses are necessary for microbiome studies, especially older 16S studies. Through our re-analysis, we classified and identified more phyla and genera across studies, which supports the notion that reanalyses provide new insights to the microbiome field and help to assess robusticity of previously published findings by using new and updated tools and databases.}, }
@article {pmid37698853, year = {2023}, author = {Li, C and Lin, Y and Lin, R and Chen, Z and Zhou, Q and Luo, C and Mo, Z}, title = {Host miR-129-5p reverses effects of ginsenoside Rg1 on morphine reward possibly mediated by changes in B. vulgatus and serotonin metabolism in hippocampus.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2254946}, doi = {10.1080/19490976.2023.2254946}, pmid = {37698853}, issn = {1949-0984}, mesh = {Animals ; Mice ; Morphine/pharmacology ; Serotonin ; *Gastrointestinal Microbiome ; Hippocampus ; *MicroRNAs/genetics ; Reward ; }, abstract = {Morphine addiction is closely associated with dysbiosis of the gut microbiota. miRNAs play a crucial role in regulating intestinal bacterial growth and are involved in the development of disease. Ginsenoside Rg1 exhibits an anti-addiction effect and significantly improves intestinal microbiota disorders. In pseudo-germfree mice, supplementation with Bacteroides vulgatus (B. vulgatus) synergistically enhanced Rg1 to alleviate morphine addiction. However, it is currently unknown the relationship between fecal miRNAs in morphine-exposed mice and their potential modulation of gut microbiome, as well as their role in mediating the resistance of ginsenoside Rg1 to drug addiction. Here, we studied the fecal miRNA abundance in mice treated with morphine to explore the different miRNAs expressed, their association with B. vulgatus and their role in the amelioration of morphine reward by ginsenoside Rg1. Our results indicated ginsenoside Rg1 attenuated the significant increase in miR-129-5p expression observed in the feces of morphine-treated mice. The miR-129-5p, specifically, inhibited the growth of B. vulgatus by modulating the transcript of the site-tag BVU_RS11835 and increased the levels of 5-hydroxytryptophan and indole-3-carboxaldehyde in vitro. Subsequently, we noticed that oral administration of synthetic miR-129-5p increased 5-HT levels in the hippocampus and inhibited the reversal effect of ginsenoside Rg1 both on the relative abundance of B. vulgatus in the feces and CPP effect induced by morphine exposure. In short, Ginsenoside Rg1 might play an indirect role in remodeling the B. vulgatus against morphine reward by suppressing miR-129-5p expression. These results highlight the role of miR-129-5p and B. vulgatus in morphine reward and the anti-morphine addiction of ginsenoside Rg1.}, }
@article {pmid37698429, year = {2023}, author = {Wang, Z and Guo, M and Li, J and Jiang, C and Yang, S and Zheng, S and Li, M and Ai, X and Xu, X and Zhang, W and He, X and Wang, Y and Chen, Y}, title = {Composition and functional profiles of gut microbiota reflect the treatment stage, severity, and etiology of acute pancreatitis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0082923}, doi = {10.1128/spectrum.00829-23}, pmid = {37698429}, issn = {2165-0497}, abstract = {Acute pancreatitis (AP) is a type of digestive system disease with high mortality. Previous studies have shown that gut microbiota can participate in developing and treating acute pancreatitis by affecting the host's metabolism. In this study, we followed 20 AP patients to generate longitudinal gut microbiota profiles and activity during disease (before treatment, on the third day of treatment, and 1 month after discharge). We analyzed species composition and metabolic pathways' changes across the treatment phase, severity, and etiology. The diversity of the gut microbiome of patients with AP did not show much variation with treatment. In contrast, the metabolic functions of the gut microbiota, such as the essential chemical reactions that produce energy and maintain life, were partially reinstated after treatment. The severe AP (SAP) patients contained less beneficial bacteria (i.e., Bacteroides xylanisolvens, Clostridium lavalense, and Roseburia inulinivorans) and weaker sugar degradation function than mild AP patients before treatment. Moreover, etiology was one of the drivers of gut microbiome composition and explained the 3.54% variation in species' relative abundance. The relative abundance of pathways related to lipid synthesis was higher in the gut of hyperlipidemia AP patients than in biliary AP patients. The composition and functional profiles of the gut microbiota reflect the severity and etiology of AP. Otherwise, we also identified bacterial species associated with SAP, i.e., Oscillibacter sp. 57_20, Parabacteroides johnsonii, Bacteroides stercoris, Methanobrevibacter smithii, Ruminococcus lactaris, Coprococcus comes, and Dorea formicigenerans, which have the potential to identify the SAP at an early stage. IMPORTANCE Acute pancreatitis (AP) is a type of digestive system disease with high mortality. Previous studies have shown that gut microbiota can participate in the development and treatment of acute pancreatitis by affecting the host's metabolism. However, fewer studies acquired metagenomic sequencing data to associate species to functions intuitively and performed longitudinal analysis to explore how gut microbiota influences the development of AP. We followed 20 AP patients to generate longitudinal gut microbiota profiles and activity during disease and studied the differences in intestinal flora under different severities and etiologies. We have two findings. First, the gut microbiota profile has the potential to identify the severity and etiology of AP at an early stage. Second, gut microbiota likely acts synergistically in the development of AP. This study provides a reference for characterizing the driver flora of severe AP to identify the severity of acute pancreatitis at an early stage.}, }
@article {pmid37698410, year = {2023}, author = {Yama, K and Nishimoto, Y and Kumagai, K and Jo, R and Harada, M and Maruyama, Y and Aita, Y and Fujii, N and Inokuchi, T and Kawamata, R and Sako, M and Ichiba, Y and Tsutsumi, K and Kimura, M and Murakami, S and Kakizawa, Y and Kumagai, T and Yamada, T and Fukuda, S}, title = {Dysbiosis of oral microbiome persists after dental treatment-induced remission of periodontal disease and dental caries.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0068323}, doi = {10.1128/msystems.00683-23}, pmid = {37698410}, issn = {2379-5077}, abstract = {Oral diseases, such as periodontal disease and dental caries, have a high risk of recurrence and are considered to be related to dysbiosis of the oral microbiome and metabolome. It is, therefore, important to understand the state of the oral microbiome and metabolome after disease treatment to prevent recurrence. The current study sought to clarify whether oral dysbiosis improves the following remission of symptoms by dental treatment. To this end, the salivary microbiome and metabolome of healthy participants were compared to those with periodontal disease, dental caries, or both (concurrent). Saliva was collected as mouth-rinsed water and the microbiome was measured using 16S rRNA gene targeted sequencing and metabolome using capillary electrophoresis-time-of-flight mass spectrometry. Comparisons with healthy participants were performed before and after treatment, and several months after transition to self-care. Dental treatment significantly improved the oral health condition of each group; several months after treatment, oral health did not deteriorate. However, even after remission, the salivary microbiome of the two groups (oral disease and healthy) differed significantly. Additionally, after remission, significant differences, compared with healthy participants, remained in the relative abundances of disease-related bacteria and nitrate-reducing bacteria. After remission, significant differences were observed in the salivary metabolome in the healthy group in terms of threonate and pyrimidine metabolism-related component concentrations, which are assumed to reflect the high relative abundance of periodontal disease-related bacteria in the microbiome. Oral microbiome dysbiosis persisted even after dental treatment-induced disease remission with a sustained increased risk of disease when compared with healthy participants. IMPORTANCE We characterized the oral conditions, salivary microbiome, and metabolome after dental treatment by investigating the state after treatment completion and transition to self-care. Dental treatment improved oral health conditions, resulting in oral disease remission; however, the imbalanced state of the salivary microbiome continued even after remission. Although the results of this study are preliminary, owing to the small number of participants in each group when compared to larger cohort studies, they indicate that the risk of disease may remain higher than that of healthy participants, thereby demonstrating the importance of removing dental plaque containing disease-related bacteria using appropriate care even after treatment completion. We also identified bacterial species with relative abundances that differed from those of healthy participants even after remission of symptoms, which may indicate that the maturation of certain bacterial species must be controlled to improve the oral microbiome and reduce the risk of disease recurrence.}, }
@article {pmid37698408, year = {2023}, author = {Dao, J and Xing, Y and Chen, C and Chen, M and Wang, Z}, title = {Adaptation of rhizosphere bacterial communities of drought-resistant sugarcane varieties under different degrees of drought stress.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0118423}, doi = {10.1128/spectrum.01184-23}, pmid = {37698408}, issn = {2165-0497}, abstract = {Sugarcane is highly sensitive to changes in moisture, and increased drought severely restricts its growth and productivity. Recent studies have shown that plant growth-promoting microorganisms are essential to reduce the adverse effects of environmental stresses, especially drought. However, our knowledge about the dynamics of rhizosphere microbial community structure in sugarcane under varying degrees of drought stress is limited. We analyzed the effects of different degrees of drought stress on the rhizosphere microbial communities of Zhongzhe 1(ZZ1) and Zhongzhe 6(ZZ6) with differences in drought resistance, by combining soil enzyme activity, nutrient content, and physiological and morphological characteristics of sugarcane roots. The results showed that rhizosphere bacterial community began to change at a field capacity of 50%, enriching the sugarcane rhizosphere with drought-resistant bacteria. The core strains of ZZ1 and ZZ6 rhizosphere enrichment were mainly Streptomycetales, Sphingomonadales, and Rhizobiales. However, compared to ZZ1, the changes in rhizosphere bacterial abundance in ZZ6 were primarily associated with the abundance of Streptomycetales as drought levels increased. Rhizobiales and Streptomycetales, enriched in the rhizosphere of ZZ6 under drought, were positively correlated with root tip number and total root length (TRL), increasing the distribution area of roots and, thus, improving water and nutrient uptake by the roots thereby enhancing the resistance of sugarcane to drought stress. This research enhances our understanding of the composition of the rhizosphere microbial community in sugarcane under different levels of drought stress and its interaction with the roots, thereby providing valuable insights for enhancing drought resistance in sugarcane. IMPORTANCE Drought stress is expected to further increase in intensity, frequency, and duration, causing substantial losses in sugarcane yields. Here, we exposed sugarcane to varying degrees of drought treatment during growth and quantified the eventual composition of the resulting sugarcane rhizosphere bacterial community groups. We found that sugarcane rhizosphere under mild drought began to recruit specific bacterial communities to resist drought stress and used the interactions of root tip number, total root length, and drought-resistant strains to improve sugarcane survival under drought. This research provides a theoretical basis for the rhizosphere microbiome to help sugarcane improve its resistance under different levels of drought stress.}, }
@article {pmid37698033, year = {2023}, author = {Zuo, T and Liang, G and Huang, Z and Cao, Z and Bai, F and Zhou, Y and Wu, X and Wu, X and Chen, YQ and Balati, M and Maimaitiyiming, M and ,  and Lan, P}, title = {Baseline gut microbiome features prior to SARS-CoV-2 infection are associated with host symptoms in and post COVID-19.}, journal = {Journal of medical virology}, volume = {95}, number = {9}, pages = {e29083}, doi = {10.1002/jmv.29083}, pmid = {37698033}, issn = {1096-9071}, mesh = {Humans ; *Gastrointestinal Microbiome ; *COVID-19 ; SARS-CoV-2 ; *Microbiota ; China/epidemiology ; }, abstract = {The human gut microbiome varies substantially across individuals and populations and differentially tames our immunity at steady-state. Hence, we hypothesize that the large heterogeneity of gut microbiomes at steady-state may shape our baseline immunity differentially, and then mediate discrepant immune responses and symptoms when one encounters a viral infection, such as SARS-CoV-2 infection. To validate this hypothesis, we conducted an exploratory, longitudinal microbiome-COVID-19 study involving homogenous young participants from two geographically different regions in China. Subjects were recruited and sampled of fecal specimens before the 3-week surge window of COVID-19 (between December 11 and December 31, 2022) in China, and then were followed up for assessment of COVID-19 and post-COVID-19 manifestations. Our data showed that the baseline gut microbiome composition was intricately associated with different COVID-19 manifestations, particularly gastrointestinal involvement and post-COVID-19 lingering symptoms, in both an individual- and population-dependent manner. Our study intriguingly for the first time highlight that the gut microbiome at steady-state may prepare us differentially for weathering a respiratory viral infection.}, }
@article {pmid37697713, year = {2023}, author = {Wei, M and Gao, Q and Liu, J and Yang, Y and Yang, J and Fan, J and Lv, S and Yang, S}, title = {Development programming: Stress during gestation alters offspring development in sheep.}, journal = {Reproduction in domestic animals = Zuchthygiene}, volume = {}, number = {}, pages = {}, doi = {10.1111/rda.14465}, pmid = {37697713}, issn = {1439-0531}, support = {CXZZBS2023075//Innovation Ability Training Program for Doctoral Students in Hebei Province/ ; NO.31902203//National Natural Science Foundation of China/ ; }, abstract = {Inappropriate management practices of domestic animals during pregnancy can be potential stressors, resulting in complex behavioural, physiological and neurological consequences in the developing offspring. Some of these consequences can last into adulthood or propagate to subsequent generations. We systematically summarized the results of different experimental patterns using artificially increased maternal glucocorticoid levels or prenatal maternal physiological stress paradigms, mediators between prenatal maternal stress (PMS) and programming effects in the offspring and the effects of PMS on offspring phenotypes in sheep. PMS can impair birthweight, regulate the development of the hypothalamic-pituitary-adrenal axis, modify behavioural patterns and cognitive abilities and alter gene expression and brain morphology in offspring. Further research should focus on the effects of programming on gene expression, immune function, gut microbiome, sex-specific effects and maternal behaviour of offspring, especially comparative studies of gestational periods when PMS is applied, continual studies of programming effects on offspring and treatment strategies that effectively reverse the detrimental programming effects of prenatal stress.}, }
@article {pmid37697657, year = {2023}, author = {De, R and Kanungo, S and Mukhopadhyay, AK and Dutta, S}, title = {The gut microbiome of the healthy population in Kolkata, India, is a reservoir of antimicrobial resistance genes emphasizing the need of enforcing antimicrobial stewardship.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnad090}, pmid = {37697657}, issn = {1574-6968}, abstract = {Antimicrobial resistance (AMR) alleviation warrants antimicrobial stewardship (AS) entailing indispensability of epidemiological surveillance. We undertook a small-scale surveillance in Kolkata to detect the presence of antimicrobial resistance genes (ARGs) in the healthy gut microbiome. We found that it was a reservoir of ARGs against common antibiotics. A targeted PCR and sequencing-based ARGs detection against tetracyclines, macrolides, trimethoprim, sulfamethoxazole, aminoglycosides, amphenicol and mobile genetic element (MGE) markers was deployed in twenty-five fecal samples. Relative abundance and frequency of ARGs was calculated. We detected markers against all these classes of antibiotics. 100% samples carried aminoglycoside resistance marker and int1U. A comparison with our previously published diarrheal resistome from the same spatial and temporal frame revealed that a higher diversity of ARGs were detected in the community and a higher rate of isolation of tetC, msrA, tmp and sul-2 was found. The presence of common markers in the two cohorts proves that the gut microbiome has been contaminated with ARGs and which are being disseminated among different ecosystems. This is an issue of discerning concern for public health. The study raises an alarming picture of the AMR crisis in low-middle and emergent economies. It emphasizes the strict enforcement of AS in the community.}, }
@article {pmid37697271, year = {2023}, author = {Mingdong, W and Xiang, G and Yongjun, Q and Mingshuai, W and Hao, P}, title = {Causal associations between gut microbiota and urological tumors: a two-sample mendelian randomization study.}, journal = {BMC cancer}, volume = {23}, number = {1}, pages = {854}, pmid = {37697271}, issn = {1471-2407}, support = {82072833//National Natural Science Foundation of China/ ; }, mesh = {Male ; Humans ; *Gastrointestinal Microbiome/genetics ; Dysbiosis ; Genome-Wide Association Study ; Mendelian Randomization Analysis ; *Urologic Neoplasms ; *Kidney Neoplasms ; *Carcinoma, Renal Cell ; }, abstract = {BACKGROUND: Dysbiosis of gut microbiota has been linked to numerous diseases, including cancer. The unique role of gut microbiota in urological tumors is gaining prominence. However, it is still controversial whether the dysbiosis of gut microbiota should be one of the etiological factors of bladder cancer (BCa), prostate cancer (PCa) or kidney cancer (KCa).<br><br>MATERIALS AND METHODS: The microbiome genome-wide association study (GWAS) from the MiBioGen consortium (18,340 samples of 24 population-based cohorts) was utilized as the exposure data. Additionally, outcomes data (951 BCa cases and 307,092 controls; 1,631 KCa cases and 238,678 controls; 79,148 PCa cases and 61,106 controls) were extracted from the GWAS of the FinnGen and PRACTICAL consortia. To detect the potential causative bacterial traits for BCa, PCa, and KCa, a two-sample Mendelian randomization (MR) analysis was performed, employing the inverse-variance weighted or Wald ratio method. Sensitivity analyses were subsequently conducted to explore the robustness of the primary results. Finally, the reverse MR analysis was undertaken to mitigate the reverse causation.<br><br>RESULTS: This study suggested that Bifidobacterium (p&#x2009;=&#x2009;0.030), Actinobacteria (p&#x2009;=&#x2009;0.037 for phylum, 0.041 for class), and Ruminococcustorques group (p&#x2009;=&#x2009;0.018), exhibited an association with an increased risk of BCa using either the inverse-variance weighted or Wald ratio method. By utilizing the Wald ratio method, Allisonella (p&#x2009;=&#x2009;0.004, p&#x2009;=&#x2009;0.038) was associated with a decreased risk of BCa and PCa, respectively. Furthermore, Ruminococcustorques group (p&#x2009;=&#x2009;0.028) and Erysipelatoclostridium (p&#x2009;=&#x2009;0.048) were causally linked to an elevated risk of KCa.<br><br>CONCLUSIONS: This MR study supports that genetically predicted gut microbiota is causally related to BCa, PCa and KCa. Additionally, distinct bacterial traits are identified in relation to each tumor type.}, }
@article {pmid37697256, year = {2023}, author = {Wang, B and Guo, J and Liu, X and Yu, Y and Wu, J and Wang, Y}, title = {Prediction of the effects of small molecules on the gut microbiome using machine learning method integrating with optimal molecular features.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {338}, pmid = {37697256}, issn = {1471-2105}, support = {2021ZKMS006//Southwest Medical University Applied Basic Research Program Project/ ; 2023NSFSC0593//Sichuan Science and Technology Program of China/ ; 22ZYZYTS0191//Sichuan Science and Technology Program of China/ ; 2022YFS0614//Sichuan Science and Technology Program of China/ ; 82074129//the National Natural Science Foundation of China/ ; 2022-SYF-46//Luzhou Science and Technology Program of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Research Design ; Algorithms ; Consensus ; Machine Learning ; }, abstract = {BACKGROUND: The human gut microbiome (HGM), consisting of trillions of microorganisms, is crucial to human health. Adverse drug use is one of the most important causes of HGM disorder. Thus, it is necessary to identify drugs or compounds with anti-commensal effects on HGM in the early drug discovery stage. This study proposes a novel anti-commensal effects classification using a machine learning method and optimal molecular features. To improve the prediction performance, we explored combinations of six fingerprints and three descriptors to filter the best characterization as molecular features.<br><br>RESULTS: The final consensus model based on optimal features yielded the F1-score of 0.725&#x2009;&#xb1;&#x2009;0.014, ACC of 82.9&#x2009;&#xb1;&#x2009;0.7%, and AUC of 0.791&#x2009;&#xb1;&#x2009;0.009 for five-fold cross-validation. In addition, this novel model outperformed the prior studies by using the same algorithm. Furthermore, the important chemical descriptors and misclassified anti-commensal compounds are analyzed to better understand and interpret the model. Finally, seven structural alerts responsible for the chemical anti-commensal effect are identified, implying valuable information for drug design.<br><br>CONCLUSION: Our study would be a promising tool for screening anti-commensal compounds in the early stage of drug discovery and assessing the potential risks of these drugs in vivo.}, }
@article {pmid37697223, year = {2023}, author = {Manohar, K and Hosfield, BD and Mesfin, FM and Colgate, C and Shelley, WC and Liu, J and Zeng, L and Brokaw, JP and Markel, TA}, title = {Chondroitin sulfate supplementation improves clinical outcomes in a murine model of necrotizing enterocolitis.}, journal = {Physiological reports}, volume = {11}, number = {17}, pages = {e15819}, pmid = {37697223}, issn = {2051-817X}, support = {R01 DK133418/DK/NIDDK NIH HHS/United States ; R01 HD105301/HD/NICHD NIH HHS/United States ; }, mesh = {Female ; Infant, Newborn ; Humans ; Animals ; Mice ; Chondroitin Sulfates/therapeutic use ; *Enterocolitis, Necrotizing/drug therapy ; Disease Models, Animal ; *Fetal Diseases ; Dietary Supplements ; Cytokines ; }, abstract = {Necrotizing enterocolitis (NEC) continues to be a devastating disease in preterm neonates and has a paucity of medical management options. Chondroitin sulfate (CS) is a naturally occurring glycosaminoglycan (GAG) in human breast milk (HM) and has been shown to reduce inflammation. We hypothesized that supplementation with CS in an experimental NEC model would alter microbial diversity, favorably alter the cytokine profile, and (like other sulfur compounds) improve outcomes in experimental NEC via the eNOS pathway. NEC was induced in 5-day-old pups. Six groups were studied (n = 9-15/group): (1) WT breastfed and (2) Formula fed controls, (3) WT NEC, (4) WT NEC + CS, (5) eNOS KO (knockout) NEC, and (6) eNOS KO NEC + CS. Pups were monitored for clinical sickness score and weights. On postnatal day 9, the pups were killed. Stool was collected from rectum and microbiome analysis was done with 16 s rRNA sequencing. Intestinal segments were examined histologically using a well-established injury scoring system and segments were homogenized and analyzed for cytokine profile. Data were analyzed using GraphPad Prism with p < 0.05 considered significant. CS supplementation in formula improved experimental NEC outcomes when compared to NEC alone. CS supplementation resulted in similar improvement in NEC in both the WT and eNOS KO mice. CS supplementation did not result in microbial changes when compared to NEC alone. Our data suggest that although CS supplementation improved outcomes in NEC, this protection is not conferred via the eNOS pathway or alteration of microbial diversity. CS therapy in NEC does improve the intestinal cytokine profile and further experiments will explore the mechanistic role of CS in altering immune pathways in this disease.}, }
@article {pmid37697153, year = {2023}, author = {}, title = {BugSigDB - a database for identifying unusual abundance patterns in human microbiome studies.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37697153}, issn = {1546-1696}, }
@article {pmid37697152, year = {2023}, author = {Geistlinger, L and Mirzayi, C and Zohra, F and Azhar, R and Elsafoury, S and Grieve, C and Wokaty, J and Gamboa-Tuz, SD and Sengupta, P and Hecht, I and Ravikrishnan, A and Gonçalves, RS and Franzosa, E and Raman, K and Carey, V and Dowd, JB and Jones, HE and Davis, S and Segata, N and Huttenhower, C and Waldron, L}, title = {BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37697152}, issn = {1546-1696}, support = {5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5U24CA180996//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; }, abstract = {The literature of human and other host-associated microbiome studies is expanding rapidly, but systematic comparisons among published results of host-associated microbiome signatures of differential abundance remain difficult. We present BugSigDB, a community-editable database of manually curated microbial signatures from published differential abundance studies accompanied by information on study geography, health outcomes, host body site and experimental, epidemiological and statistical methods using controlled vocabulary. The initial release of the database contains >2,500 manually curated signatures from >600 published studies on three host species, enabling high-throughput analysis of signature similarity, taxon enrichment, co-occurrence and coexclusion and consensus signatures. These data allow assessment of microbiome differential abundance within and across experimental conditions, environments or body sites. Database-wide analysis reveals experimental conditions with the highest level of consistency in signatures reported by independent studies and identifies commonalities among disease-associated signatures, including frequent introgression of oral pathobionts into the gut.}, }
@article {pmid37696941, year = {2023}, author = {Parrish, A and Boudaud, M and Grant, ET and Willieme, S and Neumann, M and Wolter, M and Craig, SZ and De Sciscio, A and Cosma, A and Hunewald, O and Ollert, M and Desai, MS}, title = {Akkermansia muciniphila exacerbates food allergy in fibre-deprived mice.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {37696941}, issn = {2058-5276}, abstract = {Alterations in the gut microbiome, including diet-driven changes, are linked to the rising prevalence of food allergy. However, little is known about how specific gut bacteria trigger the breakdown of oral tolerance. Here we show that depriving specific-pathogen-free mice of dietary fibre leads to a gut microbiota signature with increases in the mucin-degrading bacterium Akkermansia muciniphila. This signature is associated with intestinal barrier dysfunction, increased expression of type 1 and 2 cytokines and IgE-coated commensals in the colon, which result in an exacerbated allergic reaction to food allergens, ovalbumin and peanut. To demonstrate the causal role of A. muciniphila, we employed a tractable synthetic human gut microbiota in gnotobiotic mice. The presence of A. muciniphila within the microbiota, combined with fibre deprivation, resulted in stronger anti-commensal IgE coating and innate type-2 immune responses, which worsened symptoms of food allergy. Our study provides important insights into how gut microbes can regulate immune pathways of food allergy in a diet-dependent manner.}, }
@article {pmid37696898, year = {2023}, author = {Yin, H and Yu, J and Wu, W and Li, X and Hu, R}, title = {Analysis of the microbiome in maternal, intrauterine and fetal environments based on 16S rRNA genes following different durations of membrane rupture.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15010}, pmid = {37696898}, issn = {2045-2322}, support = {81571460//National Natural Science Foundation of China/ ; }, abstract = {The incidence of chorioamnionitis and neonatal sepsis increases with the increasing time of rupture of membranes. Changes in the amount and categories of microbiomes in maternal and fetal environments after membrane rupture have yet to be discussed. In order to determine the microbiome diversity and signature in the maternal, intrauterine, and fetal environments of different durations following membrane rupture, we collected samples of fetal membrane, amniotic fluid, cord blood and maternal peripheral blood from singleton pregnant women and divided them into five groups according to the duration of membrane rupture. DNA was isolated from the samples, and the V3V4 region of bacterial 16S rRNA genes was sequenced. We found that the alpha diversity of the fetal membrane microbiome increased significantly 12 h after membrane rupture, while the beta diversity of the amniotic fluid microbiome increased 24 h after membrane rupture. In cord blood, the mean proportion of Methylobacterium and Halomonadaceae reached the highest 12 h after membrane rupture, and the mean proportion of Prevotella reached the highest 24 h after membrane rupture. The LEfSe algorithm showed that Ruminococcus, Paludibaculum, Lachnospiraceae, and Prevotella were detected earlier in cord blood or maternal blood and then detected in fetal membranes or amniotic fluid, which may suggest a reverse infection model. In conclusion, the microbes may invade the placenta 12 h after membrane rupture and invaded the amniotic cavity 24 h after membrane rupture. In addition to the common ascending pattern of infection, the hematogenous pathway of intrauterine infection should also be considered among people with rupture of membranes.}, }
@article {pmid37696621, year = {2023}, author = {Bisgaard, H and Mikkelsen, M and Rasmussen, MA and Sevelsted, A and Schoos, AM and Brustad, N and Eliasen, AU and Thorsen, J and Chawes, B and Gürdeniz, G and Morin, A and Stark, K and Stokholm, J and Ober, C and Pedersen, CET and Bønnelykke, K}, title = {Atopic and non-atopic effects of fish oil supplementation during pregnancy.}, journal = {Thorax}, volume = {}, number = {}, pages = {}, doi = {10.1136/thorax-2022-219725}, pmid = {37696621}, issn = {1468-3296}, abstract = {BACKGROUND: We recently conducted a double-blinded randomised controlled trial showing that fish-oil supplementation during pregnancy reduced the risk of persistent wheeze or asthma in the child by 30%. Here, we explore the mechanisms of the intervention.<br><br>METHODS: 736 pregnant women were given either placebo or n-3 long-chain polyunsaturated fatty acids (LCPUFAs) in the third trimester in a randomised controlled trial. Deep clinical follow-up of the 695 children in the trial was done at 12 visits until age 6 years, including assessment of genotype at the fatty acid desaturase (FADS) locus, plasma fatty acids, airway DNA methylation, gene expression, microbiome and metabolomics.<br><br>RESULTS: Supplementation with n-3 LCPUFA reduced the overall risk of non-atopic asthma by 73% at age 6 (relative risk (RR) 0.27 (95% CI 0.06 to 0.85), p=0.042). In contrast, there was no overall effect on asthma with atopic traits (RR 1.42 (95% CI 0.63 to 3.38), p=0.40), but this was significantly modified by maternal FADS genotype and LCPUFA blood levels (interaction p<0.05), and supplementation did reduce the risk of atopic asthma in the subgroup of mothers with FADS risk variants and/or low blood levels of n-3 LCPUFA before the intervention (RR 0.31 (95% CI 0.11 to 0.75), p=0.016). Furthermore, n-3 LCPUFA significantly reduced the number of infections (croup, gastroenteritis, tonsillitis, otitis media and pneumonia) by 16% (incidence rate ratio 0.84 (95% CI 0.74 to 0.96), p=0.009).<br><br>CONCLUSIONS: n-3 LCPUFA supplementation in pregnancy showed protective effects on non-atopic asthma and infections. Protective effects on atopic asthma depended on maternal FADS genotype and n-3 LCPUFA levels. This indicates that the fatty acid pathway is involved in multiple mechanisms affecting the risk of asthma subtypes and infections.<br><br>TRIAL REGISTRATION NUMBER: NCT00798226.}, }
@article {pmid37696473, year = {2023}, author = {Kelly, SA and O'Connell, NH and Thompson, TP and Dillon, L and Wu, J and Creevey, C and Kiely, P and Slevin, B and Powell, J and Gilmore, BF and Dunne, CP}, title = {Large-scale characterisation of hospital wastewater system microbiomes and clinical isolates from infected patients: profiling of multidrug-resistant microbial species.}, journal = {The Journal of hospital infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhin.2023.09.001}, pmid = {37696473}, issn = {1532-2939}, abstract = {Hospital-acquired infection (HAI) and infectious agents exhibiting antimicrobial resistance (AMR) are challenges globally. Environmental patient-facing wastewater apparatus including handwashing sinks, showers and toilets are increasingly identified as sources of infectious agents and AMR genes. We performed large-scale metagenomic analysis of the wastewater system in a large teaching hospital in the Republic of Ireland experiencing multidrug-resistant HAI outbreaks. Immediately prior to refurbishment of a medical ward where HAI has been endemic, wastewater pipe sections (n=20) were removed. These comprised toilet u-bends, sink and shower drains and, following DNA extraction, each underwent metagenomic analysis. Diverse taxonomic and resistome profiles were observed, with members of phyla Proteobacteria and Actinobacteria dominating (38.23 ± 5.68% and 15.78 ± 3.53%, respectively). Genomes of five clinical isolates were analysed. These antimicrobial-resistant bacterial isolates were from patients >48 hours post-admission to the ward. Genomic analysis determined that the isolates bore a high number of antimicrobial resistance genes (ARGs). Comparison of resistome profiles of these isolates and wastewater pipe metagenomes revealed a high degree of similarity, with many identical ARGs shared between clinical isolates and the wastewater environment, suggesting probable acquisition post-admission. The highest numbers of ARGs observed were those encoding resistance to significant clinically- and commonly-used antibiotic classes. Average nucleotide identity analysis confirmed presence of highly similar or identical genomes in the clinical isolates and wastewater pipes. These unique large-scale analyses reinforce the need for regular cleaning and decontamination of patient-facing hospital wastewater pipes and effective infection control policies to prevent the transmission of nosocomial infection and emergence of AMR within potential wastewater reservoirs.}, }
@article {pmid37695394, year = {2023}, author = {Wei, N and Tan, J}, title = {Correction to: Environment and Host Genetics Influence the Biogeography of Plant Microbiome Structure.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-023-02300-z}, pmid = {37695394}, issn = {1432-184X}, }
@article {pmid37695333, year = {2023}, author = {Rajesh, KM and Kinra, M and Ranadive, N and Pawaskar, GM and Mudgal, J and Raval, R}, title = {Effect of chronic low-dose treatment with chitooligosaccharides on microbial dysbiosis and inflammation associated chronic ulcerative colitis in Balb/c mice.}, journal = {Naunyn-Schmiedeberg's archives of pharmacology}, volume = {}, number = {}, pages = {}, pmid = {37695333}, issn = {1432-1912}, support = {200900123//Manipal Academy for Higher Education/ ; 200900123//Manipal Academy for Higher Education/ ; }, abstract = {The study aimed to investigate the potential of low dose chitooligosaccharide (COS) in ameliorating dextran sodium sulfate (DSS) induced chronic colitis by regulating microbial dysbiosis and pro-inflammatory responses. Chronic colitis was induced in BALB/c mice by DSS (4% w/v, 3 cycles of 5 days) administration. The mice were divided into four groups: vehicle, DSS, DSS + mesalamine and DSS+COS. COS and mesalamine were administered orally, daily once, from day 1 to day 30 at a dose of 20 mg/kg and 50 mg/kg respectively. The disease activity index (DAI), colon length, histopathological score, microbial composition, and pro-inflammatory cytokine expression were evaluated. COS (20 mg/kg, COS[Low]) administration reduced the disease activity index, and colon shortening, caused by DSS significantly. Furthermore, COS[Low] restored the altered microbiome in the gut and inhibited the elevated pro-inflammatory cytokines (IL-1 and IL-6) in the colon against DSS-induced chronic colitis in mice. Moreover, COS[Low] treatment improved the probiotic microflora thereby restoring the gut homeostasis. In conclusion, this is the first study where microbial dysbiosis and pro-inflammatory responses were modulated by chronic COS[Low] treatment against DSS-induced chronic colitis in Balb/c mice. Therefore, COS supplementation at a relatively low dose could be efficacious for chronic inflammatory bowel disease.}, }
@article {pmid37695138, year = {2023}, author = {Borton, MA and Shaffer, M and Hoyt, DW and Jiang, R and Ellenbogen, JB and Purvine, S and Nicora, CD and Eder, EK and Wong, AR and Smulian, AG and Lipton, MS and Krzycki, JA and Wrighton, KC}, title = {Targeted curation of the gut microbial gene content modulating human cardiovascular disease.}, journal = {mBio}, volume = {}, number = {}, pages = {e0151123}, doi = {10.1128/mbio.01511-23}, pmid = {37695138}, issn = {2150-7511}, abstract = {Despite the promise of the gut microbiome to predict human health, few studies expose the molecular-scale processes underpinning such forecasts. We mined over 200,000 gut-derived genomes from cultivated and uncultivated microbial lineages to inventory the gut microorganisms and their gene content that control trimethylamine-induced cardiovascular disease. We assigned an atherosclerotic profile to the 6,341 microbial genomes that encoded metabolisms associated with heart disease, creating the Methylated Amine Gene Inventory of Catabolism database (MAGICdb). From microbiome gene expression data sets, we demonstrate that MAGICdb enhanced the recovery of disease-relevant genes and identified the most active microorganisms, unveiling future therapeutic targets. From the feces of healthy and diseased subjects, we show that MAGICdb predicted cardiovascular disease status as effectively as traditional lipid blood tests. This functional microbiome catalog is a public, exploitable resource, designed to enable a new era of microbiota-based therapeutics and diagnostics. IMPORTANCE One of the most-cited examples of the gut microbiome modulating human disease is the microbial metabolism of quaternary amines from protein-rich foods. By-products of this microbial processing promote atherosclerotic heart disease, a leading cause of human mortality globally. Our research addresses current knowledge gaps in our understanding of this microbial metabolism by holistically inventorying the microorganisms and expressed genes catalyzing critical atherosclerosis-promoting and -ameliorating reactions in the human gut. This led to the creation of an open-access resource, the Methylated Amine Gene Inventory of Catabolism database, the first systematic inventory of gut methylated amine metabolism. More importantly, using this resource we deliver here, we show for the first time that these gut microbial genes can predict human disease, paving the way for microbiota-inspired diagnostics and interventions.}, }
@article {pmid37695126, year = {2023}, author = {Eickhardt-Dalbøge, CS and Ingham, AC and Nielsen, HV and Fuursted, K and Stensvold, CR and Andersen, LO and Larsen, MK and Kjær, L and Christensen, SF and Knudsen, TA and Skov, V and Ellervik, C and Olsen, LR and Hasselbalch, HC and Elmer Christensen, JJ and Nielsen, XC}, title = {Pronounced gut microbiota signatures in patients with JAK2V617F-positive essential thrombocythemia.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0066223}, doi = {10.1128/spectrum.00662-23}, pmid = {37695126}, issn = {2165-0497}, abstract = {Essential thrombocythemia (ET) is part of the Philadelphia chromosome-negative myeloproliferative neoplasms. It is characterized by an increased risk of thromboembolic events and also to a certain degree hypermetabolic symptoms. The gut microbiota is an important initiator of hematopoiesis and regulation of the immune system, but in patients with ET, where inflammation is a hallmark of the disease, it is vastly unexplored. In this study, we compared the gut microbiota via amplicon-based 16S rRNA gene sequencing of the V3-V4 region in 54 patients with ET according to mutation status Janus-kinase 2 (JAK2V617F)-positive vs JAK2V617F-negative patients with ET, and in 42 healthy controls (HCs). Gut microbiota richness was higher in patients with ET (median-observed richness, 283.5; range, 75-535) compared with HCs (median-observed richness, 191.5; range, 111-300; P < 0.001). Patients with ET had a different overall bacterial composition (beta diversity) than HCs (analysis of similarities [ANOSIM]; R = 0.063, P = 0.004). Patients with ET had a significantly lower relative abundance of taxa within the Firmicutes phylum compared with HCs (51% vs 59%, P = 0.03), and within that phylum, patients with ET also had a lower relative abundance of the genus Faecalibacterium (8% vs 15%, P < 0.001), an important immunoregulative bacterium. The microbiota signatures were more pronounced in patients harboring the JAK2V617F mutation, and highly similar to patients with polycythemia vera as previously described. These findings suggest that patients with ET may have an altered immune regulation; however, whether this dysregulation is induced in part by, or is itself inducing, an altered gut microbiota remains to be investigated. IMPORTANCE Essential thrombocythemia (ET) is a cancer characterized by thrombocyte overproduction. Inflammation has been shown to be vital in both the initiation and progression of other myeloproliferative neoplasms, and it is well known that the gut microbiota is important in the regulation of our immune system. However, the gut microbiota of patients with ET remains uninvestigated. In this study, we characterized the gut microbiota of patients with ET compared with healthy controls and thereby provide new insights into the field. We show that the gut microbiota of patients with ET differs significantly from that of healthy controls and the patients with ET have a lower relative abundance of important immunoregulative bacteria. Furthermore, we demonstrate that patients with JAK2V617F-positive ET have pronounced gut microbiota signatures compared with JAK2V617F-negative patients. Thereby confirming the importance of the underlying mutation, the immune response as well as the composition of the microbiota.}, }
@article {pmid37695121, year = {2023}, author = {Rojas, CA and Gardy, J and Eisen, JA and Ganz, HH}, title = {Recovery of 52 bacterial genomes from the fecal microbiome of the domestic cat (Felis catus) using Hi-C proximity ligation and shotgun metagenomics.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0060123}, doi = {10.1128/MRA.00601-23}, pmid = {37695121}, issn = {2576-098X}, abstract = {We used Hi-C proximity ligation with shotgun sequencing to retrieve metagenome-assembled genomes (MAGs) from the fecal microbiomes of two domestic cats (Felis catus). The genomes were assessed for completeness and contamination, classified taxonomically, and annotated for putative antimicrobial resistance (AMR) genes.}, }
@article {pmid37695076, year = {2023}, author = {Sarode, GV and Mazi, TA and Neier, K and Shibata, NM and Jospin, G and Harder, NHO and Caceres, A and Heffern, MC and Sharma, AK and More, SK and Dave, M and Schroeder, SM and Wang, L and LaSalle, JM and Lutsenko, S and Medici, V}, title = {The role of intestine in metabolic dysregulation in murine Wilson disease.}, journal = {Hepatology communications}, volume = {7}, number = {10}, pages = {}, doi = {10.1097/HC9.0000000000000247}, pmid = {37695076}, issn = {2471-254X}, support = {R01 DK104770/DK/NIDDK NIH HHS/United States ; R01 AA027075/AA/NIAAA NIH HHS/United States ; R01 DK071865/DK/NIDDK NIH HHS/United States ; UL1 TR001860/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Hepatolenticular Degeneration/genetics ; Lipid Metabolism/genetics ; Disease Models, Animal ; Sphingolipids ; Intestines ; }, abstract = {BACKGROUND: The clinical manifestations of Wilson disease (WD) are related to copper accumulation in the liver and the brain, but little is known about other tissue involvement regarding metabolic changes in WD. In vitro studies suggested that the loss of intestinal ATP7B affects metabolic dysregulation in WD. We tested this hypothesis by evaluating the gut microbiota and lipidome in 2 mouse models of WD and by characterizing a new mouse model with a targeted deletion of Atp7b in the intestine.<br><br>METHODS: Cecal content 16S sequencing and untargeted hepatic and plasma lipidome analyses in the Jackson Laboratory toxic-milk and the Atp7b null global knockout mouse models of WD were profiled and integrated. Intestine-specific Atp7b knockout mice (Atp7b&#x394;IEC) were generated and characterized using targeted lipidome analysis following a high-fat diet challenge.<br><br>RESULTS: Gut microbiota diversity was reduced in animal models of WD. Comparative prediction analysis revealed amino acid, carbohydrate, and lipid metabolism functions to be dysregulated in the WD gut microbial metagenome. Liver and plasma lipidomic profiles showed dysregulated triglyceride and diglyceride, phospholipid, and sphingolipid metabolism in WD models. However, Atp7b&#x394;IEC mice did not show gut microbiome differences compared to wild type. When challenged with a high-fat diet, Atp7b&#x394;IEC mice exhibited profound alterations to fatty acid desaturation and sphingolipid metabolism pathways as well as altered APOB48 distribution in intestinal epithelial cells.<br><br>CONCLUSIONS: Gut microbiome and lipidome underlie systemic metabolic manifestations in murine WD. Intestine-specific ATP7B deficiency affected both intestinal and systemic response to a high-fat challenge but not the microbiome profile, at least at early stages. WD is a systemic disease in which intestinal-specific ATP7B loss and diet influence the phenotype and the lipidome profile.}, }
@article {pmid37694693, year = {2023}, author = {Thiran, A and Petta, I and Blancke, G and Thorp, M and Planckaert, G and Jans, M and Andries, V and Barbry, K and Gilis, E and Coudenys, J and Hochepied, T and Vanhove, C and Gracey, E and Dumas, E and Manuelo, T and Josipovic, I and van Loo, G and Elewaut, D and Vereecke, L}, title = {Sterile triggers drive joint inflammation in TNF- and IL-1β-dependent mouse arthritis models.}, journal = {EMBO molecular medicine}, volume = {}, number = {}, pages = {e17691}, doi = {10.15252/emmm.202317691}, pmid = {37694693}, issn = {1757-4684}, support = {EOS-G0H2522N-40007505//Fonds Wetenschappelijk Onderzoek (FWO)/ ; //Foundation for Research in Rheumatology (FOREUM)/ ; GOA031-22BOF//UGent | Bijzonder Onderzoeksfonds UGent (BOF)/ ; BOF-01N01019//UGent | Bijzonder Onderzoeksfonds UGent (BOF)/ ; STA010-19BOF//UGent | Bijzonder Onderzoeksfonds UGent (BOF)/ ; }, abstract = {Arthritis is the most common extra-intestinal complication in inflammatory bowel disease (IBD). Conversely, arthritis patients are at risk for developing IBD and often display subclinical gut inflammation. These observations suggest a shared disease etiology, commonly termed "the gut-joint-axis." The clinical association between gut and joint inflammation is further supported by the success of common therapeutic strategies and microbiota dysbiosis in both conditions. Most data, however, support a correlative relationship between gut and joint inflammation, while causative evidence is lacking. Using two independent transgenic mouse arthritis models, either TNF- or IL-1β dependent, we demonstrate that arthritis develops independently of the microbiota and intestinal inflammation, since both lines develop full-blown articular inflammation under germ-free conditions. In contrast, TNF-driven gut inflammation is fully rescued in germ-free conditions, indicating that the microbiota is driving TNF-induced gut inflammation. Together, our study demonstrates that although common inflammatory pathways may drive both gut and joint inflammation, the molecular triggers initiating such pathways are distinct in these tissues.}, }
@article {pmid37694585, year = {2023}, author = {Ma, Q and Li, X and Jiang, H and Fu, X and You, L and You, F and Ren, Y}, title = {Mechanisms underlying the effects, and clinical applications, of oral microbiota in lung cancer: current challenges and prospects.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-22}, doi = {10.1080/1040841X.2023.2247493}, pmid = {37694585}, issn = {1549-7828}, abstract = {The oral cavity contains a site-specific microbiota that interacts with host cells to regulate many physiological processes in the human body. Emerging evidence has suggested that changes in the oral microbiota can increase the risk of lung cancer (LC), and the oral microbiota is also altered in patients with LC. Human and animal studies have shown that oral microecological disorders and/or specific oral bacteria may play an active role in the occurrence and development of LC through direct and/or indirect mechanisms. These studies support the potential of oral microbiota in the clinical treatment of LC. Oral microbiota may therefore be used in the prevention and treatment of LC and to improve the side effects of anticancer therapy by regulating the balance of the oral microbiome. Specific oral microbiota in LC may also be used as screening or predictive biomarkers. This review summarizes the main findings in research on oral microbiome-related LC and discusses current challenges and future research directions.}, }
@article {pmid37694489, year = {2023}, author = {D'Hooghe, SMJ and Bosch, G and Sun, M and Cools, A and Becker, AAMJ and Hendriks, WH and Janssens, GPJ}, title = {How important is food structure when cats eat mice?.}, journal = {The British journal of nutrition}, volume = {}, number = {}, pages = {1-37}, doi = {10.1017/S0007114523002039}, pmid = {37694489}, issn = {1475-2662}, abstract = {Feeding whole prey to felids has shown to benefit their gastrointestinal health. Whether this effect is caused by the chemical or physical nature of whole prey is unknown. Fifteen domestic cats, as a model for strict carnivores, were either fed minced mice (MM) or whole mice (WM), to determine the effect of food structure on digestibility, mean urinary excretion time of [15]N, intestinal microbial activity and fermentation products. Faeces samples were collected after feeding all cats a commercially available extruded diet (EXT) for 10 days before feeding for 19 days the MM and WM diets with faeces and urine collected from d11-15. Samples for microbiota composition and determination of mean urinary excretion time were obtained from d16-19. The physical structure of the mice diet (minced or not) did not affect large intestinal fermentation as total SCFA and BCFA, and most biogenic amine (BA) concentrations were not different (P>0.10). When changing from EXT to the mice diets, the microbial community composition shifted from a carbolytic (Prevotellaceae) to proteolytic (Fusobacteriaceae) profile and led to a reduced faecal acetic to propionic acid ratio, SCFA, total BCFA (P<0.001), NH3 (P=0.04), total BA (P<0.001) and para-cresol (P=0.08). The results of this study indicate that food structure within a whole-prey diet is less important than the overall diet type, with major shifts in microbiome and decrease in potentially harmful fermentation products when diet changes from extruded to mice. This urges for careful consideration of the consequences of prey-based diets for gut health in cats.}, }
@article {pmid37694281, year = {2023}, author = {Kageyama, S and Inoue, R and Park, J and Hosomi, K and Yumioka, H and Suka, T and Teramoto, K and Syauki, AY and Doi, M and Sakaue, H and Miyake, M and Mizuguchi, K and Kunisawa, J and Irie, Y}, title = {Changes in Fecal Gut Microbiome of Home Healthcare Patients with Disabilities through Consumption of Malted Rice Amazake.}, journal = {Physiological genomics}, volume = {}, number = {}, pages = {}, doi = {10.1152/physiolgenomics.00062.2023}, pmid = {37694281}, issn = {1531-2267}, support = {2019C08//Okayama Prefectural University Creative Research Grant/ ; JP20gm1010006h004//Japan Agency for Medical Research and Development (AMED)/ ; 20AC5004//Ministry of Health and Welfare of Japan and Public /Private R&amp;D Investment Strategic Expansion PrograM/ ; JP23KJ1860//Grant-in-Aid for JSPS Fellows/ ; }, abstract = {The aim of this study was to investigate changes in gut microbiome both during and after the consumption of malted rice amazake (MR-Amazake), a fermented food from Japan, in home healthcare patients with disabilities including patients with severe motor and intellectual disabilities (SMID). We monitored 12 patients who consumed MR-Amazake for six weeks, investigating them before and after the intervention as well as six weeks after the end of intake to compare their physical condition, diet, the type of their medication, Constipation Assessment Scale (CAS), and an analysis of their comprehensive fecal microbiome using 16S rRNA sequencing. Their constipation symptom significantly alleviated and principal coordinates analysis revealed that 30% of patients showed significant changes in gut microbiome after MR-Amazake ingestion. Furthermore, Bifidobacterium was strongly associated with these changes. These changes were observed only during MR-Amazake intake; the original gut microbiome was restored when MR-Amazake intake was discontinued. These results suggest that six weeks is a reasonable period of time for MR-Amazake to change human gut microbiome and that continuous consumption of MR-Amazake is required to sustain such changes.}, }
@article {pmid37694136, year = {2023}, author = {Bubeck, AM and Urbain, P and Horn, C and Jung, AS and Ferrari, L and Ruple, HK and Podlesny, D and Zorn, S and Laupsa-Borge, J and Jensen, C and Lindseth, I and Lied, GA and Dierkes, J and Mellgren, G and Bertz, H and Matysik, S and Krautbauer, S and Liebisch, G and Schoett, HF and Dankel, SN and Fricke, WF}, title = {High-fat diet impact on intestinal cholesterol conversion by the microbiota and serum cholesterol levels.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107697}, pmid = {37694136}, issn = {2589-0042}, abstract = {Cholesterol-to-coprostanol conversion by the intestinal microbiota has been suggested to reduce intestinal and serum cholesterol availability, but the relationship between intestinal cholesterol conversion and the gut microbiota, dietary habits, and serum lipids has not been characterized in detail. We measured conserved proportions of cholesterol high and low-converter types in individuals with and without obesity from two distinct, independent low-carbohydrate high-fat (LCHF) dietary intervention studies. Across both cohorts, cholesterol conversion increased in previous low-converters after LCHF diet and was positively correlated with the fecal relative abundance of Eubacterium coprostanoligenes. Lean cholesterol high-converters had increased serum triacylglycerides and decreased HDL-C levels before LCHF diet and responded to the intervention with increased LDL-C, independently of fat, cholesterol, and saturated fatty acid intake. Our findings identify the cholesterol high-converter type as a microbiome marker, which in metabolically healthy lean individuals is associated with increased LDL-C in response to LCHF.}, }
@article {pmid37694134, year = {2023}, author = {Williams, A and Stephens, TG and Shumaker, A and Bhattacharya, D}, title = {Peeling back the layers of coral holobiont multi-omics data.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107623}, pmid = {37694134}, issn = {2589-0042}, abstract = {The integration of multiple 'omics' datasets is a promising avenue for answering many important and challenging questions in biology, particularly those relating to complex ecological systems. Although multi-omics was developed using data from model organisms with significant prior knowledge and resources, its application to non-model organisms, such as coral holobionts, is less clear-cut. We explore, in the emerging rice coral model Montipora capitata, the intersection of holobiont transcriptomic, proteomic, metabolomic, and microbiome amplicon data and investigate how well they correlate under high temperature treatment. Using a typical thermal stress regime, we show that transcriptomic and proteomic data broadly capture the stress response of the coral, whereas the metabolome and microbiome datasets show patterns that likely reflect stochastic and homeostatic processes associated with each sample. These results provide a framework for interpreting multi-omics data generated from non-model systems, particularly those with complex biotic interactions among microbial partners.}, }
@article {pmid37693618, year = {2023}, author = {Hamidi, B and Steed, LL and Curry, SR and Salgado, CD and Alekseyenko, AV}, title = {The hidden microbiome of hospital infection surveillance testing: biomarkers of health outcomes in MRSA and VRE colonization.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-3299277/v1}, pmid = {37693618}, abstract = {Background Hospital-acquired infections present a major concern for healthcare systems in the U.S. and worldwide. Drug-resistant infections result in increased costs and prolonged hospital stays. Methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) are responsible for many drug-resistant infections in the U.S. We undertook two parallel studies aimed to investigate the differences in the microbial communities of individuals colonized with MRSA (or VRE) as compared to their respective non-colonized counterparts matched for age, sex, race, ethnicity, unit of admission, and diagnostic-related group, when available. Results The VRE study showed considerably more Enterococcus genus communities in the VRE colonized samples. Our findings for both MRSA and VRE studies suggest a strong association between 16S rRNA gene alpha diversity, beta diversity, and colonization status. When we assessed the colonized microbial communities in isolation, the differences disappeared, suggesting that the colonized microbial communities drove the change. Isolating Staphylococcus , we saw significant differences expressed across colonization in specific sequence variants. Conclusions The differences seen in the microbial communities from MRSA (or VRE) colonized samples as compared to non-colonized match-pairs are driven by the isolated communities of the Staphylococcus (or Enterococcus) genus, the removal of which results in the disappearance of any differences in the diversity observed across the match-pairs.}, }
@article {pmid37693563, year = {2023}, author = {Ocius, KL and Kolli, SH and Ahmad, SS and Dressler, JM and Chordia, MD and Jutras, BL and Rutkowski, MR and Pires, MM}, title = {Non-invasive Analysis of Peptidoglycan from Living Animals.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.07.21.549941}, pmid = {37693563}, abstract = {The role of the intestinal microbiota in host health is increasingly revealed in its contributions to disease states. The host-microbiome interaction is multifactorial and dynamic. One of the factors that has recently been strongly associated with host physiological responses is peptidoglycan from bacterial cell walls. Peptidoglycan from gut commensal bacteria activate peptidoglycan sensors in human cells, including the Nucleotide-binding oligomerization domain containing protein 2 (NOD2). When present in the gastrointestinal tract, both the polymeric form (sacculi) and de-polymerized fragments can modulate host physiology, including checkpoint anticancer therapy efficacy, body temperature and appetite, and postnatal growth. To leverage this growing area of biology towards therapeutic prescriptions, it will be critical to directly analyze a key feature of the host-microbiome interaction from living hosts in a reproducible and non-invasive way. Here we show that metabolically labeled peptidoglycan/sacculi can be readily isolated from fecal samples collected from both mice and humans. Analysis of fecal samples provided a non-invasive route to probe the gut commensal community including the metabolic synchronicity with the host circadian clock. Together, these results pave the way for non-invasive diagnostic tools to interrogate the causal nature of peptidoglycan in host health and disease.}, }
@article {pmid37693522, year = {2023}, author = {Célio Dias, SJ and Marcelo Der Torossian, T and Yiqian, D and Álvaro, RDR and Thomas S B, S and Hui, C and Anthony, F and Michael, K and Chengkai, Z and Amy, H and Jelena, S and Anna, V and Xing-Ming, Z and Peer, B and Jaime, HC and Cesar, FN and Luis Pedro, C}, title = {Computational exploration of the global microbiome for antibiotic discovery.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.31.555663}, pmid = {37693522}, abstract = {Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine learning-based approach to predict prokaryotic antimicrobial peptides (AMPs) by leveraging a vast dataset of 63,410 metagenomes and 87,920 microbial genomes. This led to the creation of AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, the majority of which were previously unknown. We observed that AMP production varies by habitat, with animal-associated samples displaying the highest proportion of AMPs compared to other habitats. Furthermore, within different human-associated microbiota, strain-level differences were evident. To validate our predictions, we synthesized and experimentally tested 50 AMPs, demonstrating their efficacy against clinically relevant drug-resistant pathogens both in vitro and in vivo. These AMPs exhibited antibacterial activity by targeting the bacterial membrane. Additionally, AMPSphere provides valuable insights into the evolutionary origins of peptides. In conclusion, our approach identified AMP sequences within prokaryotic microbiomes, opening up new avenues for the discovery of antibiotics.}, }
@article {pmid37693491, year = {2023}, author = {Lazzaro, A and Colorado, ASB and Neff, CP and Nusbacher, N and Boyd, K and Fiorillo, S and Martin, C and Siebert, J and Campbell, T and Borok, M and Palmer, B and Lozupone, C}, title = {Antiretroviral treatment is less effective at reducing gut microbiome-associated inflammation and T cell activation in people living with HIV in rural versus urban Zimbabwe.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-3300723/v1}, pmid = {37693491}, abstract = {The widespread availability of antiretroviral therapy (ART) for people living with HIV (PLWH) has dramatically reduced mortality and improved life expectancy. However, even with suppression of HIV-1 replication, chronic immune activation and elevated inflammation persist. Chronic immune activation has been linked to a pro-inflammatory gut microbiome composition, exacerbated by compromised intestinal barrier integrity that occurs after HIV infection. Individuals living in urban versus rural areas of sub-Saharan Africa have differences in environmental factors such as water source or diet that may impact gut microbiome composition, yet immune phenotype and gut microbiome composition response to ART in PLWH living in rural versus urban areas of sub-Saharan Africa have not been compared. Here, we measured immune phenotypes and fecal microbiome composition in PLWH and healthy participants recruited from the urban Mabvuku polyclinic in the city of Harare, Zimbabwe and the Mutoko District hospital located in a district 146 km from Harare that services surrounding rural villages. PLWH were either ART naïve at baseline and sampled again after 24 weeks of treatment with efavirenz/lamivudine/tenofovir disoproxil fumarate (EFV/3TC/TDF) and the prophylactic antibiotic cotrimoxazole or were ART experienced at both timepoints. Although expected reductions in the inflammatory marker IL-6, T-cell activation, and exhaustion were observed in individuals who had suppressed HIV-1 with treatment, these changes were significant only when considering individuals in the urban and not the rural area. Gut microbiome composition showed more marked differences from healthy controls in the ART experienced compared to ART naïve cohort, and consistent longitudinal changes were also observed in ART naïve PLWH after 24 weeks of treatment, including a reduction in alpha diversity and altered composition. However, gut microbiome composition showed a more pronounced relationship with chronic immune activation and exhaustion phenotypes in the ART naïve compared to ART experienced PLWH, suggesting a particularly significant role for the gut microbiome in disease progression in uncontrolled infection.}, }
@article {pmid37693399, year = {2023}, author = {Torres, MDT and Brooks, E and Cesaro, A and Sberro, H and Nicolaou, C and Bhatt, AS and de la Fuente-Nunez, C}, title = {Human gut metagenomic mining reveals an untapped source of peptide antibiotics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.31.555711}, pmid = {37693399}, abstract = {Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally mined 444,054 families of putative small proteins from 1,773 human gut metagenomes, identifying 323 peptide antibiotics encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro , with 59% displaying activity against either pathogens or commensals. Since these peptides were unique compared to previously reported antimicrobial peptides, we termed them s mORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergized with each other, and modulated gut commensals, indicating that they may play a role in reconfiguring microbiome communities in addition to counteracting pathogens. The lead candidates were anti-infective in both murine skin abscess and deep thigh infection models. Notably, prevotellin-2 from Prevotella copri presented activity comparable to the commonly used antibiotic polymyxin B. We report the discovery of hundreds of peptide sequences in the human gut.}, }
@article {pmid37692610, year = {2023}, author = {Okoye, C and Tran, M and Soladoye, E and Akahara, DE and Emeasoba, CM and Ojinna, BT and Anasonye, E and Obadare, OO and Diala, CS and Salaudeen, BH and Evbayekha, EO and Okobi, OE}, title = {A Review of 10-Year Survivability of Immunotherapy in the Management of Colon Cancer.}, journal = {Cureus}, volume = {15}, number = {8}, pages = {e43189}, pmid = {37692610}, issn = {2168-8184}, abstract = {Colon cancer is one of the most common cancers in the United States of America. In addition to conventional treatment approaches such as surgery, chemotherapy, and radiation for colorectal cancer, immunotherapy has gained recognition over the past few years. However, its effectiveness in colorectal cancer treatment is controversial. Our study investigates the survival and progression-free rates of immunotherapy for different types of colorectal cancer over the last 10 years. We conducted literature reviews from various clinical trials and research studies to evaluate immunotherapy's role in colorectal cancer treatment. We also investigated how it affects clinical outcomes. We discovered a range of effective immunotherapy approaches targeting various growth factors and signaling pathways. These modalities include monoclonal antibodies aimed at growth factors such as epidermal growth factor (EGF), vascular endothelial growth factor (VEGF), hepatocyte growth factor (HGF), human epidermal growth factor receptor 2 (HER2), and downstream signaling pathways such as mitogen-activated protein kinase (MAPK), kirsten rat sarcoma viral oncogene (KRAS), B-raf proto-oncogene, serine/threonine kinase (BRAF), and phosphatase and tensin homolog (PTEN). Additionally, we identified immune checkpoint inhibitors, such as cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) inhibitors and programmed cell death ligand 1 (PD-L1) inhibitors, as well as target therapy and adoptive cell therapy as promising immunotherapeutic options. Nevertheless, the application of immunotherapy remains highly limited due to various factors influencing survival and progression-free rates, including tumor microenvironment, microsatellite instability, immune checkpoint expression, and gut microbiome. Additionally, its effectiveness is restricted to a small subgroup of patients, accompanied by side effects and the development of drug resistance mechanisms. To unlock its full potential, further clinical trials and research on molecular pathways in colorectal cancer are imperative. This will ultimately enhance drug discovery success and lead to more effective clinical management approaches.}, }
@article {pmid37692426, year = {2023}, author = {Senizza, B and Araniti, F and Lewin, S and Wende, S and Kolb, S and Lucini, L}, title = {Trichoderma spp.-mediated mitigation of heat, drought, and their combination on the Arabidopsis thaliana holobiont: a metabolomics and metabarcoding approach.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1190304}, doi = {10.3389/fpls.2023.1190304}, pmid = {37692426}, issn = {1664-462X}, abstract = {INTRODUCTION: The use of substances to increase productivity and resource use efficiency is now essential to face the challenge of feeding the rising global population with the less environmental impact on the ecosystems. Trichoderma-based products have been used as biopesticides, to inhibit pathogenic microorganisms, and as biostimulants for crop growth, nutrient uptake promotion, and resistance to abiotic stresses.<br><br>METHODS: In this work, plant metabolomics combined with roots and rhizosphere bacterial metabarcoding were exploited to inspect the performance of Trichoderma spp. biostimulants on Arabidopsis thaliana under drought, heat and their combination and its impact on plant holobiont.<br><br>RESULTS AND DISCUSSION: An overall modulation of N-containing compounds, phenylpropanoids, terpenes and hormones could be pointed out by metabolomics. Moreover, metabarcoding outlined an impact on alpha and beta-diversity with an abundance of Proteobacteria, Pseudomonadales, Burkholderiales, Enterobacteriales and Azospirillales. A holobiont approach was applied as an integrated analytical strategy to resolve the coordinated and complex dynamic interactions between the plant and its rhizosphere bacteria using Arabidopsis thaliana as a model host species.}, }
@article {pmid37692393, year = {2023}, author = {Zhang, MY and Zhang, XH and Wang, XY and Liu, YL and An, JH and Wang, DH and Cai, ZG and Hou, R}, title = {Intestinal acetic acid regulates the synthesis of sex pheromones in captive giant pandas.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1234676}, doi = {10.3389/fmicb.2023.1234676}, pmid = {37692393}, issn = {1664-302X}, abstract = {As a typical solitary animal, adult giant pandas rely on chemical signals (sex pheromones) to transmit reproductive information during oestrous. Although researchers have confirmed that the gut microbiota is related to the emission and reception of sex pheromones, there is no clear correlation between the gut microbes and the synthesis of sex pheromone of giant pandas, that is, which gut microbes and microbial metabolites are participate in the synthesis of giant panda's sex pheromone. As a mirror of gut microbiota, fecal microbiota can reflect the composition of gut microbiota and its interaction with host to some extent. The purpose of this study is to explore how the gut microbes affect the synthesis of sex pheromones in captive giant pandas by combining analysis of the fecal microbiome and metabolomics. The results of correlation and microbial function analysis show that intestinal microorganisms such as Veillonellaceae and Lactobacillilaceae are associated with the synthesis of short chain fatty acid (acetic acid) and volatile ester metabolites, such as 1-butanol, 3-methyl, acetate, acetic acid, hexyl ester and 3-hexen-1-ol, acetate, (Z). In summary, based on this study, we believe that volatile metabolites such as fecal acetate participate in the process of mate preference of captive giant pandas and affect their expression of natural mating behavior. The possible mechanism is that the gut microbes can promote the synthesis of key chemical signaling substances in perianal glands through mediated intermediate fecal metabolites, thus affecting the normal information exchange between giant pandas individuals. The results of this study have greatly enriched our understanding of gut microbes regulating the synthesis of sex pheromones in giant pandas.}, }
@article {pmid37692387, year = {2023}, author = {Wang, X and Zheng, Y and Chen, X and Peng, C and Zhou, S and Shen, S and Zhao, S and Wang, T}, title = {2bRAD-M reveals the difference in microbial distribution between cancerous and benign ovarian tissues.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1231354}, doi = {10.3389/fmicb.2023.1231354}, pmid = {37692387}, issn = {1664-302X}, abstract = {The development of ovarian cancer is closely related to various factors, such as environmental, genetic and microbiological factors. In previous research, bacteria were identified in human tumors by 16S rRNA sequencing. However, the microbial biomass in tumor tissue is too low and cannot be accurately identified by 16S rRNA sequencing. In our study, we employ 2bRAD sequencing for Microbiome (2bRAD-M), a new sequencing technology capable of accurately characterizing the low biomass microbiome (bacteria, fungi and archaea) at species resolution. Here we surveyed 20 ovarian samples, including 10 ovarian cancer samples and 10 benign ovarian samples. The sequencing results showed that a total of 373 microbial species were identified in both two groups, of which 90 species shared in the two groups. The Meta statistic indicated that Chlamydophila_abortus and CAG-873_sp900550395 were increased in the ovarian cancer tissues, while Lawsonella_clevelandensis_A, Ralstonia_sp001078575, Brevundimonas_aurantiaca, Ralstonia_sp900115545, Ralstonia_pickettii, Corynebacterium_kefirresidentii, Corynebacterium_sp000478175, Brevibacillus_D_fluminis, Ralstonia_sp000620465, and Ralstonia_mannitolilytica were more abundant in the benign ovarian tissues. This is the first use of 2bRAD-M technique to provide an important hint for better understanding of the ovarian cancer microbiome.}, }
@article {pmid37692382, year = {2023}, author = {Amon, CER and Fossou, RK and Ebou, AET and Koua, DK and Kouadjo, CG and Brou, YC and Voko Bi, DRR and Cowan, DA and Zézé, A}, title = {The core bacteriobiome of Côte d'Ivoire soils across three vegetation zones.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1220655}, doi = {10.3389/fmicb.2023.1220655}, pmid = {37692382}, issn = {1664-302X}, abstract = {The growing understanding that soil bacteria play a critical role in ecosystem servicing has led to a number of large-scale biogeographical surveys of soil microbial diversity. However, most of such studies have focused on northern hemisphere regions and little is known of either the detailed structure or function of soil microbiomes of sub-Saharan African countries. In this paper, we report the use of high-throughput amplicon sequencing analyses to investigate the biogeography of soil bacteria in soils of Côte d'Ivoire. 45 surface soil samples were collected from Côte d'Ivoire, representing all major biomes, and bacterial community composition was assessed by targeting the V4-V5 hypervariable region of the 16S ribosomal RNA gene. Causative relationships of both soil physicochemical properties and climatic data on bacterial community structure were infered. 48 phyla, 92 classes, 152 orders, 356 families, and 1,234 genera of bacteria were identified. The core bacteriobiome consisted of 10 genera ranked in the following order of total abundance: Gp6, Gaiella, Spartobacteria_genera_incertae_sedis, WPS-1_genera_incertae_sedis, Gp4, Rhodoplanes, Pseudorhodoplanes, Bradyrhizobium, Subdivision3_genera_incertae_sedis, and Gp3. Some of these genera, including Gp4 and WPS-1_genera_incertae_sedis, were unequally distributed between forest and savannah areas while other taxa (Bradyrhizobium and Rhodoplanes) were consistently found in all biomes. The distribution of the core genera, together with the 10 major phyla, was influenced by several environmental factors, including latitude, pH, Al and K. The main pattern of distribution that was observed for the core bacteriobiome was the vegetation-independent distribution scheme. In terms of predicted functions, all core bacterial taxa were involved in assimilatory sulfate reduction, while atmospheric dinitrogen (N2) reduction was only associated with the genus Bradyrhizobium. This work, which is one of the first such study to be undertaken at this scale in Côte d'Ivoire, provides insights into the distribution of bacterial taxa in Côte d'Ivoire soils, and the findings may serve as biological indicator for land management in Côte d'Ivoire.}, }
@article {pmid37692284, year = {2023}, author = {Li, Y and Wang, J and Wang, R and Chang, Y and Wang, X}, title = {Gut bacteria induce IgA expression in pituitary hormone-secreting cells during aging.}, journal = {iScience}, volume = {26}, number = {10}, pages = {107747}, doi = {10.1016/j.isci.2023.107747}, pmid = {37692284}, issn = {2589-0042}, abstract = {Pituitary hormone decline is a hallmark of aging. However, the precise gene regulation mechanism during pituitary aging is unclear. Here, we characterized the cell population alteration and global transcriptional change during pituitary aging through single-cell RNA sequencing (scRNA-seq). We found that mRNA-encoding components of protein translational machinery declined the most in the pituitary during aging. Remarkably, Immunoglobulin A (IgA) was found to be expressed in hormone-secreting cells, and the IgA expression level increased dramatically in aged pituitary. Moreover, the pituitary IgA expression was regulated by gut microbiota. The non-hematopoietic origin of the IgA+ cells in the pituitary was further confirmed through bone marrow transplantation. Somatotropes were identified as the most prominent IgA-producing cells through lineage tracing. Thus, pituitary hormone-secreting cells can generate IgA in an age-dependent manner, and such a process is influenced by gut bacteria.}, }
@article {pmid37692200, year = {2023}, author = {Zeldin, J and Tran, TT and Yadav, M and Chaudhary, PP and D'Souza, BN and Ratley, G and Ganesan, S and Myles, IA}, title = {Antimony Compounds Associate with Atopic Dermatitis and Influence Models of Itch and Dysbiosis.}, journal = {Environmental science &amp; technology letters}, volume = {10}, number = {5}, pages = {452-457}, doi = {10.1021/acs.estlett.3c00142}, pmid = {37692200}, issn = {2328-8930}, abstract = {Compared to the myriad of known triggers for rhinitis and asthma, environmental exposure research for atopic dermatitis (AD) is not well established. We recently reported that an untargeted search of U.S. Environmental Protection Agency (EPA) databases versus AD rates by United States (U.S.) postal codes revealed that isocyanates, such as toluene diisocyanate (TDI), are the pollutant class with the strongest spatiotemporal and epidemiologic association with AD. We further demonstrated that (di)isocyanates disrupt ceramide-family lipid production in commensal bacteria and activate the thermo-itch host receptor TRPA1. In this report, we reanalyzed regions of the U.S. with low levels of diisocyanate pollution to assess if a different chemical class may contribute. We identified antimony compounds as the top associated pollutant in such regions. Exposure to antimony compounds would be expected from brake dust in high-traffic areas, smelting plants, bottled water, and dust from aerosolized soil. Like TDI, antimony inhibited ceramide-family lipid production in Roseomonas mucosa and activated TRPA1 in human neurons. While further epidemiologic research will be needed to directly evaluate antimony exposure with surrounding AD prevalence and severity, these data suggest that compounds which are epidemiologically associated with AD, inhibit commensal lipid production, and activate TRPA1 may be causally related to AD pathogenesis.}, }
@article {pmid37692082, year = {2023}, author = {Liu, Y and Liang, Y and Li, Q and Li, Q}, title = {Comprehensive analysis of circulating cell-free RNAs in blood for diagnosing non-small cell lung cancer.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {4238-4251}, doi = {10.1016/j.csbj.2023.08.029}, pmid = {37692082}, issn = {2001-0370}, abstract = {Early screening and detection of non-small cell lung cancer (NSCLC) is crucial due to the significantly low survival rate in advanced stages. Blood-based liquid biopsy is non-invasive test to assistant disease diagnosis, while cell-free RNA is one of the promising biomarkers in blood. However, the disease related signatures have not been explored completely for most cell-free RNA transcriptome sequencing (cfRNA-Seq) datasets. To address this gap, we developed a comprehensive cfRNA-Seq pipeline for data analysis and constructed a machine learning model to facilitate noninvasive early diagnosis of NSCLC. The results of our study have demonstrated the identification of differential mRNA, lncRNAs and miRNAs from cfRNA-Seq, which have exhibited significant association with development and progression of lung cancer. The classifier based on gene expression signatures achieved an impressive area under the curve (AUC) of up to 0.9, indicating high specificity and sensitivity in both cross-validation and independent test. Furthermore, the analysis of T cell and B cell immune repertoire extracted from cfRNA-Seq have provided insights into the immune status of cancer patients, while the microbiome analysis has revealed distinct bacterial and viral profiles between NSCLC and normal samples. In our future work, we aim to validate the existence of cancer associated T cell receptors (TCR)/B cell receptors (BCR) and microorganisms, and subsequently integrate all identified signatures into diagnostic model to improve the prediction accuracy. This study not only provided a comprehensive analysis pipeline for cfRNA-Seq dataset but also highlights the potential of cfRNAs as promising biomarkers and models for early NSCLC diagnosis, emphasizing their importance in clinical settings.}, }
@article {pmid37692080, year = {2023}, author = {Sun, Z and Ning, Z and Cheng, K and Duan, H and Wu, Q and Mayne, J and Figeys, D}, title = {MetaPep: A core peptide database for faster human gut metaproteomics database searches.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {4228-4237}, doi = {10.1016/j.csbj.2023.08.025}, pmid = {37692080}, issn = {2001-0370}, abstract = {Metaproteomics has increasingly been applied to study functional changes in the human gut microbiome. Peptide identification is an important step in metaproteomics research, with sequence database search (SDS) and spectral library search (SLS) as the two main methods to identify peptides. However, the large search space in metaproteomics studies causes significant challenges for both identification methods. Moreover, with the development of mass spectrometry, it is now feasible to perform metaproteomic projects involving 100-1000 individual microbiomes. These large-scale projects create a conundrum for searching large databases. In this study, we constructed MetaPep, a core peptide database (including both collections of peptide sequences and tandem MS spectra) greatly accelerating the peptide identifications. Raw files from fifteen metaproteomics projects were re-analyzed and the identified peptide-spectrum matches (PSMs) were used to construct the MetaPep database. The constructed MetaPep database achieved rapid and accurate identification of peptides for human gut metaproteomics. MetaPep has a large collection of peptides and spectra that have been identified in published human gut metaproteomics datasets. MetaPep database can be used as an important resource in the current stage of human gut metaproteomics research. This study showed the possibility of applying a core peptide database as a generic metaproteomics workflow. MetaPep could also be an important resource for future human gut metaproteomics research, such as DIA (data-independent acquisition) analysis.}, }
@article {pmid37691931, year = {2023}, author = {Xue, X and Li, R and Chen, Z and Li, G and Liu, B and Guo, S and Yue, Q and Yang, S and Xie, L and Zhang, Y and Zhao, J and Tan, R}, title = {The role of the symbiotic microecosystem in cancer: gut microbiota, metabolome, and host immunome.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1235827}, doi = {10.3389/fimmu.2023.1235827}, pmid = {37691931}, issn = {1664-3224}, abstract = {The gut microbiota is not just a simple nutritional symbiosis that parasitizes the host; it is a complex and dynamic ecosystem that coevolves actively with the host and is involved in a variety of biological activities such as circadian rhythm regulation, energy metabolism, and immune response. The development of the immune system and immunological functions are significantly influenced by the interaction between the host and the microbiota. The interactions between gut microbiota and cancer are of a complex nature. The critical role that the gut microbiota plays in tumor occurrence, progression, and treatment is not clear despite the already done research. The development of precision medicine and cancer immunotherapy further emphasizes the importance and significance of the question of how the microbiota takes part in cancer development, progression, and treatment. This review summarizes recent literature on the relationship between the gut microbiome and cancer immunology. The findings suggest the existence of a "symbiotic microecosystem" formed by gut microbiota, metabolome, and host immunome that is fundamental for the pathogenesis analysis and the development of therapeutic strategies for cancer.}, }
@article {pmid37691844, year = {2023}, author = {Hegde, S and Rauch, HE and Hughes, GL and Shariat, N}, title = {Identification and characterization of two CRISPR/Cas systems associated with the mosquito microbiome.}, journal = {Access microbiology}, volume = {5}, number = {8}, pages = {}, doi = {10.1099/acmi.0.000599.v4}, pmid = {37691844}, issn = {2516-8290}, abstract = {The microbiome profoundly influences many traits in medically relevant vectors such as mosquitoes, and a greater functional understanding of host-microbe interactions may be exploited for novel microbial-based approaches to control mosquito-borne disease. Here, we characterized two novel clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems in Serratia sp. Ag1, which was isolated from the gut of an Anopheles gambiae mosquito. Two distinct CRISPR/Cas systems were identified in Serratia Ag1, CRISPR1 and CRISPR2. Based on cas gene composition, CRISPR1 is classified as a type I-E CRISPR/Cas system and has a single array, CRISPR1. CRISPR2 is a type I-F system with two arrays, CRISPR2.1 and CRISPR2.2. RT-PCR analyses show that all cas genes from both systems are expressed during logarithmic growth in culture media. The direct repeat sequences of CRISPRs 2.1 and 2.2 are identical and found in the arrays of other Serratia spp., including S. marcescens and S. fonticola , whereas CRISPR1 is not. We searched for potential spacer targets and revealed an interesting difference between the two systems: only 9 % of CRISPR1 (type I-E) targets are in phage sequences and 91 % are in plasmid sequences. Conversely, ~66 % of CRISPR2 (type I-F) targets are found within phage genomes. Our results highlight the presence of CRISPR loci in gut-associated bacteria of mosquitoes and indicate interplay between symbionts and invasive mobile genetic elements over evolutionary time.}, }
@article {pmid37691753, year = {2023}, author = {Malik, A and Malik, MI}, title = {Fecal Microbiota Transplantation in Human Immunodeficiency Virus-Infected Patient Population: A Systematic Review and Meta-Analysis.}, journal = {Gastroenterology research}, volume = {16}, number = {4}, pages = {209-216}, doi = {10.14740/gr1624}, pmid = {37691753}, issn = {1918-2805}, abstract = {BACKGROUND: Patients with human immunodeficiency virus (HIV) infection suffer from alterations in gut microbiota due to recurrent gastrointestinal infections and systemic inflammation. Fecal microbiota transplantation (FMT) appears to be a potential therapy; however, there are concerns about its safety. Likewise, no previous meta-analysis evaluated FMT efficacy in HIV-infected patients.<br><br>METHODS: We conducted a thorough electronic search on PubMed, Scopus, OVID, Web of Science, and Cochrane CENTRAL for clinical studies assessing the safety and efficacy of FMT in patients with HIV and gastrointestinal dysbiosis, where FMT was indicated to restore the disrupted microbiota.<br><br>RESULTS: FMT significantly restored the typical microbiome in patients with Clostridium difficile (C. difficile) and non-C. difficile and reduced the risk of gastrointestinal infections in HIV patients receiving antiretroviral therapy (odds ratio (OR) = 0.774, 95% confidence interval (CI): (0.62, 0.966)). Furthermore, adverse events, such as distention and bloating, associated with FMT were comparable between HIV and health controls (OR = 0.60, 95% CI: (0.07, 4.6)), with no statistical difference.<br><br>CONCLUSIONS: Current evidence demonstrated that FMT is safe and effective in HIV patients suffering from alterations in gut microbiota. We recommend further multi-centric clinical studies to address the optimal transplant amount and source for FMT. To the best of our knowledge, this is the first meta-analysis to assess the safety and efficacy of FMT in patients with HIV.}, }
@article {pmid37691735, year = {2023}, author = {Orenstein, R and Hecht, G and Harvey, A and Tillotson, G and Khanna, S}, title = {Two-year durability of REBYOTA™ (RBL), a live biotherapeutic for the prevention of recurrent Clostridioides difficile infections.}, journal = {Open forum infectious diseases}, volume = {10}, number = {9}, pages = {ofad456}, doi = {10.1093/ofid/ofad456}, pmid = {37691735}, issn = {2328-8957}, }
@article {pmid37691669, year = {2023}, author = {Pindling, S and Klugman, M and Lan, Q and Hosgood, HD}, title = {Narrative review: respiratory tract microbiome and never smoking lung cancer.}, journal = {Journal of thoracic disease}, volume = {15}, number = {8}, pages = {4522-4529}, doi = {10.21037/jtd-22-885}, pmid = {37691669}, issn = {2072-1439}, abstract = {BACKGROUND AND OBJECTIVE: The lung microbiome was previously thought to be a sterile environment where only gaseous exchange takes place, but recent studies have shown the presence of microbiota in the lung. This review investigates the current literature on the effects of an environmental driven dysbiosis on the healthy oral and respiratory microbiome and its relationship to lung cancer risk in never-smokers.<br><br>METHODS: An online electronic search was performed on PubMed of all English-language literature using combinations of the following keywords: "lung cancer", "dysbiosis", "non-smokers", "oral microbiome", and "respiratory microbiome". All population-based studies reporting results on oral and/or respiratory microbiome in adults were considered for our narrative review.<br><br>KEY CONTENT AND FINDINGS: Metagenomic analyses have been performed on isolated samples from healthy participants and compared to samples from those with lung cancer. Research shows that a decrease in alpha diversity of microbes in the oral microbiome is associated with increased risk of lung cancer, along with differences in beta diversity in the sputum of lung cancer cases and healthy controls. Further, several studies have observed that significant changes in the abundance of genera such as increased abundance of Lactobacillales, Bacilli, and Firmicutes associated with an increased lung cancer risk among participants with exposure to certain household solid fuels.<br><br>CONCLUSIONS: These findings suggest potential carcinogenic processes such as increased inflammation associated with changes in flora. Additionally, studies showed that increase in certain taxa such as Bacteroides and Spirochetes might have a protective effect on lung cancer risk. The review also provides insight into how understanding the microbial changes can be beneficial for lung cancer treatment and disease-free survival. Larger studies in different populations need to be performed to strengthen the current associations between microbial diversity and lung cancer risk.}, }
@article {pmid37691637, year = {2023}, author = {Kim, KR and Kim, SM and Kim, JH}, title = {A pilot study of alterations of the gut microbiome in canine chronic kidney disease.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1241215}, doi = {10.3389/fvets.2023.1241215}, pmid = {37691637}, issn = {2297-1769}, abstract = {INTRODUCTION: Gut dysbiosis has been noted in humans and animals with chronic kidney disease (CKD). However, little is known about the gut microbiome in canine patients with CKD. This study aimed to analyze and compare the gut microbiome profiles of healthy and CKD dogs, including differences in the gut microbiome between each CKD stage.<br><br>METHODS: The study was conducted on 29 client-owned dogs who underwent physical examination, complete blood count (CBC), serum biochemistry, and urinalysis. The gut microbiome profile of healthy dogs (n&#x2009;=&#x2009;10) and dogs with CKD (n&#x2009;=&#x2009;19) was analyzed employing 16S rRNA sequencing.<br><br>RESULTS: Significant differences were seen in the composition of the gut microbiome, with increased operational taxonomic units from the phylum Proteobacteria (p&#x2009;=&#x2009;0.035), family Enterobacteriaceae (p&#x2009;<&#x2009;0.001), and genus Enterococcus (p&#x2009;=&#x2009;0.002) in dogs with CKD, and a decrease in the genus Ruminococcus (p&#x2009;=&#x2009;0.007). Furthermore, an increase in both the progression of CKD and abundance of genus Klebsiella (Jonckheere-Terpstra test statistic value (JT)&#x2009;=&#x2009;2.852, p&#x2009;=&#x2009;0.004) and Clostridium (JT&#x2009;=&#x2009;2.018, p&#x2009;=&#x2009;0.044) was observed.<br><br>DISCUSSION: Our study demonstrated that in dogs with CKD, the composition of the gut microbiome varied depending on the stage of CKD. Alterations in gut microbiome composition observed in CKD patients are characterized by an increase in proteolytic bacteria and a decrease in saccharolytic bacteria. These findings suggest specific gut microbiota could be targeted for clinical management of uremic dogs with CKD.}, }
@article {pmid37691412, year = {2023}, author = {Bernabeu, M and Gharibzahedi, SMT and Ganaie, AA and Macha, MA and Dar, BN and Castagnini, JM and Garcia-Bonillo, C and Meléndez-Martínez, AJ and Altintas, Z and Barba, FJ}, title = {The potential modulation of gut microbiota and oxidative stress by dietary carotenoid pigments.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/10408398.2023.2254383}, pmid = {37691412}, issn = {1549-7852}, abstract = {Gut microbiota plays a crucial role in regulating the response to immune checkpoint therapy, therefore modulation of the microbiome with bioactive molecules like carotenoids might be a very effective strategy to reduce the risk of chronic diseases. This review highlights the bio-functional effect of carotenoids on Gut Microbiota modulation based on a bibliographic search of the different databases. The methodology given in the preferred reporting items for systematic reviews and meta-analyses (PRISMA) has been employed for developing this review using papers published over two decades considering keywords related to carotenoids and gut microbiota. Moreover, studies related to the health-promoting properties of carotenoids and their utilization in the modulation of gut microbiota have been presented. Results showed that there can be quantitative changes in intestinal bacteria as a function of the type of carotenoid. Due to the dependency on several factors, gut microbiota continues to be a broad and complex study subject. Carotenoids are promising in the modulation of Gut Microbiota, which favored the appearance of beneficial bacteria, resulting in the protection of villi and intestinal permeability. In conclusion, it can be stated that carotenoids may help to protect the integrity of the intestinal epithelium from pathogens and activate immune cells.}, }
@article {pmid37690926, year = {2023}, author = {Jiang, L and Fan, JG}, title = {The role of the gut microbiome in chronic liver diseases: Present insights and future outlook.}, journal = {Hepatobiliary &amp; pancreatic diseases international : HBPD INT}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.hbpd.2023.09.003}, pmid = {37690926}, issn = {1499-3872}, }
@article {pmid37690859, year = {2023}, author = {Gangneux, JP and Rhodes, JL and Papon, N}, title = {Airway microbiome: environmental exposure-respiratory health nexus.}, journal = {Trends in molecular medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molmed.2023.08.011}, pmid = {37690859}, issn = {1471-499X}, abstract = {Toxicants such as smoke, biofuel, and pollutants constantly challenge our respiratory health, but little is known about the pathophysiological processes involved. In a new report, Lin et al. provide evidence that our bacterial and fungal lung populations orchestrate the interplay between environmental exposure and lung functions, thereby conditioning health outcomes.}, }
@article {pmid37690850, year = {2023}, author = {Inoue, D and Nakamura, S and Sugiyama, T and Ike, M}, title = {Potential of Predatory Bacteria to Colonize the Duckweed Microbiome and Change Its Structure: A Model Study Using the Obligate Predatory Bacterium, Bacteriovorax sp. HI3.}, journal = {Microbes and environments}, volume = {38}, number = {3}, pages = {}, doi = {10.1264/jsme2.ME23040}, pmid = {37690850}, issn = {1347-4405}, abstract = {Modifying the duckweed microbiome is a major challenge for enhancing the effectiveness of duckweed-based wastewater treatment and biomass production technologies. We herein examined the potential of the exogenous introduction of predatory bacteria to change the duckweed microbiome. Bacteriovorax sp. HI3, a model predatory bacterium, colonized the core of the Lemna microbiome, and its predatory behavior changed the microbiome structure, which correlated with colonization density. These results reveal that bacterial predatory interactions may be important drivers that shape the duckweed microbiome, suggesting their potential usefulness in modifying the microbiome.}, }
@article {pmid37690725, year = {2023}, author = {Zhu, SL and Gu, FF and Tang, YF and Liu, XH and Jia, MH and Valencak, TG and Liu, JX and Sun, HZ}, title = {Dynamic fecal microenvironment properties enable predictions and understanding of peripartum blood oxidative status and non-esterified fatty acids in dairy cows.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2022-23066}, pmid = {37690725}, issn = {1525-3198}, abstract = {The transition period in dairy cows is a critical stage and peripartum oxidative status, negative energy balance (NEB) and inflammation are highly prevalent. Fecal microbial metabolism is closely associated with blood oxidative status and nonesterified fatty acids (NEFA) levels. Here, we investigated dynamic changes in total oxidative status markers and NEFA in blood, fecal microbiome and metabolome of 30 dairy cows during transition (-21d, -7d, +7d, +21d relative to calving). Then the Bayesian network and 9 machine learning algorithms were applied to dismantle their relationship. Our results show that the oxidative status indicator (OSI) of -21d, -7d, +7d was higher than +21d (P < 0.001). The plasma concentration of nonesterified fatty acids (NEFA) peaked on +7d (P < 0.001). For fecal microenvironment, a decline in bacterial α diversity was observed at postpartum (P < 0.001) and in bacterial interactions at +7d (P = 0.014). Conversely, microbial metabolites involved in carbohydrate, lipid and energy metabolism increased on +7d (P < 0.05). A correlation analysis revealed that 11 and 10 microbial metabolites contributed to OSI and NEFA variations, respectively (Arc. strength >0.5). The support vector machine (SVM) radial model showed the highest average predictive accuracy (100% and 88.9% in the test and external data sets) for OSI using 1 metabolite and 3 microbiota. SVM radial model also showed the highest average diagnostic accuracy (100% and 91% in the test and external data sets) for NEFA with 2 metabolites and 3 microbiota. Our results reveal a relationship between variation in the fecal microenvironment and indicators of oxidative status, NEB and inflammation, which provide a theoretical basis for the prevention and precise regulation of peripartum oxidative status and NEB.}, }
@article {pmid37690584, year = {2023}, author = {Borrego-Ruiz, A and Borrego, JJ}, title = {An updated overview on the relationship between human gut microbiome dysbiosis and psychiatric and psychological disorders.}, journal = {Progress in neuro-psychopharmacology &amp; biological psychiatry}, volume = {}, number = {}, pages = {110861}, doi = {10.1016/j.pnpbp.2023.110861}, pmid = {37690584}, issn = {1878-4216}, abstract = {There is a lot of evidence establishing that nervous system development is related to the composition and functions of the gut microbiome. In addition, the central nervous system (CNS) controls the imbalance of the intestinal microbiota, constituting a bidirectional communication system. At present, various gut-brain crosstalk routes have been described, including immune, endocrine and neural circuits via the vagal pathway. Several empirical data have associated gut microbiota alterations (dysbiosis) with neuropsychiatric diseases, such as Alzheimer's disease, autism and Parkinson's disease, and with other psychological disorders like anxiety, depression, and cognitive dysfunctions. Fecal microbiota transplantation (FMT) therapy has shown that the gut microbiota can transfer behavioral features to recipient animals, which provides strong evidence to establish a causal-effect relationship. Interventions, based on prebiotics, probiotics or synbiotics, have demonstrated an important influence of microbiota on neurological disorders by both the synthesis of neuroactive compounds that interact with the nervous system and by the regulation of inflammatory and endocrine processes. Further research is needed to demonstrate the influence of gut microbiota dysbiosis on psychiatric and psychological disorders, and how microbiota-based interventions may be used as potential therapeutic tools.}, }
@article {pmid37690443, year = {2023}, author = {Li, Y and Zou, C and Li, J and Wang, W and Wang, F and Guo, Y}, title = {Airway Microbiome Composition and Co-Occurrence Network Are Associated with Inflammatory Phenotypes of Asthma.}, journal = {International archives of allergy and immunology}, volume = {}, number = {}, pages = {1-10}, doi = {10.1159/000533315}, pmid = {37690443}, issn = {1423-0097}, abstract = {INTRODUCTION: The composition and co-occurrence network of the airway microbiome might influence the asthma inflammatory phenotype. Airway microbiota change with asthma phenotypes, and the structure of the bacterial community in the airway might differ between different asthma inflammatory phenotypes and may also influence therapy results. Identifying airway microbiota can help to investigate the role that microbiota play in the asthma inflammatory process.<br><br>METHODS: Induced sputum from 55 subjects and 12 healthy subjects from Beijing, China, was collected and analyzed for bacterial microbiota. Microbiome diversity, composition, co-occurrence networks, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were predicted and compared between the study groups.<br><br>RESULTS: Significant differences in the sputum microbiome composition, co-occurrence network, and predicted functional pathways were observed between the two inflammatory phenotypes. Asthmatics in the low FeNO group exhibited lower &#x3b1;-diversity in the sputum microbiota and had higher abundance of the phylum Proteobacteria compared with that of the high FeNO group. The network in the high FeNO group was more "closed" and "connected" compared with that of the low FeNO group, and an alteration in the abundance of keystone species T. socranskii was found. Significantly different predicted metabolic subfunctions including nucleotide metabolism, lipid metabolism, energy metabolism, replication and repair, and drug resistance antimicrobial and carbohydrate metabolism between the two studied phenotypes were also observed.<br><br>CONCLUSION: Our findings confirm that the airway microbiota is associated with the asthma inflammation process. The differences in the airway microbiome composition and co-occurrence network may affect distinct asthma inflammatory phenotypes, suggesting the possibility that more targeted therapies could be applied based on the airway bacterial genera.}, }
@article {pmid37690228, year = {2023}, author = {Zhang, Z and Lu, W and Liu, P and Li, M and Ge, X and Yu, B and Wu, Z and Liu, G and Ding, N and Cui, B and Chen, X}, title = {Microbial modifications with Lycium barbarum L. oligosaccharides decrease hepatic fibrosis and mitochondrial abnormalities in mice.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {120}, number = {}, pages = {155068}, doi = {10.1016/j.phymed.2023.155068}, pmid = {37690228}, issn = {1618-095X}, abstract = {BACKGROUND: Lycium barbarum L. is a typical Chinese herbal and edible plant and are now consumed globally. Low molecular weight L. barbarum L. oligosaccharides (LBO) exhibit better antioxidant activity and gastrointestinal digestibility in vitro than high molecular weight polysaccharides. However, the LBO on the treatment of liver disease is not studied.<br><br>PURPOSE: Modification of the gut microbial ecosystem by LBO is a promising treatment for liver fibrosis.<br><br>STUDY DESIGN AND METHODS: Herein, LBO were prepared and characterized. CCl4-treated mice were orally gavaged with LBO and the effects on hepatic fibrosis and mitochondrial abnormalities were evaluated according to relevant indicators (gut microbiota, faecal metabolites, and physiological and biochemical indices).<br><br>RESULTS: The results revealed that LBO, a potential prebiotic source, is a pyranose cyclic oligosaccharide possessing &#x3b1;-glycosidic and &#x3b2;-glycosidic bonds. Moreover, LBO supplementation restored the configuration of the bacterial community, enhanced the proliferation of beneficial species in the gastrointestinal tract (e.g., Bacillus, Tyzzerella, Fournierella and Coriobacteriaceae UCG-002), improved microbial metabolic alterations (i.e., carbohydrate metabolism, vitamin metabolism and entero-hepatic circulation), and increased antioxidants, including doxepin, in mice. Finally, LBO administration reduced serum inflammatory cytokine and hepatic hydroxyproline levels, improved intestinal and hepatic mitochondrial functions, and ameliorated mouse liver fibrosis.<br><br>CONCLUSION: These findings indicate that LBO can be utilized as a prebiotic and has a remarkable ability to mitigate liver fibrosis.}, }
@article {pmid37690105, year = {2023}, author = {Jackson, TW and House, JS and Henriquez, AR and Schladweiler, MC and Jackson, KM and Fisher, AA and Snow, SJ and Alewel, DI and Motsinger-Reif, AA and Kodavanti, UP}, title = {Multi-tissue transcriptomic and serum metabolomic assessment reveals systemic implications of acute ozone-induced stress response in male Wistar Kyoto rats.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {19}, number = {9}, pages = {81}, pmid = {37690105}, issn = {1573-3890}, support = {DE-SC0014664//Oak Ridge Institute for Science and Education/ ; DE-SC0014664//Oak Ridge Institute for Science and Education/ ; DE-SC0014664//Oak Ridge Institute for Science and Education/ ; }, abstract = {Air pollutant exposures have been linked to systemic disease; however, the underlying mechanisms between responses of the target tissue and systemic effects are poorly understood. A prototypic inducer of stress, ozone causes respiratory and systemic multiorgan effects through activation of a neuroendocrine stress response. The goal of this study was to assess transcriptomic signatures of multiple tissues and serum metabolomics to understand how neuroendocrine and adrenal-derived stress hormones contribute to multiorgan health outcomes. Male Wistar Kyoto rats (12-13 weeks old) were exposed to filtered air or 0.8 ppm ozone for 4-hours, and blood/tissues were collected immediately post-exposure. Each tissue had distinct expression profiles at baseline. Ozone changed 1,640 genes in lung, 274 in hypothalamus, 2,516 in adrenals, 1,333 in liver, 1,242 in adipose, and 5,102 in muscle (adjusted p-value < 0.1, absolute fold-change > 50%). Serum metabolomic analysis identified 863 metabolites, of which 447 were significantly altered in ozone-exposed rats (adjusted p-value < 0.1, absolute fold change > 20%). A total of 6 genes were differentially expressed in all 6 tissues. Glucocorticoid signaling, hypoxia, and GPCR signaling were commonly changed, but ozone induced tissue-specific changes in oxidative stress, immune processes, and metabolic pathways. Genes upregulated by TNF-mediated NFkB signaling were differentially expressed in all ozone-exposed tissues, but those defining inflammatory response were tissue-specific. Upstream predictor analysis identified common mediators of effects including glucocorticoids, although the specific genes responsible for these predictors varied by tissue. Metabolomic analysis showed major changes in lipids, amino acids, and metabolites linked to the gut microbiome, concordant with transcriptional changes identified through pathway analysis within liver, muscle, and adipose tissues. The distribution of receptors and transcriptional mechanisms underlying the ozone-induced stress response are tissue-specific and involve induction of unique gene networks and metabolic phenotypes, but the shared initiating triggers converge into shared pathway-level responses. This multi-tissue transcriptomic analysis, combined with circulating metabolomic assessment, allows characterization of the systemic inhaled pollutant-induced stress response.}, }
@article {pmid37689957, year = {2023}, author = {Wang, S and De Paepe, K and Van de Wiele, T and Fu, X and Wang, S and Zhang, B and Huang, Q}, title = {Starch-entrapped microspheres enhance gut microbiome-mediated anti-obesity effects of resistant starch in high-fat diet induced obese C57BL/6J mice.}, journal = {Food research international (Ottawa, Ont.)}, volume = {172}, number = {}, pages = {113215}, doi = {10.1016/j.foodres.2023.113215}, pmid = {37689957}, issn = {1873-7145}, mesh = {Animals ; Mice ; Mice, Inbred C57BL ; *Resistant Starch ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Dysbiosis ; Microspheres ; Obesity ; Starch/pharmacology ; Amylose ; }, abstract = {The prevalence of obesity is growing worldwide and has been extensively linked to gut microbiota dysbiosis. In addition to exercise and physical activity, fiber-rich foods may be a first-line prophylactic to manage obesity. This study investigated in vivo dietary intervention with high-amylose maize starch (HAMS) and starch-entrapped microspheres (MS) to treat high-fat diet induced metabolic disorder and gut microbiome dysbiosis in mice. MS more efficiently controlled body weight as well as adipose tissue mass compared to HAMS. Furthermore, MS significantly reduced blood glucose, insulin, lipid and pro-inflammatory cytokine levels compared to the high-fat diet, while the effects of HAMS were less pronounced. The MS-altered gut microbiota composition favoring Streptococcaceae, Bacilli, Firmicutes and unclassified Clostridiales was predicted to promote fatty acid, pantothenate and Coenzyme A biosynthesis. In line with this, elevated fecal short chain fatty acid (SCFA), in particular, propionate concentration was observed in MS-fed mice. Our study provides novel insights into the mechanistic action of MS on intestinal homeostasis, providing a basis for future dietary therapeutic applications.}, }
@article {pmid37689944, year = {2023}, author = {Wittwer, AE and Lee, SG and Ranadheera, CS}, title = {Potential associations between organic dairy products, gut microbiome, and gut health: A review.}, journal = {Food research international (Ottawa, Ont.)}, volume = {172}, number = {}, pages = {113195}, doi = {10.1016/j.foodres.2023.113195}, pmid = {37689944}, issn = {1873-7145}, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome ; Milk ; Biological Transport ; *Fatty Acids, Omega-3 ; Inflammation ; }, abstract = {Organic products have received longstanding, widespread attention for their nutritional and ecological benefits, as they are said to have certain positive health attributes and contain fewer harmful compounds than conventional (or non-organic) products. We reviewed the recent literature to examine potential associations between nutrient composition, gut microbiota, and gut health effects in recent comparative studies of organic and conventional dairy products. Trends of increased ratios of omega-3 to omega-6 polyunsaturated fatty acids and unsaturated to saturated fat, increased fat-soluble vitamin content, and decreased levels of certain pernicious contaminants in organic milk were observed across the studies reviewed. Studies of the metabolism of these nutrients in both in vitro and in vivo settings, and their or their metabolites' interaction with the intestinal epithelium show that nutrients enriched in organic dairy products may support host nutrient uptake and mediate gut inflammation. Research on the effects of single food products or classes of food products on gut health is rare. The extent of these benefits is highly likely to be mediated by both the magnitude of the difference in nutrient types and quantities, and by dietary intake levels of dairy products. Intervention studies directly examining the different effects of organic and conventional dairy products on gut health in humans are needed to further elucidate this relationship.}, }
@article {pmid37689914, year = {2023}, author = {Ye, J and Li, Y and Wang, X and Yu, M and Liu, X and Zhang, H and Meng, Q and Majeed, U and Jian, L and Song, W and Xue, W and Luo, Y and Yue, T}, title = {Positive interactions among Corynebacterium glutamicum and keystone bacteria producing SCFAs benefited T2D mice to rebuild gut eubiosis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {172}, number = {}, pages = {113163}, doi = {10.1016/j.foodres.2023.113163}, pmid = {37689914}, issn = {1873-7145}, mesh = {Animals ; Mice ; *Diabetes Mellitus, Type 2 ; *Corynebacterium glutamicum ; Fatty Acids, Volatile ; Butyrates ; Bacteria ; Levivirus ; }, abstract = {Accumulating evidences strongly support the correlations between the compositions of gut microbiome and therapeutic effects on Type 2 diabetes (T2D). Notably, gut microbes such as Akkermansia muciniphila are found able to regulate microecological balance and alleviate dysmetabolism of mice bearing T2D. In order to search out similarly functional bacteria, bacteriophage MS2 with a good specificity to bacteria carrying fertility (F) factor were used to treat T2D mice. Based on multi-omics analysis of microbiome and global metabolism of mice, we observed that gavage of bacteriophage MS2 and metformin led to a significant increase in the abundance of Corynebacterium glutamicum and A. muciniphila, respectively. Consequently, the gut microbiota were remodeled, leading to variations in metabolites and a substantial increase in short-chain fatty acids (SCFAs). In which, the amount of acetate, propionate, and butyrate presented negative correlations to that of proinflammatory cytokines, which was beneficial to repairing the intestinal barriers and improving their functions. Moreover, main short fatty acid (SCFA) producers exhibited positive interactions, further facilitating the restoration of gut eubiosis. These findings revealed that C. glutamicum and its metabolites may be potential dietary supplements for the treatment of T2D. Moreover, our research contributes to a novel understanding of the underlying mechanism by which functional foods exert their anti-diabetic effects.}, }
@article {pmid37689892, year = {2023}, author = {Dong, R and Peng, K and Shi, L and Niu, Q and Rafique, H and Liu, Y and Yuan, L and Zou, L and Li, L and Messia, MC and Hu, X}, title = {Oat bran prevents high-fat-diet induced muscular dysfunction, systemic inflammation and oxidative stress through reconstructing gut microbiome and circulating metabolome.}, journal = {Food research international (Ottawa, Ont.)}, volume = {172}, number = {}, pages = {113127}, doi = {10.1016/j.foodres.2023.113127}, pmid = {37689892}, issn = {1873-7145}, mesh = {Animals ; Mice ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Avena ; Metabolome ; Oxidative Stress ; Dietary Fiber ; Inflammation/prevention &amp; control ; }, abstract = {Western-type diet characterized by high fat emerges a promoter of skeletal muscle dysfunctions. Oat bran was typically considered a healthy food of premium quality for its abundant dietary fiber. The present study comprehensively explored the effects of a diet rich in oat bran on skeletal muscle disfunctions in high-fat diet (HFD) fed mice. Dietary-fiber-rich oat bran significantly ameliorated HFD-induced skeletal muscle function abnormalities, as evidenced by a phenotype improvement in mice grip strength and endurance treadmill running distance, accompanied with the regulation of muscle functions related gene expressions, namely Fis1, Cytc, Mhy2 and Mhy4. Oat bran suppressed the production of systemic inflammatory cytokines while promoted superoxide dismutase and glutathione. Furthermore, oat bran significantly impacted gut microbiota composition by promoting short chain fatty acids (SCFAs) producers and certain probiotic genera, along with the enhancement of SCFAs. Oat bran also significantly decreased the circulating levels of inflammation-related metabolites and played roles in MAPK signaling, thereafter influencing skeletal muscle functions. Collectively, benefits from integration of biomedical indicators, microbiomics, and metabolomics demonstrates the benefits of oat bran consumption on prevention of HFD-related muscular dysfunctions via alleviating HFD-induced inflammation, gut dysbiosis, and systemic metabolism, pinpointing a novel mechanism underlying the muscle-promoting property of oat bran.}, }
@article {pmid37689844, year = {2023}, author = {Li, L and Yan, S and Liu, S and Wang, P and Li, W and Yi, Y and Qin, S}, title = {In-depth insight into correlations between gut microbiota and dietary fiber elucidates a dietary causal relationship with host health.}, journal = {Food research international (Ottawa, Ont.)}, volume = {172}, number = {}, pages = {113133}, doi = {10.1016/j.foodres.2023.113133}, pmid = {37689844}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome ; Diet ; *Microbiota ; Nutritional Status ; Dietary Fiber ; }, abstract = {Dietary fiber exerts a wide range of biological benefits on host health, which not only provides a powerful source of nutrition for gut microbiota but also supplies key microbial metabolites that directly affect host health. This review mainly focuses on the decomposition and metabolism of dietary fiber and the essential genera Bacteroides and Bifidobacterium in dietary fiber fermentation. Dietary fiber plays an essential role in host health by impacting outcomes related to obesity, enteritis, immune health, cancer and neurodegenerative diseases. Additionally, the gut microbiota-independent pathway of dietary fiber affecting host health is also discussed. Personalized dietary fiber intake combined with microbiome, genetics, epigenetics, lifestyle and other factors has been highlighted for development in the future. A higher level of evidence is needed to demonstrate which microbial phenotype benefits from which kind of dietary fiber. In-depth insights into the correlation between gut microbiota and dietary fiber provide strong theoretical support for the precise application of dietary fiber, which elucidates a dietary causal relationship with host health.}, }
@article {pmid37689641, year = {2023}, author = {Ding, H and Xu, Y and Cheng, Y and Zhou, H and Dong, S and Wu, J and Lv, J and Hu, X and Tang, O}, title = {Gut microbiome profile of Chinese hypertension patients with and without type 2 diabetes mellitus.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {254}, pmid = {37689641}, issn = {1471-2180}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/complications ; East Asian People ; *Hypertension/complications ; }, abstract = {BACKGROUND: The coexistence of hypertension and type 2 diabetes mellitus (T2DM) may largely increase the risk for cardiovascular disease. However, there is no clear consensus on the association between hypertension and the risk of diabetes. Gut microbiota plays important roles in the development of hypertension and T2DM, but whether there is difference between hypertension patients with or without T2DM has not been explored yet.<br><br>METHODS: We recruited 101 hypertension patients in this study (72 patients without T2DM named HT group and 29 patients with T2DM named HT-T2DM group). Their blood samples were collected for testing clinical characteristics and fecal samples were tested for bacterial DNA using 16&#xa0;S ribosomal RNA gene sequencing targeting the V3 and V4 region. The data of 40 samples were downloaded from project PRJNA815750 as health control (HC group) in this study. The community composition and structure of the microbiome, taxonomic difference, co-occurrence network and functional enrichment were analyzed by alpha/beta diversity, LEfSe, Fruchterman Reingold's algorithm and PICRUSt2 functional analysis, respectively.<br><br>RESULTS: Alpha and beta diversity analysis showed significant differences in microbial community richness and composition among the three groups. The HC group had a significantly higher Simpson index and a distinct microbiota community compared to the HT and HT-T2DM groups, as demonstrated by significant differences in unweighted and weighted UniFrac distances. The LEfSe analysis identified specific taxa that had significantly different abundance among the groups, such as Bacteroides uniformis, Blautia wexlerae, Alistipes putredinis, and Prevotella stercorea in the HC group, Prevotella copri and Phascolarctobacterium faecium in the HT group, and Klebsiella pneumoniae in the HT-T2DM group. Co-occurrence network analysis indicates that Prevotella copri, Mediterraneibacter gnavus, Alistipes onderdonkii and some unidentified species act as key nodes in the network. Differentially functional pathway identified by PICRUSt2 were concentrated in nutrition and energy metabolism, as well as the biosynthesis of other secondary metabolites.<br><br>CONCLUSIONS: Our study found significant differences in microbial community richness, composition, and function among the healthy controls, hypertension patients with and without T2DM. Some specific taxa may explain this difference and serve as potential therapeutic targets for hypertension, T2DM, and their coexistence.}, }
@article {pmid37689446, year = {2023}, author = {Zhang, K and He, C and Qiu, Y and Li, X and Hu, J and Fu, B}, title = {ASSOCIATION OF ORAL MICROBIOTA AND PERIODONTAL DISEASE WITH LUNG CANCER: A SYSTEMATIC REVIEW AND META-ANALYSIS.}, journal = {The journal of evidence-based dental practice}, volume = {23}, number = {3}, pages = {101897}, doi = {10.1016/j.jebdp.2023.101897}, pmid = {37689446}, issn = {1532-3390}, mesh = {Humans ; *Lung Neoplasms ; Case-Control Studies ; *Microbiota ; *Periodontal Diseases ; Research Design ; }, abstract = {OBJECTIVES: Evidence of oral microbiota perturbations has been accumulated for lung cancers. This review focused on the oral microbiota alterations in population suffering from lung cancer. In addition, we also discussed conflicting data about the association between oral microbiota dysbiosis and risk of lung cancer.<br><br>METHODS: A systematic search was conducted in Medline, Embase, PubMed, and Cochrane Library databases. The studies evaluated diversity and abundance of oral microbes in healthy and lung cancer individuals as well as association of periodontal disease and pathogens with lung cancer. Of 3559 studies, 28 included studies were performed in qualitative analysis, and 25 studies were used in meta-analyses for quantitative assessment. Heterogeneity was analyzed by using I&#xb2; and chi-squared Q test statistics. Statistical analyses were performed by using the RevMan 5.4 software.<br><br>RESULTS: Compared with the control, lung cancer patients had lower alpha diversity (Shannon: SMD&#x202f;=&#x202f;-0.54; 95% CI, -0.90 to -0.19; P < .01, I[2]&#x202f;=&#x202f;71%). In nested case-control studies, individuals with decreased alpha diversity tended to have an increased risk of lung cancer (observed species: HR&#x202f;=&#x202f;0.90; 95% CI, 0.85-0.96; P < .01, I[2]&#x202f;=&#x202f;0%; Shannon: HR&#x202f;=&#x202f;0.89; 95% CI, 0.83-0.95; P < .01, I[2]&#x202f;=&#x202f;0%). Overall, no strong evidence of association of relative abundance with specific oral microbes with lung cancers was found because of inconsistent data. No associations were found between periodontal pathogens and lung cancer risk (red complex: HR&#x202f;=&#x202f;1.12, 95% CI: 0.42-3.02, P&#x202f;=&#x202f;.82, I[2]&#x202f;=&#x202f;62%; orange complex: HR =1.77, 95% CI: 0.78-3.98, P&#x202f;=&#x202f;.17, I[2]&#x202f;=&#x202f;36%), expect for Fusobacterium nucleatum (HR&#x202f;=&#x202f;2.27, 95% CI: 1.13-4.58, P&#x202f;=&#x202f;.02, I[2]&#x202f;=&#x202f;0%). The positive association of periodontal disease with lung cancer risk was found (HR&#x202f;=&#x202f;1.58, 95% CI: 1.25-2.00, P < .001, I[2]= 0%) with increase of periodontal diseases severity (HR&#x202f;=&#x202f;2.39, 95% CI: 1.57-3.66, P < .001, I[2]&#x202f;=&#x202f;0%). However, such association was not found in never-smoker participants (HR&#x202f;=&#x202f;1.00, 95% CI: 0.76-1.31, P&#x202f;=&#x202f;.37, I[2]= 7%).<br><br>CONCLUSIONS: Lower alpha diversity of oral microbiome may be associated with a greater risk of lung cancer and might serve as a predictive signal of lung cancer risk. There was no strong evidence of relative abundance of oral microbial taxa and periodontal pathogens in lung cancer patients. Fusobacterium nucleatum might be a potential microbial candidate of biomarkers in lung cancer. Periodontal disease may be positively associated with lung cancer risk by confounding of smoking, but not an independent risk factor.}, }
@article {pmid37689427, year = {2023}, author = {Carbonero-Pacheco, J and Rey, MD and Moreno-García, J and Moreno, J and García-Martínez, T and Mauricio, JC}, title = {Microbial diversity in sherry wine biofilms and surrounding mites.}, journal = {Food microbiology}, volume = {116}, number = {}, pages = {104366}, doi = {10.1016/j.fm.2023.104366}, pmid = {37689427}, issn = {1095-9998}, mesh = {Animals ; *Mites ; *Wine ; Biofilms ; Biotechnology ; Food ; }, abstract = {Sherry wines are film wines produced in the Jerez-Xérès-Sherry and Montilla-Moriles regions in southern Spain which require an aging process under flor biofilms, known as "biological aging". The presence of mites in Sherry wine wineries has been reported and associated with improved wine volatile properties. This work analyzes the microbial diversity in flor biofilms and mites in Sherry wine wineries using Matrix-Assisted Laser Desorption/Ionization Time of Flight (MALDI-TOF) and ITS/gene amplification. Two mite species, Carpoglyphus lactis and Tyrophagus putrescentiae, were spotted in the sampled winery and 32 microorganism species were identified in their exoskeleton or surrounding biofilms. To our knowledge, 26 of these species were never described before in sherry wine environments. We hypothesized that mites feed on the flor biofilms as well as another type of biofilm located in barrel cracks, known by winemakers as "natas" (cream in English). These non-studied biofilms showed the highest microbiome diversity among all samples (followed by C. lactis spotted nearby) thus, representing a niche of microorganisms with potential biotechnological interest. Besides mites, Drosophila flies were spotted in the sampling areas. The role of flies and mites as vectors that transport microorganisms among different niches (i.e., flor biofilms and natas) is discussed.}, }
@article {pmid37689277, year = {2023}, author = {Ke, S and Hartmann, J and Ressler, KJ and Liu, YY and Koenen, KC}, title = {The emerging role of the gut microbiome in posttraumatic stress disorder.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2023.09.005}, pmid = {37689277}, issn = {1090-2139}, abstract = {Posttraumatic stress disorder (PTSD) occurs in some people following exposure to a terrifying or catastrophic event involving actual/threatened death, serious injury, or sexual violence. PTSD is a common and debilitating mental disorder that imposes a significant burden on individuals, their families, health services, and society. Moreover, PTSD is a risk factor for chronic diseases such as coronary heart disease, stroke, diabetes, as well as premature mortality. Furthermore, PTSD is associated with dysregulated immune function. Despite the high prevalence of PTSD, the mechanisms underlying its etiology and manifestations remain poorly understood. Compelling evidence indicates that the human gut microbiome, a complex community of microorganisms living in the gastrointestinal tract, plays a crucial role in the development and function of the host nervous system, complex behaviors, and brain circuits. The gut microbiome may contribute to PTSD by influencing inflammation, stress responses, and neurotransmitter signaling, while bidirectional communication between the gut and brain involves mechanisms such as microbial metabolites, immune system activation, and the vagus nerve. In this literature review, we summarize recent findings on the role of the gut microbiome in PTSD in both human and animal studies. We discuss the methodological limitations of existing studies and suggest future research directions to further understand the role of the gut microbiome in PTSD.}, }
@article {pmid37689266, year = {2023}, author = {Shasha, D and Grupel, D and Treigerman, O and Prajgrod, G and Paran, Y and Haham, D and Ben-Ami, R and Albukrek, D and Zacay, G}, title = {The Clinical Significance of Dientamoeba fragilis and Blastocystis in Human Stool - Retrospective Cohort Study.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2023.09.003}, pmid = {37689266}, issn = {1469-0691}, abstract = {OBJECTIVE: The aim of this study was to assess the clinical significance of Dientamoeba fragilis (DF) and Blastocystis species (Bs) in human stool.<br><br>METHODS: Observational study of patients &#x2265;18&#xa0;years, who were tested by stool multiplex PCR for bacteria and parasites between April 2019 and March 2022. While DF and Bs are part of the PCR kit, these results are not routinely reported to the patient or the ordering physician. The main outcomes were: the incidence of symptoms during 14&#xa0;days before the referral to stool PCR test, and the incidence of several clinical outcomes during 60&#xa0;days following the PCR test (symptoms, referrals to further evaluation, prescription of symptomatic or antibiotic treatment).<br><br>RESULTS: 27,918 patients were tested by stool PCR during the three study years. 6,215 (22.3%) and 5,337 (19.2%) were positive for DF and Bs, respectively. The incidence of symptoms before the test was similar in those positive for Bs or DF and those with all-negative PCR (adjusted OR (aOR) and 95% confidence interval (CI) of 0.87 (0.80-0.95) and 0.82 (0.76-0.88) for Bs and DF, respectively), while significantly higher (2.47(2.23-2.73)) in those positive for the other multiplex PCR assay components. During the 60&#xa0;days following the test the prevalence of any of the outcomes was similar in those positive for Bs or DF and those with negative PCR (aOR and 95% CI of 0.92 (0.83-1.02) and 0.89 (0.81-0.97) for symptoms, 0.84 (0.75-0.94) and 0.93 (0.85-1.01) for referrals, 0.88 (0.75-1.03) and 0.82 (0.71-0.94) for symptomatic treatment and 0.88 (0.75-1.02) and 0.86 (0.75-0.98) for antibiotic treatment in the Bs and DF positive individuals, respectively). The PCR cycle threshold was not associated with any of the outcomes.<br><br>CONCLUSIONS: Positive stool PCR for DF or Bs was not associated with any of the measured clinical outcomes.}, }
@article {pmid37688810, year = {2023}, author = {Yan, S and Ren, X and Zheng, L and Wang, X and Liu, T}, title = {A systematic analysis of residue and risk of cyantraniliprole in the water-sediment system: Does metabolism reduce its environmental risk?.}, journal = {Environment international}, volume = {179}, number = {}, pages = {108185}, doi = {10.1016/j.envint.2023.108185}, pmid = {37688810}, issn = {1873-6750}, abstract = {As a representative variety of diamide insecticides, cyantraniliprole has broad application prospects. In this study, the fate and risk of cyantraniliprole and its main metabolite J9Z38 in a water-sediment system were investigated. The present result showed that more J9Z38 was adsorbed in the sediment at the end of exposure. However, the bioaccumulation capacity of cyantraniliprole in zebrafish was higher than that of J9Z38. Cyantraniliprole had stronger influence on the antioxidant system and detoxification system of zebrafish than J9Z38. Moreover, cyantraniliprole induced more significant oxidative stress effect and more differentially expressed genes (DEGs) in zebrafish. Cyantraniliprole had significantly influence on the expression of RyR-receptor-related genes, which was confirmed by resolving their binding modes with key receptor proteins using AlphaFold2 and molecular docking techniques. In the sediment, both cyantraniliprole and J9Z38 had inhibitory effects on microbial community structure diversity and metabolic function, especially cyantraniliprole. The methane metabolism pathway, mediated by methanogens such as Methanolinea, Methanoregula, and Methanosaeta, may be the main pathway of degradation of cyantraniliprole and J9Z38 in sediments. The present results demonstrated that metabolism can reduce the environmental risk of cyantraniliprole in water-sediment system to a certain extent.}, }
@article {pmid37688509, year = {2023}, author = {Santacroce, L and Passarelli, PC and Azzolino, D and Bottalico, L and Charitos, IA and Cazzolla, AP and Colella, M and Topi, S and Godoy, FG and D'Addona, A}, title = {Oral microbiota in human health and disease: A perspective.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {}, number = {}, pages = {15353702231187645}, doi = {10.1177/15353702231187645}, pmid = {37688509}, issn = {1535-3699}, abstract = {The evolution of medical knowledge about oral microbiota has increased awareness of its important role for the entire human body health. A wide range of microbial species colonizing the oral cavity interact both with each other and with their host through complex pathways. Usually, these interactions lead to a harmonious coexistence (i.e. eubiosis). However, several factors - including diet, poor oral hygiene, tobacco smoking, and certain medications, among others - can disrupt this weak homeostatic balance (i.e. dysbiosis) with potential implications on both oral (i.e. development of caries and periodontal disease) and systemic health. This article is thus aimed at providing an overview on the importance of oral microbiota in mediating several physiological and pathological conditions affecting human health. In this context, strategies based on oral hygiene and diet as well as the role of probiotics supplementation are discussed.}, }
@article {pmid37688396, year = {2023}, author = {Zhang, L and San Valentin, EMD and John, TM and Jenq, RR and Do, KA and Hanna, EY and Peterson, CB and Reyes-Gibby, CC}, title = {Influence of oral microbiome on longitudinal patterns of oral mucositis severity in patients with squamous cell carcinoma of the head and neck.}, journal = {Cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/cncr.35001}, pmid = {37688396}, issn = {1097-0142}, support = {R01DE022891/NH/NIH HHS/United States ; R21DE026837/NH/NIH HHS/United States ; P30CA016672/NH/NIH HHS/United States ; R01 HL158796/NH/NIH HHS/United States ; R01 HL124112/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: This study investigated the influence of oral microbial features on the trajectory of oral mucositis (OM) in patients with squamous cell carcinoma of the head and neck.<br><br>METHODS: OM severity was assessed and buccal swabs were collected at baseline, at the initiation of cancer treatment, weekly during cancer treatment, at the termination of cancer treatment, and after cancer treatment termination. The oral microbiome was characterized via the 16S ribosomal RNA V4 region with the Illumina platform. Latent class mixed-model analysis was used to group individuals with similar trajectories of OM severity. Locally estimated scatterplot smoothing was used to fit an average trend within each group and to assess the association between the longitudinal OM scores and longitudinal microbial abundances.<br><br>RESULTS: Four latent groups (LGs) with differing patterns of OM severity were identified for 142 subjects. LG1 has an early onset of high OM scores. LGs 2 and 3 begin with relatively low OM scores until the eighth and 11th week, respectively. LG4 has generally flat OM scores. These LGs did not vary by treatment or clinical or demographic variables. Correlation analysis showed that the abundances of Bacteroidota, Proteobacteria, Bacteroidia, Gammaproteobacteria, Enterobacterales, Bacteroidales, Aerococcaceae, Prevotellaceae, Abiotrophia, and Prevotella_7 were positively correlated with OM severity across the four LGs. Negative correlation was observed with OM severity for a few microbial features: Abiotrophia and Aerococcaceae for LGs 2 and 3; Gammaproteobacteria and Proteobacteria for LGs 2, 3, and 4; and Enterobacterales for LGs 2 and 4.<br><br>CONCLUSIONS: These findings suggest the potential to personalize treatment for OM.<br><br>PLAIN LANGUAGE SUMMARY: Oral mucositis (OM) is a common and debilitating after effect for patients treated for squamous cell carcinoma of the head and neck. Trends in the abundance of specific microbial features may be associated with patterns of OM severity over time. Our findings suggest the potential to personalize treatment plans for OM via tailored microbiome interventions.}, }
@article {pmid37688332, year = {2023}, author = {Siddiqui, R and Khan, NA}, title = {Is the gut microbiome of insects a potential source to meet UN sustainable development goals to eliminate plastic pollution?.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.13166}, pmid = {37688332}, issn = {1758-2229}, abstract = {As insects such as cockroaches can endure high radiation, flourish in unsanitary circumstances, thrive on germ-infested feed, and can even digest the organic polymer cellulose, the gut microbiota of these species likely produces enzymes contributing to their ability to digest a variety of materials. The use of cockroaches as a bio-resource to eliminate plastic is discussed. We explore whether species such as cockroaches are a potential bio-resource to eliminate plastic pollution and contribute to the sustainable development goals adopted by the United Nations as well as the global community to reduce and/or eliminate plastic pollution.}, }
@article {pmid37687337, year = {2023}, author = {López-Pozo, M and Adams, WW and Demmig-Adams, B}, title = {Lemnaceae as Novel Crop Candidates for CO2 Sequestration and Additional Applications.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {17}, pages = {}, pmid = {37687337}, issn = {2223-7747}, support = {NNX16AO69A//Translational Research Institute for Space Health through Cooperative Agreement/ ; }, abstract = {Atmospheric carbon dioxide (CO2) is projected to be twice as high as the pre-industrial level by 2050. This review briefly highlights key responses of terrestrial plants to elevated CO2 and compares these with the responses of aquatic floating plants of the family Lemnaceae (duckweeds). Duckweeds are efficient at removing CO2 from the atmosphere, which we discuss in the context of their exceptionally high growth rates and capacity for starch storage in green tissue. In contrast to cultivation of terrestrial crops, duckweeds do not contribute to CO2 release from soils. We briefly review how this potential for contributions to stabilizing atmospheric CO2 levels is paired with multiple additional applications and services of duckweeds. These additional roles include wastewater phytoremediation, feedstock for biofuel production, and superior nutritional quality (for humans and livestock), while requiring minimal space and input of light and fertilizer. We, furthermore, elaborate on other environmental factors, such as nutrient availability, light supply, and the presence of a microbiome, that impact the response of duckweed to elevated CO2. Under a combination of elevated CO2 with low nutrient availability and moderate light supply, duckweeds' microbiome helps maintain CO2 sequestration and relative growth rate. When incident light intensity increases (in the presence of elevated CO2), the microbiome minimizes negative feedback on photosynthesis from increased sugar accumulation. In addition, duckweed shows a clear propensity for absorption of ammonium over nitrate, accepting ammonium from their endogenous N2-fixing Rhizobium symbionts, and production of large amounts of vegetative storage protein. Finally, cultivation of duckweed could be further optimized using hydroponic vertical farms where nutrients and water are recirculated, saving both resources, space, and energy to produce high-value products.}, }
@article {pmid37687126, year = {2023}, author = {Ratajczak, K and Piotrowska-Cyplik, A and Cyplik, P}, title = {Analysis of the Effect of Various Potential Antimicrobial Agents on the Quality of the Unpasteurized Carrot Juice.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {17}, pages = {}, pmid = {37687126}, issn = {1420-3049}, support = {005/RID/2018/19//Polish Ministry of Science and Higher Education's program: "Regional Excellence Initiative" in the years 2019-2023/ ; }, mesh = {*Daucus carota ; Food ; *Anti-Infective Agents/pharmacology ; Disinfection ; Plant Extracts/pharmacology ; }, abstract = {Short shelf-life and poor microbial quality of minimally processed foods of plant origin pose a serious problem for the food industry. Novel techniques of minimal treatment combined with disinfection are being researched, and, for fresh juice, the addition of antimicrobial agents appears to be a promising route. In this research, fresh, nonfiltered, unpasteurized carrot juice was mixed with four potential antimicrobials (bourbon vanilla extract, peppermint extract, cannabidiol oil, and grapefruit extract). All four variants and the reference pure carrot juice were analyzed for metapopulational changes, microbial changes, and physicochemical changes. The potential antimicrobials used in the research have improved the overall microbial quality of carrot juice across 4 days of storage. However, it is important to notice that each of the four agents had a different spectrum of effectiveness towards the groups identified in the microflora of carrot juice. Additionally, the antimicrobials have increased the diversity of the carrot juice microbiome but did not prevent the occurrence of pathogenic bacteria. In conclusion, the use of antimicrobial agents such as essential oils or their derivatives may be a promising way of improving the microbial quality and prolonging the shelf-life of minimally processed foods, such as fresh juices, but the technique requires further research.}, }
@article {pmid37686891, year = {2023}, author = {Liwinski, T and Lang, UE}, title = {Folate and Its Significance in Depressive Disorders and Suicidality: A Comprehensive Narrative Review.}, journal = {Nutrients}, volume = {15}, number = {17}, pages = {}, pmid = {37686891}, issn = {2072-6643}, mesh = {Humans ; Suicidal Ideation ; *Suicide ; Folic Acid/therapeutic use ; Glutamic Acid ; *Depressive Disorder ; }, abstract = {Depressive disorders pose significant challenges to global public health, necessitating effective prevention and management strategies. Notably, the occurrence of suicide frequently coincides with depressive episodes. Suicide is as a paramount global health concern that demands efficacious preventive strategies. Current psychiatric approaches heavily rely on pharmacological interventions but have had limited success in addressing the global burden of mental health issues. Suboptimal nutrition, with its impact on the neuroendocrine system, has been implicated in the underlying pathology of depressive disorders. Folate, a group of water-soluble compounds, plays a crucial role in various central nervous system functions. Depressed individuals often exhibit low levels of serum and red blood cell folate. Multiple studies and systematic reviews have investigated the efficacy of folic acid and its derivative, L-methylfolate, which can cross the blood-brain barrier, as stand-alone or adjunct therapies for depression. Although findings have been mixed, the available evidence generally supports the use of these compounds in depressed individuals. Recent studies have established links between the one-carbon cycle, folate-homocysteine balance, immune system function, glutamate excitation via NMDA (N-methyl-D-aspartate) receptors, and gut microbiome eubiosis in mood regulation. These findings provide insights into the complex neurobiological mechanisms underlying the effects of folate and related compounds in depression. Through a comprehensive review of the existing literature, this study aims to advance our understanding of the therapeutic potential of folic acid and related compounds in depression treatment. It also seeks to explore their role in addressing suicidal tendencies and shed light on the neurobiological mechanisms involved, leveraging the latest discoveries in depression research.}, }
@article {pmid37686884, year = {2023}, author = {Gao, K and Chen, C and Ke, X and Fan, Q and Wang, H and Li, Y and Chen, S}, title = {Improvements of Age-Related Cognitive Decline in Mice by Lactobacillus helveticus WHH1889, a Novel Strain with Psychobiotic Properties.}, journal = {Nutrients}, volume = {15}, number = {17}, pages = {}, pmid = {37686884}, issn = {2072-6643}, support = {2022C02017//the Science and Technology Projects of Zhejiang Province/ ; 2022C04034//the Key R &amp; D Projects of Zhejiang Province/ ; }, mesh = {Animals ; Mice ; 5-Hydroxytryptophan ; *Lactobacillus helveticus ; Serotonin ; Tryptophan ; *Cognitive Dysfunction/prevention &amp; control ; }, abstract = {A gradual decline in cognitive function occurs with age. Accumulating evidence suggests that certain probiotic strains exert beneficial effects on age-related cognitive decline. Our previous study revealed that Lactobacillus helveticus WHH1889 attenuated symptoms of anxiety and depression in depressed mice via shaping the 5-hydroxytryptamine (5-HT) and 5-hydroxytryptophan (5-HTP) metabolism and gut microbial community, indicating the psychobiotic potential of WHH1889. In the present study, the effects of WHH1889 on age-related cognitive decline were investigated. WHH1889 was orally administrated (1 × 10[9] CFU/day) for twelve weeks in aged mice, and their cognitive behaviors, neurochemical factors, cognitive-related gene expressions, neuroinflammation, and serum tryptophan pathway-targeted metabolic profiling, as well as gut microbiome composition were assessed. WHH1889 demonstrated improvement of the cognitive behaviors via the novel object recognition test (NORT), the active shuttle avoidance test (ASAT), the Y-maze test, and the passive avoidance test (PAT). The hippocampal neuronal loss; the declined concentrations of BDNF, 5-HT, and 5-HTP; the decreased gene expressions of neurodegeneration biomarkers; and the increased production of hippocampal inflammatory cytokines in aged mice were restored by WHH1889. In addition, WHH1889 increased the 5-HT/5HTP levels and decreased the serum levels of tryptophan-derived metabolites (e.g., kynurenine, xanthurenic acid, 3-hydroxykynurenine, and 3-hydroxyanthranilic acid). Furthermore, WHH1889 was revealed to shape the gut microbiota community by reversing the relative abundances of Bacteroidota and Firmicutes. The present findings suggest that L. helveticus WHH1889 exerted cognitive improving effects on aged mice, which was associated with the modulation of 5-HT and 5-HTP metabolism and gut microbial composition. The supplementation of WHH1889 may therefore be a promising therapeutic agent for age-related cognitive deficits.}, }
@article {pmid37686860, year = {2023}, author = {Xu, F and Yu, Z and Liu, Y and Du, T and Yu, L and Tian, F and Chen, W and Zhai, Q}, title = {A High-Fat, High-Cholesterol Diet Promotes Intestinal Inflammation by Exacerbating Gut Microbiome Dysbiosis and Bile Acid Disorders in Cholecystectomy.}, journal = {Nutrients}, volume = {15}, number = {17}, pages = {}, pmid = {37686860}, issn = {2072-6643}, support = {32122067//Qixiao Zhai/ ; 32021005//Qixiao Zhai/ ; BK20200084//Wei Chen/ ; JUSRP622013//Qixiao Zhai/ ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Dysbiosis ; Cholesterol ; *Hypercholesterolemia ; Cholecystectomy/adverse effects ; Bile Acids and Salts ; Disease Models, Animal ; Inflammation/etiology ; }, abstract = {Patients with post-cholecystectomy (PC) often experience adverse gastrointestinal conditions, such as PC syndrome, colorectal cancer (CRC), and non-alcoholic fatty liver disease (NAFLD), that accumulate over time. An epidemiological survey further revealed that the risk of cholecystectomy is associated with high-fat and high-cholesterol (HFHC) dietary intake. Mounting evidence suggests that cholecystectomy is associated with disrupted gut microbial homeostasis and dysregulated bile acids (BAs) metabolism. However, the effect of an HFHC diet on gastrointestinal complications after cholecystectomy has not been elucidated. Here, we aimed to investigate the effect of an HFHC diet after cholecystectomy on the gut microbiota-BA metabolic axis and elucidate the association between this alteration and the development of intestinal inflammation. In this study, a mice cholecystectomy model was established, and the levels of IL-Iβ, TNF-α, and IL-6 in the colon were increased in mice fed an HFHC diet for 6 weeks. Analysis of fecal BA metabolism showed that an HFHC diet after cholecystectomy altered the rhythm of the BA metabolism by upregulating liver CPY7A1, CYP8B1, and BSEP and ileal ASBT mRNA expression levels, resulting in increased fecal BA levels. In addition, feeding an HFHC diet after cholecystectomy caused a significant dysbiosis of the gut microbiota, which was characterized by the enrichment of the metabolic microbiota involved in BAs; the abundance of pro-inflammatory gut microbiota and related pro-inflammatory metabolite levels was also significantly higher. In contrast, the abundance of major short-chain fatty acid (SCFA)-producing bacteria significantly decreased. Overall, our study suggests that an HFHC diet after cholecystectomy promotes intestinal inflammation by exacerbating the gut microbiome and BA metabolism dysbiosis in cholecystectomy. Our study also provides useful insights into the maintenance of intestinal health after cholecystectomy through dietary or probiotic intervention strategies.}, }
@article {pmid37686754, year = {2023}, author = {Guo, Q and Li, Y and Dai, X and Wang, B and Zhang, J and Cao, H}, title = {Polysaccharides: The Potential Prebiotics for Metabolic Associated Fatty Liver Disease (MAFLD).}, journal = {Nutrients}, volume = {15}, number = {17}, pages = {}, doi = {10.3390/nu15173722}, pmid = {37686754}, issn = {2072-6643}, support = {TJWJ2022QN010//Tianjin Health Science and Technology/ ; 2022KJ243//Scientific research project of Tianjin Municipal Commission of Education/ ; }, abstract = {Metabolic (dysfunction) associated fatty liver disease (MAFLD) is recognized as the most prevalent chronic liver disease globally. However, its pathogenesis remains incompletely understood. Recent advancements in the gut-liver axis offer novel insights into the development of MAFLD. Polysaccharides, primarily derived from fungal and algal sources, abundantly exist in the human diet and exert beneficial effects on glycometabolism, lipid metabolism, inflammation, immune modulation, oxidative stress, and the release of MAFLD. Numerous studies have demonstrated that these bioactivities of polysaccharides are associated with their prebiotic properties, including the ability to modulate the gut microbiome profile, maintain gut barrier integrity, regulate metabolites produced by gut microbiota such as lipopolysaccharide (LPS), short-chain fatty acids (SCFAs), and bile acids (BAs), and contribute to intestinal homeostasis. This narrative review aims to present a comprehensive summary of the current understanding of the protective effects of polysaccharides on MAFLD through their interactions with the gut microbiota and its metabolites. Specifically, we highlight the potential molecular mechanisms underlying the prebiotic effects of polysaccharides, which may give new avenues for the prevention and treatment of MAFLD.}, }
@article {pmid37686712, year = {2023}, author = {Santangelo, A and Corsello, A and Spolidoro, GCI and Trovato, CM and Agostoni, C and Orsini, A and Milani, GP and Peroni, DG}, title = {The Influence of Ketogenic Diet on Gut Microbiota: Potential Benefits, Risks and Indications.}, journal = {Nutrients}, volume = {15}, number = {17}, pages = {}, doi = {10.3390/nu15173680}, pmid = {37686712}, issn = {2072-6643}, abstract = {The ketogenic diet (KD) restricts carbohydrate consumption, leading to an increase in ketone bodies, such as acetoacetate, β-hydroxybutyrate, and acetone, which are utilized as energy substrates. This dietary approach impacts several biochemical processes, resulting in improved clinical management of various disorders, particularly in childhood. However, the exact mechanisms underlying the efficacy of KD remain unclear. Interestingly, KD may also impact the gut microbiota, which plays a pivotal role in metabolism, nutrition, and the development of the immune and nervous systems. KD has gained popularity for its potential benefits in weight loss, blood sugar control, and certain neurological conditions. This narrative review sums up KD-related studies published over 30 years. While short-term studies have provided valuable insights into the effects of KD on the gut microbiota, persistent uncertainties surround its long-term efficacy and potential for inducing dysbiosis. The significant influence of KD on epigenetic mechanisms, intracellular pathways, and gut microbial composition underscores its potential as a therapeutic choice. However, a judicious consideration of the potential risks associated with the strict adherence to a low-carbohydrate, high-fat, and high-protein regimen over prolonged periods is imperative. As KDs gain popularity among the adolescent and young adult demographic for weight management, it becomes imperative to undertake additional research to comprehensively assess their impact on nutritional status and gut microbiota, ensuring a holistic and sustainable approach to medical nutrition.}, }
@article {pmid37686707, year = {2023}, author = {Al-Ishaq, RK and Kubatka, P and Büsselberg, D}, title = {Sweeteners and the Gut Microbiome: Effects on Gastrointestinal Cancers.}, journal = {Nutrients}, volume = {15}, number = {17}, pages = {}, doi = {10.3390/nu15173675}, pmid = {37686707}, issn = {2072-6643}, support = {NPRP 14S-0311-210033//Qatar National Research Fund/ ; }, abstract = {Worldwide, the demand for natural and synthetic sweeteners in the food industry as an alternative to refined sugar is increasing. This has prompted more research to be conducted to estimate its safety and effects on health. The gut microbiome is critical in metabolizing selected sweeteners which might affect overall health. Recently, more studies have evaluated the relationship between sweeteners and the gut microbiome. This review summarizes the current knowledge regarding the role played by the gut microbiome in metabolizing selected sweeteners. It also addresses the influence of the five selected sweeteners and their metabolites on GI cancer-related pathways. Overall, the observed positive effects of sweetener consumption on GI cancer pathways, such as apoptosis and cell cycle arrest, require further investigation in order to understand the underlying mechanism.}, }
@article {pmid37686576, year = {2023}, author = {Maddern, AS and Coller, JK and Bowen, JM and Gibson, RJ}, title = {The Association between the Gut Microbiome and Development and Progression of Cancer Treatment Adverse Effects.}, journal = {Cancers}, volume = {15}, number = {17}, pages = {}, doi = {10.3390/cancers15174301}, pmid = {37686576}, issn = {2072-6694}, abstract = {Adverse effects are a common consequence of cytotoxic cancer treatments. Over the last two decades there have been significant advances in exploring the relationship between the gut microbiome and these adverse effects. Changes in the gut microbiome were shown in multiple clinical studies to be associated with the development of acute gastrointestinal adverse effects, including diarrhoea and mucositis. However, more recent studies showed that changes in the gut microbiome may also be associated with the long-term development of psychoneurological changes, cancer cachexia, and fatigue. Therefore, the aim of this review was to examine the literature to identify potential contributions and associations of the gut microbiome with the wide range of adverse effects from cytotoxic cancer treatments.}, }
@article {pmid37686487, year = {2023}, author = {Mauceri, R and Coppini, M and Vacca, D and Bertolazzi, G and Cancila, V and Tripodo, C and Campisi, G}, title = {No Clear Clustering Dysbiosis from Salivary Microbiota Analysis by Long Sequencing Reads in Patients Affected by Oral Squamous Cell Carcinoma: A Single Center Study.}, journal = {Cancers}, volume = {15}, number = {17}, pages = {}, doi = {10.3390/cancers15174211}, pmid = {37686487}, issn = {2072-6694}, abstract = {BACKGROUND: Advancements in DNA sequencing technology have facilitated the assessment of the connection between the oral microbiome and various diseases. The aim of the present study was to investigate the salivary microbiota composition employing for the first time in the literature the Oxford Nanopore Technology in patients affected by oral squamous cell carcinoma (OSCC).<br><br>METHODS: Unstimulated saliva samples of 31 patients were collected (24 OSCC patients and 7 controls). DNA was extracted using the QIAamp DNA Blood Kit and metagenomic long sequencing reads were performed using the MinION device.<br><br>RESULTS: In the OSCC group, 13 were males and 11 were females, with a mean age of 65.5 &#xb1; 13.9 years; in the control group, 5 were males and 2 were females, with a mean age of 51.4 &#xb1; 19.2 years. The border of the tongue was the most affected OSCC site. The microorganisms predominantly detected in OSCC patients were Prevotella, Chlamydia, Tissierellia, Calothrix, Leotiomycetes, Firmicutes and Zetaproteobacteria.<br><br>CONCLUSIONS: This study confirmed the predominance of periodontopathic bacteria in the salivary microbiome in the OSCC group. If a direct correlation between oral dysbiosis and OSCC onset was proven, it could lead to new prevention strategies and early diagnostic tools.}, }
@article {pmid37686320, year = {2023}, author = {Ma, Y and Yang, L and Jiang, M and Zhao, X and Xue, P}, title = {Connecting Cryptococcal Meningitis and Gut Microbiome.}, journal = {International journal of molecular sciences}, volume = {24}, number = {17}, pages = {}, doi = {10.3390/ijms241713515}, pmid = {37686320}, issn = {1422-0067}, support = {82173554//National Natural Science Foundation of China/ ; BK20201444//Natural Science Foundation of Jiangsu Province/ ; 2020//Qing Lan Project for Excellent Young Key Teachers of Colleges and Universities of Jiangsu Province/ ; 202310304049Z//Nantong University student innovation training program project/ ; }, abstract = {Fungal pathogens of the Cryptococcus neoformans species complex (C. neoformans SC) are a major cause of fungal meningitis in immunocompromised individuals. As with other melanotic microorganisms associated with human diseases, the cell-wall-associated melanin of C. neoformans SC is a major virulence factor that contributes to its ability to evade host immune responses. The levels of melanin substrate and the regulation of melanin formation could be influenced by the microbiota-gut-brain axis. Moreover, recent studies show that C. neoformans infections cause dysbiosis in the human gut microbiome. In this review, we discuss the potential association between cryptococcal meningitis and the gut microbiome. Additionally, the significant potential of targeting the gut microbiome in the diagnosis and treatment of this debilitating disease is emphasized.}, }
@article {pmid37686314, year = {2023}, author = {Santos, FP and Carvalhos, CA and Figueiredo-Dias, M}, title = {New Insights into Photobiomodulation of the Vaginal Microbiome-A Critical Review.}, journal = {International journal of molecular sciences}, volume = {24}, number = {17}, pages = {}, doi = {10.3390/ijms241713507}, pmid = {37686314}, issn = {1422-0067}, abstract = {The development of new technologies such as sequencing has greatly enhanced our understanding of the human microbiome. The interactions between the human microbiome and the development of several diseases have been the subject of recent research. In-depth knowledge about the vaginal microbiome (VMB) has shown that dysbiosis is closely related to the development of gynecologic and obstetric disorders. To date, the progress in treating or modulating the VMB has lagged far behind research efforts. Photobiomodulation (PBM) uses low levels of light, usually red or near-infrared, to treat a diversity of conditions. Several studies have demonstrated that PBM can control the microbiome and improve the activity of the immune system. In recent years, increasing attention has been paid to the microbiome, mostly to the gut microbiome and its connections with many diseases, such as metabolic disorders, obesity, cardiovascular disorders, autoimmunity, and neurological disorders. The applicability of PBM therapeutics to treat gut dysbiosis has been studied, with promising results. The possible cellular and molecular effects of PBM on the vaginal microbiome constitute a theoretical and promising field that is starting to take its first steps. In this review, we will discuss the potential mechanisms and effects of photobiomodulation in the VMB.}, }
@article {pmid37686269, year = {2023}, author = {Machado, M and Silva, S and Costa, EM}, title = {Are Antimicrobial Peptides a 21st-Century Solution for Atopic Dermatitis?.}, journal = {International journal of molecular sciences}, volume = {24}, number = {17}, pages = {}, doi = {10.3390/ijms241713460}, pmid = {37686269}, issn = {1422-0067}, support = {UIDB/50016/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; 2022.07206.CEECIND//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disorder that is the result of various environmental, bacterial and genetic stimuli, which culminate in the disruption of the skin's barrier function. Characterized by highly pruritic skin lesions, xerosis and an array of comorbidities among which skin infections are the most common, this condition results in both a significant loss of quality of life and in the need for life-long treatments (e.g., corticosteroids, monoclonal antibodies and regular antibiotic intake), all of which may have harmful secondary effects. This, in conjunction with AD's rising prevalence, made the development of alternative treatment strategies the focus of both the scientific community and the pharmaceutical industry. Given their potential to both manage the skin microbiome, fight infections and even modulate the local immune response, the use of antimicrobial peptides (AMPs) from more diverse origins has become one of the most promising alternative solutions for AD management, with some being already used with some success towards this end. However, their production and use also exhibit some limitations. The current work seeks to compile the available information and provide a better understanding of the state of the art in the understanding of AMPs' true potential in addressing AD.}, }
@article {pmid37686253, year = {2023}, author = {Houghton, CA}, title = {The Rationale for Sulforaphane Favourably Influencing Gut Homeostasis and Gut-Organ Dysfunction: A Clinician's Hypothesis.}, journal = {International journal of molecular sciences}, volume = {24}, number = {17}, pages = {}, doi = {10.3390/ijms241713448}, pmid = {37686253}, issn = {1422-0067}, abstract = {Given the increasing scientific, clinical and consumer interest in highly prevalent functional gastrointestinal disorders, appropriate therapeutic strategies are needed to address the many aspects of digestive dysfunction. Accumulating evidence for the crucifer-derived bioactive molecule sulforaphane in upstream cellular defence mechanisms highlights its potential as a therapeutic candidate in targeting functional gastrointestinal conditions, as well as systemic disorders. This article catalogues the evolution of and rationale for a hypothesis that multifunctional sulforaphane can be utilised as the initial step in restoring the ecology of the gut ecosystem; it can do this primarily by targeting the functions of intestinal epithelial cells. A growing body of work has identified the colonocyte as the driver of dysbiosis, such that targeting gut epithelial function could provide an alternative to targeting the microbes themselves for the remediation of microbial dysbiosis. The hypothesis discussed herein has evolved over several years and is supported by case studies showing the application of sulforaphane in gastrointestinal disorders, related food intolerance, and several systemic conditions. To the best of our knowledge, this is the first time the effects of sulforaphane have been reported in a clinical environment, with several of its key properties within the gut ecosystem appearing to be related to its nutrigenomic effects on gene expression.}, }
@article {pmid37686011, year = {2023}, author = {Kononova, S and Kashparov, M and Xue, W and Bobkova, N and Leonov, S and Zagorodny, N}, title = {Gut Microbiome Dysbiosis as a Potential Risk Factor for Idiopathic Toe-Walking in Children: A Review.}, journal = {International journal of molecular sciences}, volume = {24}, number = {17}, pages = {}, doi = {10.3390/ijms241713204}, pmid = {37686011}, issn = {1422-0067}, support = {075-03-2023-106//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Idiopathic toe walking (ITW) occurs in about 5% of children. Orthopedic treatment of ITW is complicated by the lack of a known etiology. Only half of the conservative and surgical methods of treatment give a stable positive result of normalizing gait. Available data indicate that the disease is heterogeneous and multifactorial. Recently, some children with ITW have been found to have genetic variants of mutations that can lead to the development of toe walking. At the same time, some children show sensorimotor impairment, but these studies are very limited. Sensorimotor dysfunction could potentially arise from an imbalanced production of neurotransmitters that play a crucial role in motor control. Using the data obtained in the studies of several pathologies manifested by the association of sensory-motor dysfunction and intestinal dysbiosis, we attempt to substantiate the notion that malfunction of neurotransmitter production is caused by the imbalance of gut microbiota metabolites as a result of dysbiosis. This review delves into the exciting possibility of a connection between variations in the microbiome and ITW. The purpose of this review is to establish a strong theoretical foundation and highlight the benefits of further exploring the possible connection between alterations in the microbiome and TW for further studies of ITW etiology.}, }
@article {pmid37685710, year = {2023}, author = {Izdebska, WM and Daniluk, J and Niklinski, J}, title = {Microbiome and MicroRNA or Long Non-Coding RNA-Two Modern Approaches to Understanding Pancreatic Ductal Adenocarcinoma.}, journal = {Journal of clinical medicine}, volume = {12}, number = {17}, pages = {}, doi = {10.3390/jcm12175643}, pmid = {37685710}, issn = {2077-0383}, abstract = {Pancreatic ductal adenocarcinoma (PDAC) is one of humans' most common and fatal neoplasms. Nowadays, a number of PDAC studies are being conducted in two different fields: non-coding RNA (especially microRNA and long non-coding RNA) and microbiota. It has been recently discovered that not only does miRNA affect particular bacteria in the gut microbiome that can promote carcinogenesis in the pancreas, but the microbiome also has a visible impact on the miRNA. This suggests that it is possible to use the combined impact of the microbiome and noncoding RNA to suppress the development of PDAC. Nevertheless, insufficient research has focused on bounding both approaches to the diagnosis, treatment, and prevention of pancreatic ductal adenocarcinoma. In this article, we summarize the recent literature on the molecular basis of carcinogenesis in the pancreas, the two-sided impact of particular types of non-coding RNA and the pancreatic cancer microbiome, and possible medical implications of the discovered phenomenon.}, }
@article {pmid37685622, year = {2023}, author = {Wyszyńska, M and Czelakowska, A and Rosak, P and Kasperski, J and Łopacińska, M and Ghanem, A and Mertas, A and Skucha-Nowak, M}, title = {The Impact of COVID-19 on the Oral Bacterial Flora in Patients Wearing Complete Dentures and on the Level of Exhaled Nitric Oxide as a Marker of Inflammation.}, journal = {Journal of clinical medicine}, volume = {12}, number = {17}, pages = {}, doi = {10.3390/jcm12175556}, pmid = {37685622}, issn = {2077-0383}, support = {PCN- 1-151/N/1/K//Medical University of Silesia/ ; PCN-1-130/N/1/K//Medical University of Silesia/ ; PCN-1-190/N/0/K//Medical University of Silesia/ ; }, abstract = {BACKGROUND: Exhaled nitric oxide is helpful in the diagnosis of the inflammation process. The study aimed to analyze the impact of the COVID-19 disease on the oral bacterial flora of patients using complete dentures with a diagnostic device that measures the level of NO in exhaled air.<br><br>MATERIALS AND METHODS: The study included patients using upper and lower acrylic complete dentures. All patients participating in the study were vaccinated against COVID-19. The patients were divided into two groups. A dental examination was conducted in each group. The NO concentration was measured using the Vivatmo Pro device. An oral microbiological examination was performed by taking a swab from the bottom of the mouth.<br><br>RESULTS: There were no statistically significant differences in the distribution of NO in relation to the number of bacteria from isolated families in the study and control groups and no statistically significant correlations between the level of NO and the number of bacteria from all families in the control and study group. Significantly higher NO values were present in the vaccinated and COVID-19-positive history population compared to the vaccinated and with no COVID-19 history population (patients with no clinical symptoms of infection or unaware they had COVID-19).<br><br>CONCLUSIONS: There are statistically significant differences in NO distribution in the considered populations: vaccinated and sick, and vaccinated and with a negative history of COVID-19. The measurement of NO in exhaled air can be a complementary, non-invasive diagnostic and inflammation monitoring method.}, }
@article {pmid37685600, year = {2023}, author = {Sadowsky, RL and Sulejmani, P and Lio, PA}, title = {Atopic Dermatitis: Beyond the Skin and Into the Gut.}, journal = {Journal of clinical medicine}, volume = {12}, number = {17}, pages = {}, doi = {10.3390/jcm12175534}, pmid = {37685600}, issn = {2077-0383}, abstract = {Atopic dermatitis (AD) is a common, chronic and recurring inflammatory skin disorder characterized by an intensely pruritic, eczematous dermatitis. The etiology of AD is thought to involve a combination of environmental, genetic, and immunologic factors. Emerging research has investigated factors that may impact individual risk for developing AD, disease severity, and treatment response. One component is the gut microbiome, which is considered to play an essential role in maintaining the homeostasis of several organ systems. The gut microbiome has been described as a major regulator of the "gut-skin axis," yet some studies have yielded conflicting evidence regarding the strength of the association of gut microbiota dysbiosis with AD. This review discusses recent insights into the role of the gut microbiome in AD pathogenesis and its interplay among other complex systems that govern the current assessments of and treatments for AD.}, }
@article {pmid37685376, year = {2023}, author = {Unal, M and Bostanci, E and Ozkul, C and Acici, K and Asuroglu, T and Guzel, MS}, title = {Crohn's Disease Prediction Using Sequence Based Machine Learning Analysis of Human Microbiome.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {13}, number = {17}, pages = {}, doi = {10.3390/diagnostics13172835}, pmid = {37685376}, issn = {2075-4418}, abstract = {Human microbiota refers to the trillions of microorganisms that inhabit our bodies and have been discovered to have a substantial impact on human health and disease. By sampling the microbiota, it is possible to generate massive quantities of data for analysis using Machine Learning algorithms. In this study, we employed several modern Machine Learning techniques to predict Inflammatory Bowel Disease using raw sequence data. The dataset was obtained from NCBI preprocessed graph representations and converted into a structured form. Seven well-known Machine Learning frameworks, including Random Forest, Support Vector Machines, Extreme Gradient Boosting, Light Gradient Boosting Machine, Gaussian Naïve Bayes, Logistic Regression, and k-Nearest Neighbor, were used. Grid Search was employed for hyperparameter optimization. The performance of the Machine Learning models was evaluated using various metrics such as accuracy, precision, fscore, kappa, and area under the receiver operating characteristic curve. Additionally, Mc Nemar's test was conducted to assess the statistical significance of the experiment. The data was constructed using k-mer lengths of 3, 4 and 5. The Light Gradient Boosting Machine model overperformed over other models with 67.24%, 74.63% and 76.47% accuracy for k-mer lengths of 3, 4 and 5, respectively. The LightGBM model also demonstrated the best performance in each metric. The study showed promising results predicting disease from raw sequence data. Finally, Mc Nemar's test results found statistically significant differences between different Machine Learning approaches.}, }
@article {pmid37685075, year = {2023}, author = {Caponio, G and Vendemia, M and Mallardi, D and Marsico, AD and Alba, V and Gentilesco, G and Forte, G and Velasco, R and Coletta, A}, title = {Pesticide Residues and Berry Microbiome after Ozonated Water Washing in Table Grape Storage.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {17}, pages = {}, doi = {10.3390/foods12173144}, pmid = {37685075}, issn = {2304-8158}, support = {ARS01_00640 - POFACS", D.D. 1211/2020 and 1104/2021//Italian Ministry of University and Research (MUR)/ ; }, abstract = {Nowadays, different systems for reducing pesticides in table grapes are being tested at different production stages either in the field or in postharvest. The present study tested ozonated water treatments at the beginning of the cold storage of the Princess[®] seedless table grape variety to reduce the residue contents of some pesticides and to evaluate their effect on gray mold and the berry microbiome. An ozone generator capable of producing an ozone concentration ranging from 18 to 65 Nm[3] was utilized for obtaining three ozone concentration levels in water: 3, 5 and 10 mg/L. Ozonated water was placed in a 70 L plastic box where 500 g grape samples closed in perforated plastic clamshell containers were immersed utilizing two washing times (5 and 10 min). Overall, six ozonated water treatments were tested. After the ozonated water treatments, all samples were stored for 30 days at 2 °C and 95% relative humidity to simulate commercial practices. The pesticide residue contents were determined before the ozonated water treatments (T0) and 30 days after the cold storage (T1). The treatments with ozonated water washing reduced the pesticide residues up to 100%, while the SO2 control treatment reduced the pesticide residues ranging from 20.7 to 60.7%. Using 3 mg/L ozonated water to wash grapes for 5 min represented the optimal degradation conditions for all of the analyzed pesticides, except for fludioxonil, which degraded better with a washing time of 10 min. The ozone treatments did not significantly reduce the gray mold and the fungal and bacterial microbiome, while a relevant reduction was observed in the yeast population.}, }
@article {pmid37685071, year = {2023}, author = {Nishigaki, A and Previdelli, R and Alexander, JL and Balarajah, S and Roberts, L and Marchesi, JR}, title = {Identification of a Sub-Clinical Salmonella spp. Infection in a Dairy Cow Using a Commercially Available Stool Storage Kit.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {17}, pages = {}, doi = {10.3390/ani13172807}, pmid = {37685071}, issn = {2076-2615}, abstract = {Stool sampling is a useful tool for diagnosing gastrointestinal disease in veterinary medicine. The sub-clinical disease burden of Salmonella spp. in cattle can become significant for farmers. However, current methods of faecal sampling in a rural setting for diagnosis are not consistently sufficient for the preservation of Salmonella spp. in faeces. This study evaluated the use of a commercial stool storage kit for bacterial preservation in cow faecal samples compared to unpreserved stools placed into refrigeration at different time-points. A stool sample was collected per-rectum from one apparently healthy Holstein-Freisen cow. The sample was weighed and aliquoted into two sterile Falcon tubes and into two commercial kit tubes. The aliquots were then placed into refrigeration at 4 °C at 0, 24, and 96 h after processing. One commercial kit tube was not aliquoted and remained at ambient temperature. After 2 weeks, DNA was extracted from the samples and analysed using endpoint PCR, revealing a sub-clinical infection with Salmonella spp. The bacterium was best preserved when the stool was stored in the commercial kit at ambient temperature and re-homogenised immediately prior to DNA extraction. The unpreserved stool did not maintain obvious levels of Salmonella spp. after 24 h at ambient temperature. This commercial kit should be considered for use in the diagnosis of salmonellosis in cattle.}, }
@article {pmid37685027, year = {2023}, author = {Miao, Y and Zhao, X and Lei, J and Ding, J and Feng, H and Wu, K and Liu, J and Wang, C and Ye, D and Wang, X and Wang, J and Yang, Z}, title = {Characterization of Lung Microbiomes in Pneumonic Hu Sheep Using Culture Technique and 16S rRNA Gene Sequencing.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {17}, pages = {}, doi = {10.3390/ani13172763}, pmid = {37685027}, issn = {2076-2615}, support = {CARS-39-14//China Wool sheep Industry and Technology System project/ ; }, abstract = {Hu sheep, a locally bred species in China known for its high productivity, is currently suffering from pneumonia. Here, we combine high-throughput 16SrRNA gene sequencing and bacterial culturing to examine the bacterial community in pneumonic Hu Sheep lungs (p < 0.05). The results showed that the abundance and diversity of lung bacteria in healthy sheep were significantly higher than those in pneumonia sheep (p = 0.139), while there was no significant difference between moderate and severe pneumonia. Furthermore, the composition of the lung microbiota community underwent significant alterations between different levels of pneumonia severity. The application of LEfSe analysis revealed a notable enrichment of Mannheimiae within the lungs of sheep afflicted with moderate pneumonia (p < 0.01), surpassing the levels observed in their healthy counterparts. Additionally, Fusobacterium emerged as the prevailing bacterial group within the lungs of sheep suffering from severe pneumonia. Integrating the results of bacterial isolation and identification, we conclusively determined that Mannheimia haemolytica was the primary pathogenic bacterium within the lungs of sheep afflicted with moderate pneumonia. Furthermore, the exacerbation of pneumonia may be attributed to the synergistic interplay between Fusobacterium spp. and other bacterial species. Our results provide new insights for guiding preventive and therapeutic measures for pneumonia of different severities in sheep.}, }
@article {pmid37684694, year = {2023}, author = {Liu, S and Men, X and Guo, Y and Cai, W and Wu, R and Gao, R and Zhong, W and Guo, H and Ruan, H and Chou, S and Mai, J and Ping, S and Jiang, C and Zhou, H and Mou, X and Zhao, W and Lu, Z}, title = {Gut microbes exacerbate systemic inflammation and behavior disorders in neurologic disease CADASIL.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {202}, pmid = {37684694}, issn = {2049-2618}, abstract = {BACKGROUND: Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a cerebral small vessel disease that carries mutations in NOTCH3. The clinical manifestations are influenced by genetic and environmental factors that may include gut microbiome.<br><br>RESULTS: We investigated the fecal metagenome, fecal metabolome, serum metabolome, neurotransmitters, and cytokines in a cohort of 24 CADASIL patients with 28 healthy household controls. The integrated-omics study showed CADASIL patients harbored an altered microbiota composition and functions. The abundance of bacterial coenzyme A, thiamin, and flavin-synthesizing pathways was depleted in patients. Neurotransmitter balance, represented by the glutamate/GABA (4-aminobutanoate) ratio, was disrupted in patients, which was consistent with the increased abundance of two major GABA-consuming bacteria, Megasphaera elsdenii and Eubacterium siraeum. Essential inflammatory cytokines were significantly elevated in patients, accompanied by an increased abundance of bacterial virulence gene homologs. The abundance of patient-enriched Fusobacterium varium positively correlated with the levels of IL-1&#x3b2; and IL-6. Random forest classification based on gut microbial species, serum cytokines, and neurotransmitters showed high predictivity for CADASIL with AUC&#x2009;=&#x2009;0.89. Targeted culturomics and mechanisms study further showed that patient-derived F. varium infection caused systemic inflammation and behavior disorder in Notch3[R170C/+] mice potentially via induction of caspase-8-dependent noncanonical inflammasome activation in macrophages.<br><br>CONCLUSION: These findings suggested the potential linkage among the brain-gut-microbe axis in CADASIL. Video Abstract.}, }
@article {pmid37684563, year = {2023}, author = {Liang, W and Feng, Y and Yang, D and Qin, J and Zhi, X and Wu, W and Jie, Q}, title = {Oral probiotics increased the proportion of Treg, Tfr, and Breg cells to inhibit the inflammatory response and impede gestational diabetes mellitus.}, journal = {Molecular medicine (Cambridge, Mass.)}, volume = {29}, number = {1}, pages = {122}, pmid = {37684563}, issn = {1528-3658}, support = {2021-Z04-042//Panyu District Science and Technology Plan Project/ ; 20221A010084//General Guidance Project for Health Science and Technology in Guangzhou/ ; 2022-Z04-115//Panyu District Major Healthcare Project, Project/ ; }, abstract = {BACKGROUND: Children of mothers with gestational diabetes mellitus (GDM) are more prone to acquire type 2 diabetes and obesity as adults. Due to this link, early intervention strategies that alter the gut microbiome may benefit the mother and kid long-term. This work uses metagenomic and transcriptome sequencing to investigate how probiotics affect gut microbiota dysbiosis and inflammation in GDM.<br><br>METHODS: GDM and control metagenomic sequencing data were obtained from the SRA database. This metagenomic data helped us understand gut microbiota abundance and function. KEGG detected and extracted functional pathway genes. Transcriptome sequencing data evaluated GDM-related gene expression. Finally, GDM animal models were given probiotics orally to evaluate inflammatory response, regulatory immune cell fractions, and leptin protein levels.<br><br>RESULTS: GDM patients had more Fusobacteria and Firmicutes, while healthy people had more Bacteroidetes. Gut microbiota composition may affect GDM by altering the L-aspartate and L-asparagine super pathways. Mannan degradation and the super pathway of L-aspartate and L-asparagine synthesis enhanced in GDM mice with leptin protein overexpression. Oral probiotics prevent GDM by lowering leptin. Oral probiotics increased Treg, Tfr, and Breg cells, which decreased TNF-&#x3b1; and IL-6 and increased TGF-&#x3b2; and IL-10, preventing inflammation and preserving mouse pregnancy.<br><br>CONCLUSION: Dysbiosis of the gut microbiota may increase leptin expression and cause GDM. Oral probiotics enhance Treg, Tfr, and Breg cells, which limit the inflammatory response and assist mice in sustaining normal pregnancy. Thus, oral probiotics may prevent GDM, enabling targeted gut microbiota modulation and maternal and fetal health.}, }
@article {pmid37684401, year = {2023}, author = {Wang, S and Zang, M and Yang, X and Lv, L and Chen, L and Cui, J and Liu, Y and Xia, Y and Zhou, N and Yang, Z and Li, Y and Shi, B}, title = {Gut microbiome in men with chronic prostatitis/chronic pelvic pain syndrome: profiling and its predictive significance.}, journal = {World journal of urology}, volume = {}, number = {}, pages = {}, pmid = {37684401}, issn = {1433-8726}, support = {81970661//National Natural Science Foundation of China/ ; 82170790//National Natural Science Foundation of China/ ; 2020SDUCRCC021//Clinical Research Project of Shandong University/ ; grant number 2022JC004//Fundamental Research Funds for the Central Universities/ ; }, abstract = {PURPOSE: To investigate the difference in gut microbiome composition between patients with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) and healthy controls, and to assess the potential of gut microbiota as predictive markers for CP/CPPS risk.<br><br>METHODS: The present study included 41 CP/CPPS patients and 43 healthy controls in China. Fecal specimen data were obtained and analysed using 16S rRNA gene sequencing. Alpha and beta-diversity indices, relative microbiome abundances, cluster analysis, and linear discriminant analysis effect size (LEfSe) were employed. Microbial biomarkers were selected for the development of a diagnostic classification model, and the functional prediction was conducted using PICRUSt2.<br><br>RESULTS: Alpha-diversity measures revealed no statistically significant difference in bacterial community structure between CP/CPPS patients and controls. However, significant differences were observed in the relative abundances of several bacterial genera. Beta-diversity analysis revealed a distinct separation between the two groups. Significant inter-group differences were noted at various taxonomic levels, with specific bacterial genera being significantly different in abundance. The LEfSe analysis indicated that three bacterial species were highly representative and seven bacterial species were low in CP/CPPS patients as compared to the control group. A diagnostic model for CP/CPPS based on microbial biomarkers exhibited good performance. PICRUSt2 functional profiling indicated significant differences in the development and regeneration pathway.<br><br>CONCLUSION: Significant differences in the gut microbiome composition were found between groups. The study provided a novel diagnostic model for CP/CPPS based on microbiota, presenting promising potential for future therapeutic targets and non-invasive diagnostic biomarkers for CP/CPPS patients.}, }
@article {pmid37684335, year = {2023}, author = {Yeo, S and Park, H and Kim, H and Ryu, CB and Huh, CS}, title = {Selenobaculum gbiensis gen. nov. sp. nov., a new bacterium isolated from the gut microbiota of a patient with Crohn's disease.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14835}, pmid = {37684335}, issn = {2045-2322}, support = {NRF-2021R1A6A3A13038425//Ministry of Education/ ; NRF-2021R1I1A1A01057496//Ministry of Education, South Korea/ ; }, abstract = {The human gut microbiota is a complex ecology comprising approximately 10 to 100 trillion microbial cells. Most of the bacteria detected by 16s rRNA sequencing have yet to be cultured, but intensive attempts to isolate the novel bacteria have improved our knowledge of the gut microbiome composition and its roles within human host. In our culturomics study, a novel gram-negative, motile, obligately anaerobic, rod-shaped bacteria, designated as strain ICN-92133[T], was isolated from a fecal sample of a 26-year-old patient with Crohn's disease. Based on the 16s rRNA sequence of strain ICN-92133[T], the phylogeny analysis placed the strain into the family Selenomonadaceae, showing 93.91% similarity with the closely related Massilibacillus massiliensis strain DSM 102838[T]. Strain ICN-92133[T] exhibited a genome size of 2,679,003 bp with a GC content of 35.5% which was predicted to contain 26 potential virulence factors and five antimicrobial resistance genes. In comparative genomic analysis, strain ICN-92133[T] showed digital DNA-DNA Hybridization and OrthoANI values lower than 21.9% and 71.9% with the closest type strains, respectively. In addition, comparing phenotypic, biochemical, and cellular fatty acids with those of closely related strains revealed the distinctiveness of strain ICN-92133[T]. Based on the taxonogenomic results, strain ICN-92133[T] is proposed as a novel species belonging to a new genus. Therefore, we suggest the name of the new genus Selenobaculum gen. nov. within the family Selenomonadaceae and strain ICN-92133[T] (= KCTC 25622[T] = JCM 36070[T]) as a type strain of new species Selenobaculum gbiensis sp. nov.}, }
@article {pmid37683929, year = {2023}, author = {Luo, W and Skondra, D}, title = {Elucidating the Role of the Microbiome in Ocular Diseases.}, journal = {The American journal of pathology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajpath.2023.08.006}, pmid = {37683929}, issn = {1525-2191}, }
@article {pmid37683868, year = {2023}, author = {Wang, J and Zhang, C and Zhao, X and Weng, Y and Nan, X and Han, X and Li, C and Liu, B}, title = {Ingestion and biodegradation of disposable surgical masks by yellow mealworms Tenebrio molitor larvae: Differences in mask layers and effects on the larval gut microbiome.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {166808}, doi = {10.1016/j.scitotenv.2023.166808}, pmid = {37683868}, issn = {1879-1026}, abstract = {During the COVID-19 pandemic, the usage and production of face masks considerably increased, resulting in large quantities of mask waste accumulating in the natural environment. To investigate whether masks of polypropylene (PP) material could be ingested and degraded by insect worms like PP foam plastic, yellow mealworms were provided with different layers of disposable surgical masks as sole diets to for 30 d. Although mask layers, especially the middle layer of melt-blown filter, could be ingested by yellow mealworms, sole mask layer diets had adverse effects on the larval survival and growth. Analyses of Fourier transform infrared spectroscopy, differential scanning calorimeter and thermogravimetric, and gel permeation chromatography demonstrated the changes of functional groups, thermostability and molecular weights in frass compared to original masks, indicating the partial oxidation and degradation of masks. And the depolymerization of the middle layer of masks by yellow mealworms was different from that of other layers. The larval gut bacterial and fungal microbiomes were assessed by Illumina MiSeq, indicating that both of them shifted upon sole layer mask diets. Changes in relative abundances of dominant bacterial and fungal genera demonstrated the strong association between gut microbiome and mask degradation. For instance, unclassified Enterobacteriaceae was closely associated with outer layers degradation. Lactococcus and unclassified Ascomycota were responsible for middle layers degradation, while Lactococcus and Morganella for inner layers degradation. In conclusion, disposable surgical masks of PP material could be ingested and biodegraded by yellow mealworms. The diversities of gut bacterial and fungal microbiomes were associated with the differences in rigid crystalline structures of the layer masks.}, }
@article {pmid37683845, year = {2023}, author = {Kang, J and Qiu, W and Zhang, W and Liu, J and Yang, Z and Wu, Z and Ge, J}, title = {Understanding how various forms of phosphorus stress affect microbiome functions and boost plant disease resistance: Insights from metagenomic analysis.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {166899}, doi = {10.1016/j.scitotenv.2023.166899}, pmid = {37683845}, issn = {1879-1026}, abstract = {The plant's response to phosphorus (P) starvation suppresses its immunity and regulates rhizosphere microbial colonization. However, the impact of various P forms on plant disease resistance and microbial composition remains underreported. This paper examines the soybean rhizosphere microbiome facing co-stress from Fusarium oxysporum and diverse P forms. Macrogenomic analysis evaluates whether P addition enhances plant disease resistance and rhizosphere microbial function, and if such effects relate to P forms. Results show that different P forms mitigate F. oxysporum-induced plant inhibition by promoting P turnover. P forms predominantly affect microbial composition, followed by soil and plant properties. In soybean, the phosphate transport strategy (ugpA/Q) was selected to maintain high P to enhance immunity in the KH2PO4 treatment, while organo-P mineralization (phnH/F/W/G) was selected for superphosphate treatment. The Frankiales, a P-turnover microorganism, copiotrophic microorganisms, and indicator bacteria of plant properties, initially increase after F. oxysporum inoculation and then decrease post P addition, regardless of P forms. Additionally, the rhizosphere microbial community's metabolic activities and compounds significantly aid soybean defense against F. oxysporum, with functional types depending on P forms. Therefore, these findings establish a novel approach to enhance host defense against soil-borne diseases through P nutrition regulation to mediate host-driven metabolic activities of microbial communities.}, }
@article {pmid37682941, year = {2023}, author = {Julien, ME and Shih, JB and Correa Lopes, B and Vallone, LV and Suchodolski, JS and Pilla, R and Scott, EM}, title = {Alterations of the bacterial ocular surface microbiome are found in both eyes of horses with unilateral ulcerative keratitis.}, journal = {PloS one}, volume = {18}, number = {9}, pages = {e0291028}, pmid = {37682941}, issn = {1932-6203}, abstract = {Next generation sequencing (NGS) studies in healthy equine eyes have shown a more diverse ocular surface microbiota compared to culture-based techniques. This study aimed to compare the bacterial ocular surface microbiota in both eyes of horses with unilateral ulcerative keratitis (UK) with controls free of ocular disease. Conjunctival swabs were obtained from both ulcerated eyes and unaffected eyes of 15 client-owned horses with unilateral UK following informed consent, as well as from one eye of 15 healthy horses. Genomic DNA was extracted from the swabs and sequenced on an Illumina platform using primers that target the V4 region of bacterial 16S rRNA. Data were analyzed using Quantitative Insights Into Molecular Ecology (QIIME2). The ocular surface of ulcerated eyes had significantly decreased species richness compared with unaffected fellow eyes (Chao1 q = 0.045, Observed ASVs p = 0.045) with no differences in evenness of species (Shannon q = 0.135). Bacterial community structure was significantly different between either eye of horses with UK and controls (unweighted UniFrac: control vs. unaffected, p = 0.03; control vs. ulcerated, p = 0.003; unaffected vs. ulcerated, p = 0.016). Relative abundance of the gram-positive taxonomic class, Bacilli, was significantly increased in ulcerated eyes compared with controls (q = 0.004). Relative abundance of the taxonomic family Staphylococcaceae was significantly increased in ulcerated and unaffected eyes compared with controls (q = 0.030). The results suggest the occurrence of dysbiosis in infected eyes and reveal alterations in beta diversity and taxa of unaffected fellow eyes. Further investigations are necessary to better understand the role of the microbiome in the pathophysiology of ocular surface disease.}, }
@article {pmid37682902, year = {2023}, author = {Martinez-Marin, D and Helmer, RA and Kaur, G and Washburn, RL and Martinez-Zaguilan, R and Sennone, SR and Dufour, JM and Chilton, BS}, title = {Helicase-like transcription factor (HLTF)-deleted CDX/TME model of colorectal cancer increased transcription of oxidative phosphorylation genes and diverted glycolysis to boost S-glutathionylation in lymphatic intravascular metastatic niches.}, journal = {PloS one}, volume = {18}, number = {9}, pages = {e0291023}, pmid = {37682902}, issn = {1932-6203}, abstract = {Helicase-like transcription factor (HLTF) also known as SMARCA3, protects genome integrity. A tumor suppressor, HLTF is expressed in tumor cells but not in the tumor microenvironment (TME) in early-stage colorectal cancer (CRC). With disease progression, there is high concordance between epigenetic silencing of HLTF in CRC cells and negligible HLTF expression in the TME. We developed a cell line-derived xenograft (CDX) model and show for the first time that HLTF-deletion in cancer cells and the TME results in metabolic reprogramming that mitigates oxidative stress in lymphatic intravascular metastatic niches. The two metabolic pathways that derive energy from glucose-glycolysis and oxidative phosphorylation (OXPHOS)-are variously utilized by cancer cells depending upon the TME. HIF-1α, a master regulator of glycolysis, was eliminated from a role in reprogramming metabolism to satisfy CDX energetic requirements by RNAseq and spatial transcriptomics. Variability in the gut microbiome, with a putative role in altered metabolism, was also eliminated. HLTF-deleted cancer cells recovered from DNA damage at a transcriptomic level induction of DNA repair and OXPHOS genes linked to an amoeboid-associated phenotype at the tumor border (confocal microscopy). HLTF-deleted cancer and endothelial cells of lymphatic (PDPN) intravascular niches in the TME shared a site-specific protein S-glutathionylation signature (2D DIGE, MALDI-TOF/TOF mass spectrometry) for three glycolytic enzymes (PGK1 Cys379/380, PGAM1 Cys55, ENOA1 Cys119) that diverted glycolysis in support of continued glutathione biosynthesis. The collective absence of HLTF/Hltf from tumor and TME achieved redox homeostasis throughout the CDX and promoted metastasis.}, }
@article {pmid37682568, year = {2023}, author = {Moir, J and Hyman, M and Wang, J and Flores, A and Skondra, D}, title = {The Association of Antibiotic Use and the Odds of a New-Onset ICD Code Diagnosis of Age-Related Macular Degeneration: A Large National Case-Control Study.}, journal = {Investigative ophthalmology &amp; visual science}, volume = {64}, number = {12}, pages = {14}, doi = {10.1167/iovs.64.12.14}, pmid = {37682568}, issn = {1552-5783}, abstract = {PURPOSE: The widespread use of antibiotics has many well-documented impacts on the human microbiome, which may be associated with the development of various inflammatory diseases. Despite age-related macular degeneration (AMD) featuring an inflammatory pathogenesis, the relationship between antibiotics and AMD has remained unexplored. We conducted the first study to determine the association between antibiotic exposure and a new-onset International Classification of Diseases (ICD) diagnosis of AMD.<br><br>METHODS: We performed a case-control analysis of patients aged 55 and older with new-onset AMD between 2008 and 2017 from a nationwide commercial health insurance claims database. Exposure to antibiotics in the two years before the index date was determined for cases and controls matched one-to-one by age, year, region, anemia, hypertension, and a comorbidity index. Conditional multivariable logistic regression, adjusted for AMD risk factors, was performed to calculate odd ratios (OR) and 95% confidence intervals (CI).<br><br>RESULTS: Among the antibiotic classes, exposure to aminoglycosides (OR = 1.24; 95% CI, 1.22-1.26) and fluoroquinolones (OR = 1.13; 95% CI, 1.12-1.14) was associated with the greatest odds of a new-onset ICD code diagnosis of AMD. Broad-spectrum antibiotics were associated with nearly three times greater odds of a new-onset ICD code diagnosis of AMD (OR = 1.15; 95% CI, 1.13-1.16) compared to narrow-spectrum antibiotics (OR = 1.05; 95% CI, 1.03-1.07). We also identified a frequency- and duration-dependent association, with a greater cumulative number of antibiotic prescriptions or day supply of antibiotics conferring increased odds of a new-onset ICD code diagnosis of AMD.<br><br>CONCLUSIONS: Greater cumulative exposure to antibiotics, particularly fluoroquinolones, aminoglycosides, and those with broader-spectrum coverage, may be associated with the development of AMD, a finding that requires further investigation using prospective studies.}, }
@article {pmid37681948, year = {2023}, author = {Hyde, J and Brackney, DE and Steven, B}, title = {Three species of axenic mosquito larvae recruit a shared core of bacteria in a common garden experiment.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0077823}, doi = {10.1128/aem.00778-23}, pmid = {37681948}, issn = {1098-5336}, abstract = {In this study, we describe the generation of two new species of axenic mosquito, Aedes albopictus and Aedes triseriatus. Along with Aedes aegypti, axenic larvae of these three species were exposed to an environmental water source to document the assembly of the microbiome in a common garden experiment. Additionally, the larvae were reared either individually or combinatorially with the other species to characterize the effects of co-rearing on the composition of the microbiome. We found that the microbiome of the larvae was composed of a relatively low-diversity collection of bacteria from the colonizing water. The abundance of bacteria in the water was a poor predictor of their abundance in the larvae, suggesting the larval microbiome is made up of a subset of relatively rare aquatic bacteria. We found 11 bacterial 16S rRNA gene amplicon sequence variants (ASVs) that were conserved among ≥90% of the mosquitoes sampled, including 2 found in 100% of the larvae, pointing to a conserved core of bacteria capable of colonizing all three species of mosquito. Yet, the abundance of these ASVs varied widely between larvae, suggesting individuals harbored largely unique microbiome structures, even if they overlapped in membership. Finally, larvae reared in a tripartite mix of the host-species consistently showed a convergence in the structure of their microbiome, indicating that multi-species interactions between hosts potentially lead to shifts in the composition of their respective microbiomes.IMPORTANCEThis study is the first report of the axenic (free of external microbes) rearing of two species of mosquito, Aedes albopictus and Aedes triseriatus. Our previous report of axenic Aedes aegypti brings the number of axenic species to three. We designed a method to perform a common garden experiment to characterize the bacteria the three species of axenic larvae assemble from their surroundings. Furthermore, species could be reared in isolation or in multi-species combinations to assess how host-species interactions influence the composition of the microbiome. We found all three species recruited a common core of bacteria from their rearing water, with a large contingent of rare and sporadically detected bacteria. Finally, we also show that co-rearing of mosquito larvae leads to a coalescence in the composition of their microbiome, indicating that host-species interactions potentially influence the composition of the microbiome.}, }
@article {pmid37681584, year = {2023}, author = {Manchester, AC and Dow, S and Chow, L and Gagne, J and Lappin, MR}, title = {Efficacy of an elemental diet in achieving clinical remission in dogs with chronic enteropathy.}, journal = {Journal of veterinary internal medicine}, volume = {}, number = {}, pages = {}, doi = {10.1111/jvim.16846}, pmid = {37681584}, issn = {1939-1676}, abstract = {BACKGROUND: Diet may induce clinical remission in dogs with chronic enteropathy (CE). Elemental diets (EDs), providing protein as amino acids, modulate intestinal immunity and microbiome in rodents and humans.<br><br>HYPOTHESIS: Evaluate the impact of an amino acid-based kibble (EL) on CE clinical activity and gastrointestinal (GI)-relevant variables.<br><br>ANIMALS: Client-owned dogs (n&#x2009;=&#x2009;23) with inadequately controlled CE.<br><br>METHODS: Prospective, uncontrolled clinical trial. Diagnostic evaluation including upper and lower GI endoscopy was performed before study entry. Canine chronic enteropathy clinical activity index (CCECAI), serum biomarkers, and fecal microbiome were evaluated before and after 2&#x2009;weeks of EL. Dogs with stable or improved CE remained in the study for another 6&#x2009;weeks. Pre- and post-EL clinical and microbiological variables were compared statistically using a mixed model.<br><br>RESULTS: After 2&#x2009;weeks of EL, 15 of 22 dogs (68%; 95% confidence interval [CI], 47%-84%) consuming the diet were classified as responders with a median (range) decrease in CCECAI from 6 (3-12) to 2 (0-9; P&#x2009;<&#x2009;.001). Fourteen of 15 responders and 2/7 nonresponders at 2&#x2009;weeks completed the trial; all 16 were experiencing adequate control at week 8 with a median CCECAI of 2 (0-3). In total, 16/23 dogs (70%; 95% CI, 49%-84%) were responders. Feeding EL caused shifts in fecal bacterial communities, which differed between responders and nonresponders. Serum biomarker concentrations were unchanged throughout the study apart from serum alkaline phosphatase activity.<br><br>CONCLUSIONS: Exclusive feeding of EL improved clinical signs in 16 of 23 dogs with uncontrolled CE. Fecal microbiome shifts were associated with response to diet and may represent a mechanism for clinical improvement.}, }
@article {pmid37681253, year = {2023}, author = {Matthee, CA and Bierman, A and Krasnov, BR and Matthee, S and van der Mescht, L}, title = {Documenting the microbiome diversity and distribution in selected Ctenocephalides fleas from southern Africa.}, journal = {Parasitology}, volume = {}, number = {}, pages = {1-31}, doi = {10.1017/S0031182023000835}, pmid = {37681253}, issn = {1469-8161}, support = {Grant to Conrad Matthee//Universiteit Stellenbosch/ ; Grant to Sonja Matthee//Universiteit Stellenbosch/ ; Grant to Luther van der Mescht//Claude Leon Foundation/ ; }, }
@article {pmid37681179, year = {2023}, author = {He, H and Huang, J and Zhao, Z and Du, P and Li, J and Xin, J and Xu, H and Feng, W and Zheng, X}, title = {Whole genome analysis of Streptomyces sp. RerS4, a Rehmannia glutinosa rhizosphere microbe producing a new lipopeptide.}, journal = {Heliyon}, volume = {9}, number = {9}, pages = {e19543}, pmid = {37681179}, issn = {2405-8440}, abstract = {Rehmannia glutinosa, a valuable medicinal plant, is threatened by ring rot, a condition that greatly affects its yield and quality. Interactions between plant and the rhizosphere soil microbiome in the context of pathogen invasion are generally more specific, with recruitment of specialized microbes potentially antagonistic to a certain pathogen. Isolation of microorganisms from rhizosphere soil of healthy and ring rot-infected R. glutinosa was carried out to screen antifungal microbes. A strain designated RerS4 isolated from ring rot-infected R. glutinosa rhizosphere soil with strong antifungal activities was selected for further study. RerS4 was taxonomically characterized as the genus Streptomyces according to its morphology and 16S rRNA sequences that were most closely related to Streptomyces racemochromogenes NRRL B-5430[T] (99.72%) and Streptomyces polychromogenes NBRC 13072[T] (99.72%). A new lipopeptide isolated from RerS4 showed restrained proliferation, but was devoid of significant antibacterial and antioxidant activity with minimum inhibitory concentration (MIC) values of 20.3 ± 2.5 and 70.8 ± 3.7 μg/mL and half-maximal inhibitory concentration (IC50) values of 23.3 ± 0.8 and 58.8 ± 2.9 μg/mL, respectively. In addition, we report the complete genome sequence of Streptomyces sp. RerS4, which consists of a 7,301,482 bp linear chromosome and a 242,139 bp plasmid. Genome analysis revealed that Streptomyces sp. RerS4 contained 25 biosynthetic gene clusters (BGCs) for secondary metabolites, among which 68% had low similarities with known BGCs, leading us to believe that Streptomyces sp. RerS4 could produce valuable bioactive compounds.}, }
@article {pmid37680975, year = {2023}, author = {Ashy, RA}, title = {Functional analysis of bacterial genes accidentally packaged in rhizospheric phageome of the wild plant species Abutilon fruticosum.}, journal = {Saudi journal of biological sciences}, volume = {30}, number = {10}, pages = {103789}, pmid = {37680975}, issn = {1319-562X}, abstract = {The study aimed to reveal the structure and function of phageome existing in soil rhizobiome of Abutilon fruticosum in order to detect accidentally-packaged bacterial genes that encode Carbohydrate-Active enZymes (or CAZymes) and those that confer antibiotic resistance (e.g., antibiotic resistance genes or ARGs). Highly abundant genes were shown to mainly exist in members of the genera Pseudomonas, Streptomyces, Mycobacterium and Rhodococcus. Enriched CAZymes belong to glycoside hydrolase families GH4, GH6, GH12, GH15 and GH43 and mainly function in D-glucose biosynthesis via 10 biochemical passages. Another enriched CAZyme, e.g., alpha-galactosidase, of the GH4 family is responsible for the wealth of different carbohydrate forms in rhizospheric soil sink of A. fruticosum. ARGs of this phageome include the soxR and OleC genes that participate in the "antibiotic efflux pump" resistance mechanism, the parY mutant gene that participates in the "antibiotic target alteration" mechanism and the arr-1, iri, and AAC(3)-Ic genes that participate in the "antibiotic inactivation" mechanism. It is claimed that the genera Streptomyces, which harbors phages with oleC and parY mutant genes, and Pseudomonas, which harbors phages with soxR and AAC(3)-Ic genes, are approaching multidrug resistance via newly disseminating phages. These ARGs inhibit many antibiotics including oleandomycin, tetracycline, rifampin and aminoglycoside. The study highlights the possibility of accidental packaging of these ARGs in soil phageome and the risk of their horizontal transfer to human gut pathogens through the food chain as detrimental impacts of soil phageome of A. fruticosum. The study also emphasizes the beneficial impacts of phageome on soil microbiome and plant interacting in storing carbohydrates in the soil sink for use by the two entities upon carbohydrate deprivation.}, }
@article {pmid37680751, year = {2023}, author = {Xu, T and Chen, N and He, X and Chen, F}, title = {Editorial: The relationship of oral and other body sites microbiome in human diseases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1276473}, pmid = {37680751}, issn = {2235-2988}, }
@article {pmid37680634, year = {2023}, author = {Garrido-Mesa, J and Gálvez, J and Garrido-Mesa, N}, title = {Editorial: The gut-immune axis: a complex training ground impacting inflammatory pathologies.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1274761}, doi = {10.3389/fimmu.2023.1274761}, pmid = {37680634}, issn = {1664-3224}, }
@article {pmid37680535, year = {2023}, author = {Liu, R and Shen, Y and Ma, H and Li, Y and Lambo, MT and Dai, B and Shen, W and Qu, Y and Zhang, Y}, title = {Silibinin reduces in vitro methane production by regulating the rumen microbiome and metabolites.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1225643}, pmid = {37680535}, issn = {1664-302X}, abstract = {This study used Silibinin as an additive to conduct fermentation experiments, wherein its effects on rumen gas production, fermentation, metabolites, and microbiome were analyzed in vitro. The silibinin inclusion level were 0 g/L (control group), 0.075 g/L, 0.15 g/L, 0.30 g/L, and 0.60 g/L (experimental group). Fermentation parameters, total gas production, carbon dioxide (CO2), methane (CH4), hydrogen (H2), and their percentages were determined. Further analysis of the rumen microbiome's relative abundance and α/β diversity was performed on the Illumina NovaSeq sequencing platform. Qualitative and quantitative metabolomics analyses were performed to analyze the differential metabolites and metabolic pathways based on non-targeted metabolomics. The result indicated that with an increasing dose of silibinin, there was a linear reduction in total gas production, CO2, CH4, H2 and their respective percentages, and the acetic acid to propionic acid ratio. Concurrent with a linear increase in pH, when silibinin was added at 0.15 g/L and above, the total volatile fatty acid concentration decreased, the acetic acid molar ratio decreased, the propionic acid molar ratio increased, and dry matter digestibility decreased. At the same time, the relative abundance of Prevotella, Isotricha, Ophryoscolex, unclassified_Rotifera, Methanosphaera, Orpinomyces, and Neocallimastix in the rumen decreased after adding 0.60 g/L of silibinin. Simultaneously, the relative abundance of Succiniclasticum, NK4A214_group, Candidatus_Saccharimonas, and unclassified_Lachnospiraceae increased, altering the rumen species composition, community, and structure. Furthermore, it upregulated the ruminal metabolites, such as 2-Phenylacetamide, Phlorizin, Dalspinin, N6-(1,2-Dicarboxyethyl)-AMP, 5,6,7,8-Tetrahydromethanopterin, Flavin mononucleotide adenine dinucleotide reduced form (FMNH), Pyridoxine 5'-phosphate, Silibinin, and Beta-D-Fructose 6-phosphate, affecting phenylalanine metabolism, flavonoid biosynthesis, and folate biosynthesis pathways. In summary, adding silibinin can alter the rumen fermentation parameters and mitigate enteric methane production by regulating rumen microbiota and metabolites, which is important for developing novel rumen methane inhibitors.}, }
@article {pmid37680534, year = {2023}, author = {Zhang, S and Zhang, W and Ren, H and Xue, R and Wang, Z and Wang, Z and Lv, Q}, title = {Mendelian randomization analysis revealed a gut microbiota-mammary axis in breast cancer.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1193725}, pmid = {37680534}, issn = {1664-302X}, abstract = {BACKGROUND: Observational epidemiological studies suggested an association between the gut microbiota and breast cancer, but it remains unclear whether the gut microbiota causally influences the risk of breast cancer. We employed two-sample Mendelian randomization (MR) analysis to investigate this association.<br><br>METHODS: We used summary statistics of the gut microbiome from a genome-wide association study (GWAS) of 18,340 individuals in the MiBioGen study. GWAS summary statistics for overall breast cancer risk and hormone receptor subtype-specific analyses were obtained from the UK Biobank and FinnGen databases, totaling 400,000 individuals. The inverse variance-weighted (IVW) MR method was used to examine the causal relationship between the gut microbiome and breast cancer and its subtypes. Sensitivity analyses were conducted using maximum likelihood, MR-Egger, and MR pleiotropic residual sums and outliers methods.<br><br>RESULTS: The IVW estimates indicated that an increased abundance of Genus_Sellimonas is causally associated with an increased risk of ER+ breast cancer [odds ratio (OR)&#x2009;=&#x2009;1.09, p&#x2009;=&#x2009;1.72E-04, false discovery rate (FDR)&#x2009;=&#x2009;0.02], whereas an increased abundance of Genus_Adlercreutzia was protective against ER+ breast cancer (OR&#x2009;=&#x2009;0.88, p&#x2009;=&#x2009;6.62E-04, FDR&#x2009;=&#x2009;0.04). For Her2+ breast cancer, an increased abundance of Genus_Ruminococcus2 was associated with a decreased risk (OR&#x2009;=&#x2009;0.77, p&#x2009;=&#x2009;4.91E-04, FDR&#x2009;=&#x2009;0.04), whereas an increased abundance of Genus_Erysipelatoclostridium was associated with an increased risk (OR&#x2009;=&#x2009;1.25, p&#x2009;=&#x2009;6.58E-04, FDR&#x2009;=&#x2009;0.04). No evidence of heterogeneity or horizontal pleiotropy was found.<br><br>CONCLUSION: Our study revealed a gut microbiota-mammary axis, providing important data supporting the potential use of the gut microbiome as a candidate target for breast cancer prevention, diagnosis, and treatment.}, }
@article {pmid37680532, year = {2023}, author = {Katagiri, S and Ohsugi, Y and Shiba, T and Yoshimi, K and Nakagawa, K and Nagasawa, Y and Uchida, A and Liu, A and Lin, P and Tsukahara, Y and Iwata, T and Tohara, H}, title = {Homemade blenderized tube feeding improves gut microbiome communities in children with enteral nutrition.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1215236}, pmid = {37680532}, issn = {1664-302X}, abstract = {Enteral nutrition for children is supplied through nasogastric or gastrostomy tubes. Diet not only influences nutritional intake but also interacts with the composition and function of the gut microbiota. Homemade blenderized tube feeding has been administered to children receiving enteral nutrition, in addition to ready-made tube feeding. The purpose of this study was to evaluate the oral/gut microbial communities in children receiving enteral nutrition with or without homemade blenderized tube feeding. Among a total of 30 children, 6 receiving mainly ready-made tube feeding (RTF) and 5 receiving mainly homemade blenderized tube feeding (HBTF) were analyzed in this study. Oral and gut microbiota community profiles were evaluated through 16S rRNA sequencing of saliva and fecal samples. The α-diversity representing the number of observed features, Shannon index, and Chao1 in the gut were significantly increased in HBTF only in the gut microbiome but not in the oral microbiome. In addition, the relative abundances of the phylum Proteobacteria, class Gammaproteobacteria, and genus Escherichia-Shigella were significantly low, whereas that of the genus Ruminococcus was significantly high in the gut of children with HBTF, indicating HBTF altered the gut microbial composition and reducing health risks. Metagenome prediction showed enrichment of carbon fixation pathways in prokaryotes at oral and gut microbiomes in children receiving HBTF. In addition, more complex network structures were observed in the oral cavity and gut in the HBTF group than in the RTF group. In conclusion, HBTF not only provides satisfaction and enjoyment during meals with the family but also alters the gut microbial composition to a healthy state.}, }
@article {pmid37680529, year = {2023}, author = {Adejoro, DO and Jones, EE and Ridgway, HJ and Mundy, DC and Vanga, BR and Bulman, SR}, title = {Grapevines escaping trunk diseases in New Zealand vineyards have a distinct microbiome structure.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1231832}, pmid = {37680529}, issn = {1664-302X}, abstract = {Grapevine trunk diseases (GTDs) are a substantial challenge to viticulture, especially with a lack of available control measures. The lack of approved fungicides necessitates the exploration of alternative controls. One promising approach is the investigation of disease escape plants, which remain healthy under high disease pressure, likely due to their microbiome function. This study explored the microbiome of grapevines with the disease escape phenotype. DNA metabarcoding of the ribosomal internal transcribed spacer 1 (ITS1) and 16S ribosomal RNA gene was applied to trunk tissues of GTD escape and adjacent diseased vines. Our findings showed that the GTD escape vines had a significantly different microbiome compared with diseased vines. The GTD escape vines consistently harbored a higher relative abundance of the bacterial taxa Pseudomonas and Hymenobacter. Among fungi, Aureobasidium and Rhodotorula were differentially associated with GTD escape vines, while the GTD pathogen, Eutypa, was associated with the diseased vines. This is the first report of the link between the GTD escape phenotype and the grapevine microbiome.}, }
@article {pmid37680522, year = {2023}, author = {You, Y and Zhang, W and Cai, M and Guo, Q and Wang, J and Cai, Y and Lin, J}, title = {Discovery of fecal microbial signatures in patients with ankylosing spondylitis.}, journal = {Archives of rheumatology}, volume = {38}, number = {2}, pages = {217-229}, pmid = {37680522}, issn = {2618-6500}, abstract = {OBJECTIVES: This study aimed to investigate the characteristics of the gut microbiota in Chinese patients with ankylosing spondylitis (AS) and healthy controls in Quanzhou aiming to explore the correlation between microbiome changes and AS activities.<br><br>PATIENTS AND METHODS: In this study, high-throughput sequencing of the gene of 16S ribosomal RNA (16S rRNA) in fecal samples from 40 AS patients and 40 healthy controls, for a total of 80 participants (70 males, 10 females; mean age 33.7&#xb1;10.7 years; range, 15 to 58 years), was conducted between January 2018 and January 2019. Alpha and beta diversity were analyzed using the QIIME (Quantitative Insights Into Microbial Ecology) software, and differences were analyzed using Student's t-test, linear discriminant analysis coupled with effect size and Metastats. Finally, a correlation network was constructed using Pearson's analysis.<br><br>RESULTS: The alpha index values of the AS group were not significantly different from those of the control group. At the genus level, eight genera, Ruminiclostridium_9, Fusicatenibacter, Adlercreutzia, CAG-56, Intestinimonas, Lachnospira, Bacteroides, and Pseudoflavonifractor, were significantly enriched in patients with AS, whereas the abundance of uncultured_bacterium_f_Saccharimonadaceae, Prevotella_7, uncultured_bacterium_f_ Enterobacteriaceae, Cronobacter, Prevotellaceae_NK3B31_group, and Weissella were significantly decreased in patients with AS. In addition, diseaserelated gut microbial communities were detected in patients with AS.<br><br>CONCLUSION: We found differences in the gut microbiome between the patients with AS and controls and identified potential disease activity-related bacterial communities.}, }
@article {pmid37680388, year = {2023}, author = {Fernández-Pinteño, A and Pilla, R and Manteca, X and Suchodolski, J and Torre, C and Salas-Mani, A}, title = {Age-associated changes in intestinal health biomarkers in dogs.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1213287}, pmid = {37680388}, issn = {2297-1769}, abstract = {The gut microbiome is critical for maintaining host health. In healthy humans, the aging process is one of the main factors modulating the changes in the intestinal microbiota. However, little is known about the relationship between gut health, microbiota, and the aging process in dogs. The present study aims to explore the differences in the intestinal microbiota and intestinal health based on fecal biomarkers in a population of dogs of different ages. The study involved 106 dogs of different breeds aged between 0.2 and 15 years categorized as senior (>7 years; n = 40), adult (2-7 years; n = 50), and junior (< 2 years; n = 16). Fecal samples were collected during the same period at the same facilities. The analysis included the following gut health indicators: 16S rRNA gene sequencing to investigate the differences in the fecal microbiota; qPCR to determine the dysbiosis index; fecal short-chain fatty acid concentrations; fecal calprotectin; and immunoglobulin A. Beta diversity analysis revealed a significant difference with a small effect size (p = 0.003; R = 0.087) among age categories based on the unweighted UniFrac metric, but no significance was observed based on the weighted UniFrac metric or Bray-Curtis distances. There were no significant differences in the alpha diversity measures or the fecal dysbiosis index among age categories. Senior dogs had significantly higher relative abundance proportions in phyla Bacteroidota and Pseudomonadota and the genus Faecalibacterium, but not on qPCR analysis. At the family level, Ruminococcaceae, Uncl. Clostridiales.1, Veillonellaceae, Prevotellaceae, Succinivibrionaceae, and Bacteroidaceae abundances were higher in the senior category than in the adult and/or junior categories. Relative proportions, but not concentrations of fecal acetate, were higher in the senior category, while butyrate, isovaleric acid, and valeric acid were lower. The valeric acid concentration was significantly lower in the senior category than in the adult category. Calprotectin and immunoglobulin A levels did not differ significantly across groups. In conclusion, this study observed multiple minor changes in the fecal microbiota composition and the relative amount of short-chain fatty acids in dogs among different age groups, but studies in larger populations representative of all ages are warranted to refine the present results.}, }
@article {pmid37680359, year = {2023}, author = {Yuan, T and Qazi, IH and Li, J and Yang, P and Yang, H and Zhang, X and Liu, W and Liu, J}, title = {Analysis of changes in bacterial diversity in healthy and bacterial wilt mulberry samples using metagenomic sequencing and culture-dependent approaches.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1206691}, pmid = {37680359}, issn = {1664-462X}, abstract = {INTRODUCTION: Mulberry bacterial wilt is a serious destructive soil-borne disease caused by a complex and diverse group of pathogenic bacteria. Given that the bacterial wilt has been reported to cause a serious damage to the yield and quality of mulberry, therefore, elucidation of its main pathogenic groups is essential in improving our understanding of this disease and for the development of its potential control measures.<br><br>METHODS: In this study, combined metagenomic sequencing and culture-dependent approaches were used to investigate the microbiome of healthy and bacterial wilt mulberry samples.<br><br>RESULTS: The results showed that the healthy samples had higher bacterial diversity compared to the diseased samples. Meanwhile, the proportion of opportunistic pathogenic and drug-resistant bacterial flora represented by Acinetobacter in the diseased samples was increased, while the proportion of beneficial bacterial flora represented by Proteobacteria was decreased. Ralstonia solanacearum species complex (RSSC), Enterobacter cloacae complex (ECC), Klebsiella pneumoniae, K. quasipneumoniae, K. michiganensis, K. oxytoca, and P. ananatis emerged as the main pathogens of the mulberry bacterial wilt.<br><br>DISCUSSION: In conclusion, this study provides a valuable reference for further focused research on the bacterial wilt of mulberry and other plants.}, }
@article {pmid37680119, year = {2023}, author = {Gao, K and Chen, L and Chen, C and Chen, Z and Zhang, Q and Fan, Q and Li, Y and Chen, S}, title = {Leuconostoc mesenteroides WHH1141 ameliorates ovalbumin-induced food allergy in mice.}, journal = {Journal of food science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1750-3841.16760}, pmid = {37680119}, issn = {1750-3841}, support = {//Science and Technology Projects of Zhejiang Province/ ; }, abstract = {Food allergy (FA) is acknowledged as a significant public health and food safety issue, due to its manifestation as an amplified immune reaction to food antigens. Recently, probiotics within Lactobacillus and Bifidobacterium have been highlighted as a promising strategy against allergic disease by modulating the balance of Th1/Th2 responses. However, the allergy-alleviating effects of probiotic Leuconostoc mesenteroides strains are unknown. Therefore, this study investigated the potentials of eleven L. mesenteroides strains on the Th1/Th2 balance in vitro by evaluating the expression patterns of interferon-gamma (IFN-γ) (Th1 cytokine) and interleukin-4 (IL-4) (Th2 cytokine) in mesenteric lymph node-derived lymphocytes from ovalbumin (OVA)-sensitized mice. Among strains, WHH1141 incubation caused the highest IFN-γ/IL-4 ratio. Oral administration of WHH1141 (1 × 10[9] CFU/mL) in the OVA-induced FA mouse model for 40 days improved the weight loss and FA pathological symptoms and normalized the serum immunoglobulin E levels. Meanwhile, the OVA-induced elevated gene expressions of cytokines (IL-4, IL-5, and IL-13) and tight-junction proteins (ZO-1 and Occludin) and levels of cytokines (IL-4, IL-5, and IL-13) and histamine in the jejunum were restored by WHH1141. Furthermore, WHH1141 reversed the reduced gut microbial diversity and short-chain fatty acid (SCFA) levels, specifically increased Bacteroidota abundance, and decreased Firmicutes abundance in OVA-induced mice. Overall, these findings suggest that WHH1141 exerts FA-alleviating effects on OVA-induced mice, which is involved with the inhibition of the jejunal Th2 immune responses and the modulation of gut microbiome composition and SCFA productions. PRACTICAL APPLICATION: Leuconostoc mesenteroides WHH1141 with FA-alleviating potentials may be considered a promising approach in the mitigation of FA symptoms.}, }
@article {pmid37680093, year = {2023}, author = {de la Cuesta-Zuluaga, J and Huus, KE and Youngblut, ND and Escobar, JS and Ley, RE}, title = {Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2246634}, pmid = {37680093}, issn = {1949-0984}, abstract = {Obesity (OB) and cardiometabolic disease are major public health issues linked to changes in the gut microbiome. OB and poor cardiometabolic health status (CHS) are often comorbid, which hinders efforts to identify components of the microbiome uniquely linked to either one. Here, we used a deeply phenotyped cohort of 408 adults from Colombia, including subjects with OB, unhealthy CHS, or both, to validate previously reported features of gut microbiome function and diversity independently correlated with OB or CHS using fecal metagenomes. OB was defined by body mass index, waist circumference, and body fat; CHS as healthy or unhealthy according to blood biochemistry and anthropometric data. We found that OB, more so than metabolic status, drove associations with gut microbiome structure and functions. The microbiome of obese individuals with and without co-existing unhealthy CHS was characterized by reduced metagenomic diversity, reduced fermentative potential and elevated capacity to respond to oxidative stress and produce bacterial antigens. Disease-linked features were correlated with increased host blood pressure and inflammatory markers, and were mainly contributed by members of the family Enterobacteriaceae. Our results link OB with a microbiome able to tolerate an inflammatory and oxygenated gut state, and suggest that OB is the main driver of microbiome functional differences when poor CHS is a comorbidity.}, }
@article {pmid37679873, year = {2023}, author = {Menzies, J and Sundararaj, A and Cardamone, M and McHarg, A and Leach, ST and Krishnan, U}, title = {Ketogenic diets in children with intractable epilepsy and its effects on gastrointestinal function, gut microbiome, inflammation, and quality of life.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1097/MPG.0000000000003928}, pmid = {37679873}, issn = {1536-4801}, abstract = {OBJECTIVES: The ketogenic diet (KD) is a treatment for children with intractable epilepsy (IE), it can cause gastrointestinal symptoms, and have an adverse effect on growth, nutrition and quality of life (QOL). This study investigated the extent of these side-effects by comparing children with IE on KDs to their counterparts on normal diets.<br><br>METHODS: Patients with IE were categorised into patients with KD or control groups. Gastrointestinal side effects and QOL were assessed using the PedsQL&#x2122; Gastrointestinal Symptoms Module. Cross sectional growth, gut microbiome compositions and inflammation levels were also analysed.<br><br>RESULTS: Fourteen patients on the KD and 13 control patients were enrolled. Patients had been on KD for a median duration of 15 months (Interquartile range (IQR): 9.8 to 60 months). The patients on the KD reported a trend to lower total gastrointestinal symptoms scores (more symptoms) compared to control patients, at 71.1 and 84.9 respectively (p=0.06, not significant). Patients on the KD had significantly lower QOL scores compared to control patients(p=0.01). Patients on the KD were found to have consistently lower median height/length, weight and Body mass index (BMI) z scores compared to the controls although these were not statistically significant. Patients on the KD had a lower microbial diversity, Both groups had a normal level of S100A12, a marker of gut inflammation.<br><br>CONCLUSIONS: Patients on the KD reported a trend to more gastrointestinal symptoms and more QOL concerns compared to controls. Although microbial differences were noted in patients on the KD, this did not result in detectable gut inflammation.}, }
@article {pmid37679818, year = {2023}, author = {Cui, W and Hull, L and Zizzo, A and Wang, L and Lin, B and Zhai, M and Xiao, M}, title = {The gut microbiome changes in wild type and IL-18 knockout mice after 9.0 Gy total body irradiation.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {42}, pmid = {37679818}, issn = {2524-4671}, support = {AFR-B2-10449//NIH/NIAID/RNCP All Government IAA/ ; AFR-B2-10449//NIH/NIAID/RNCP All Government IAA/ ; RAB24360//Armed Forces Radiobiology Research Institute, Uniformed Services University/ ; AFR-B2-10631//Defense Medical Research and Development Program JPC-7/ ; }, abstract = {BACKGROUND: Recent studies have shown that gut microbiome plays important roles in response to radiation exposure. IL-18, an inflammatory cytokine, is highly elevated in mice, mini-pigs and nonhuman primates after radiation exposure. Blocking IL-18 using its endogenous binding protein (IL-18BP) increases mice survival after radiation exposure by decreasing bone marrow interferon-gamma levels.<br><br>METHODS: To further characterize the roles of IL-18 in response to radiation, both wild type and IL-18 knockout (IL-18 KO) mice were exposed to 9.0&#xa0;Gy total body irradiation (TBI). The 30-day survival result demonstrated that IL-18 KO mice were significantly more resistant to radiation compared to the wild type mice (p&#x2009;<&#x2009;0.0001). Mouse faecal samples were collected at pre-radiation (d0), d1, d3, d7, d14, d21 and d29 after radiation exposure. Microbiome profiling was performed on the faecal samples using 16S and ITS sequencing technology.<br><br>RESULTS: Data analysis showed that there was significant difference in the bacterial microbiome between wild type and IL-18 KO mice. Cohousing of wild type and IL-18 KO mice decreased the bacterial microbiome difference between the two genotypes. Much fewer bacterial genera were significantly changed in wild type mice than the IL-18 KO mice after radiation exposure. The different composition of the IL-18 KO mice and wild type mice persisted even after radiation exposure. Bacterial genera that significantly correlated with other genera were identified in the IL-18 KO and wild type mice. The metabolic pathways that differentially expressed in both genotypes were identified. The animal bacterial microbiome data could be used to predict the animal's radiation status. The fungal microbiome had no significant difference regarding genotype or time after radiation exposure.<br><br>CONCLUSION: The current study helps understand the gut microbiome in different genetic backgrounds and its temporal changes after radiation exposure. Our data provide insight into the mechanisms underlying radiation-induced toxicity and help identify bacteria important in response to radiation.}, }
@article {pmid37679681, year = {2023}, author = {Wang, Y and Xu, X and Chen, H and Yang, F and Xu, B and Wang, K and Liu, Q and Liang, G and Zhang, R and Jiao, X and Zhang, Y}, title = {Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {530}, pmid = {37679681}, issn = {1471-2164}, support = {PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, abstract = {BACKGROUND: Ligilactobacillus salivarius has been frequently isolated from the gut microbiota of humans and domesticated animals and has been studied as a candidate probiotic. Badger (Meles meles) is known as a "generalist" species that consumes complex foods and exhibits tolerance and resistance to certain pathogens, which can be partly attributed to the beneficial microbes such as L. salivarius in the gut microbiota. However, our understanding of the beneficial traits and genomic features of badger-originated L. salivarius remains elusive.<br><br>RESULTS: In this study, nine L. salivarius strains were isolated from wild badgers' feces, one of which exhibited good probiotic properties. Complete genomes of the nine L. salivarius strains were generated, and comparative genomic analysis was performed with the publicly available complete genomes of L. salivarius obtained from humans and domesticated animals. The strains originating from badgers harbored a larger genome, a higher number of protein-coding sequences, and functionally annotated genes than those originating from humans and chickens. The pan-genome phylogenetic tree demonstrated that the strains originating from badgers formed a separate clade, and totally 412 gene families (12.6% of the total gene families in the pan-genome) were identified as genes gained by the last common ancestor of the badger group. The badger group harbored significantly more gene families responsible for the degradation of complex carbohydrate substrates and production of polysaccharides than strains from other hosts; many of these were acquired by gene gain events.<br><br>CONCLUSIONS: A candidate probiotic and nine L. salivarius complete genomes were obtained from the badgers' gut microbiome, and several beneficial genes were identified to be specifically present in the badger-originated strains that were gained in the evolution. Our study provides novel insights into the adaptation of L. salivarius to the intestinal habitat of wild badgers and provides valuable strain and genome resources for the development of L. salivarius as a probiotic.}, }
@article {pmid37679485, year = {2023}, author = {Fang, Y and Subedi, S}, title = {Clustering microbiome data using mixtures of logistic normal multinomial models.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14758}, pmid = {37679485}, issn = {2045-2322}, support = {2021-03812//NSERC Discovery Grant/ ; 2020-00303//Canada Research Chair Program/ ; 714187//Simons Foundation/ ; }, abstract = {Discrete data such as counts of microbiome taxa resulting from next-generation sequencing are routinely encountered in bioinformatics. Taxa count data in microbiome studies are typically high-dimensional, over-dispersed, and can only reveal relative abundance therefore being treated as compositional. Analyzing compositional data presents many challenges because they are restricted to a simplex. In a logistic normal multinomial model, the relative abundance is mapped from a simplex to a latent variable that exists on the real Euclidean space using the additive log-ratio transformation. While a logistic normal multinomial approach brings flexibility for modeling the data, it comes with a heavy computational cost as the parameter estimation typically relies on Bayesian techniques. In this paper, we develop a novel mixture of logistic normal multinomial models for clustering microbiome data. Additionally, we utilize an efficient framework for parameter estimation using variational Gaussian approximations (VGA). Adopting a variational Gaussian approximation for the posterior of the latent variable reduces the computational overhead substantially. The proposed method is illustrated on simulated and real datasets.}, }
@article {pmid37679469, year = {2023}, author = {Li, X and Chou, MY and Bonito, GM and Last, RL}, title = {Anti-fungal bioactive terpenoids in the bioenergy crop switchgrass (Panicum virgatum) may contribute to ecotype-specific microbiome composition.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {917}, pmid = {37679469}, issn = {2399-3642}, abstract = {Plant derived bioactive small molecules have attracted attention of scientists across fundamental and applied scientific disciplines. We seek to understand the influence of these phytochemicals on rhizosphere and root-associated fungi. We hypothesize that - consistent with accumulating evidence that switchgrass genotype impacts microbiome assembly - differential terpenoid accumulation contributes to switchgrass ecotype-specific microbiome composition. An initial in vitro Petri plate-based disc diffusion screen of 18 switchgrass root derived fungal isolates revealed differential responses to upland- and lowland-isolated metabolites. To identify specific fungal growth-modulating metabolites, we tested fractions from root extracts on three ecologically important fungal isolates - Linnemania elongata, Trichoderma sp. and Fusarium sp. Saponins and diterpenoids were identified as the most prominent antifungal metabolites. Finally, analysis of liquid chromatography-purified terpenoids revealed fungal inhibition structure - activity relationships (SAR). Saponin antifungal activity was primarily determined by the number of sugar moieties - saponins glycosylated at a single core position were inhibitory whereas saponins glycosylated at two core positions were inactive. Saponin core hydroxylation and acetylation were also associated with reduced activity. Diterpenoid activity required the presence of an intact furan ring for strong fungal growth inhibition. These results inform future breeding and biotechnology strategies for crop protection with reduced pesticide application.}, }
@article {pmid37679294, year = {2023}, author = {Umar, M and Bowman, JP and Asis, C and McConchie, C and Eyles, A and Stanley, R and Gracie, A}, title = {Microbial communities associated with resin canal discoloration in mango fruit.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/lambio/ovad104}, pmid = {37679294}, issn = {1472-765X}, abstract = {Resin canal discoloration (RCD) severely impacts the fruit quality of mango, diminishes consumer confidence and reduces sales, but the biological cause is still unclear. Using next-generation sequencing, the overall microbial community composition of RCD + and visually healthy mango fruit was determined for the first time to examine the possible role of bacterial and fungal pathogens in RCD. The diversity profile of bacterial and fungal communities was determined using primers targeting the 16S rRNA gene and ITS regions. Results showed that bacterial communities in healthy fruits are clustered together and significantly different from those in RCD + fruits. Tatumella and Pantoea species were the most abundant bacterial taxa on RCD + fruit, and both have been linked to disease outbreaks in a variety of fruit crops. Fungal communities were generally similar between RCD + and normal samples though non-pathogenic yeasts Meyerozyma and Naganishia tended to dominate the fungal communities on RCD + fruit. The study indicates that bacteria rather than fungal organisms are more likely to be associated with RCD in mango. This finding will facilitate the isolation and confirmation of RCD-causing organisms and the development of control strategies to manage RCD problem in mango.}, }
@article {pmid37678996, year = {2023}, author = {Weng, TH and Huang, KY and Jhong, JH and Kao, HJ and Chen, CH and Chen, YC and Weng, SL}, title = {Microbiome analysis of maternal and neonatal microbial communities associated with the different delivery modes based on 16S rRNA gene amplicon sequencing.}, journal = {Taiwanese journal of obstetrics &amp; gynecology}, volume = {62}, number = {5}, pages = {687-696}, doi = {10.1016/j.tjog.2023.07.033}, pmid = {37678996}, issn = {1875-6263}, abstract = {OBJECTIVE: With the rising number of cases of non-vaginal delivery worldwide, scientists have been concerned about the influence of the different delivery modes on maternal and neonatal microbiomes. Although the birth rate trend is decreasing rapidly in Taiwan, more than 30 percent of newborns are delivered by caesarean section every year. However, it remains unclear whether the different delivery modes could have a certain impact on the postpartum maternal microbiome and whether it affects the mother-to-newborn vertical transmission of bacteria at birth.<br><br>MATERIALS AND METHODS: To address this, we recruited 30 mother-newborn pairs to participate in this study, including 23 pairs of vaginal delivery (VD) and seven pairs of caesarean section (CS). We here investigate the development of the maternal prenatal and postnatal microbiomes across multiple body habitats. Moreover, we also explore the early acquisition of neonatal gut microbiome through a vertical multi-body site microbiome analysis.<br><br>RESULTS AND CONCLUSION: The results indicate that no matter the delivery mode, it only slightly affects the maternal microbiome in multiple body habitats from pregnancy to postpartum. On the other hand, about 95% of species in the meconium microbiome were derived from one of the maternal body habitats; notably, the infants born by caesarean section acquire bacterial communities resembling their mother's oral microbiome. Consequently, the delivery modes play a crucial role in the initial colonization of the neonatal gut microbiome, potentially impacting children's health and development.}, }
@article {pmid37678901, year = {2023}, author = {Hadley, M and Oppong, AY and Coleman, J and Powell, AM}, title = {Structural Racism and Adverse Pregnancy Outcomes Through the Lens of the Maternal Microbiome.}, journal = {Obstetrics and gynecology}, volume = {}, number = {}, pages = {}, pmid = {37678901}, issn = {1873-233X}, abstract = {Microbiome science offers a glimpse into personalized medicine by characterizing health and disease states according to an individual's microbial signatures. Without a critical examination of the use of race as a variable, microbiome studies may be susceptible to the same pitfalls as other areas of science grounded in racist biology. We will examine the use of race as a biological variable in pregnancy-related microbiome research. Emerging data from studies that investigate the intestinal microbiome in pregnancy suggest strong influence of a poor diet on adverse pregnancy outcomes. Differences in the vaginal microbiome implicated in adverse pregnancy outcomes are frequently attributed to race. We review evidence that links systemic racism to pregnancy health outcome differences with a focus on the vaginal and intestinal microbiomes as well as diet. We also review how structural racism ultimately contributes to inequitable access to healthy food and higher risk environmental exposures among pregnant people of lower socioeconomic status and exacerbates common pregnancy comorbidities.}, }
@article {pmid37548312, year = {2023}, author = {Wang, S and Tian, ZB and Chen, JW and Cong, PS and Ding, XL and Zhang, CP and Yin, XY and Yang, L and Jing, X and Mao, T and Li, XY and Sun, ZY and Jiang, JJ and Yu, YN}, title = {Effect of fucoidan on gut microbiota and its clinical efficacy in Helicobacter pylori eradication: A randomized controlled trial.}, journal = {Journal of digestive diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-2980.13215}, pmid = {37548312}, issn = {1751-2980}, support = {QDFY+X2021049//Medicine and X Project of the Affiliated Hospital of Qingdao University/ ; ZR2021MH077//Natural Science Foundation of Shandong Province/ ; SKL-BASS1801//Open Foundation of the State Key Laboratory of Bioactive Seaweed Substances/ ; }, abstract = {OBJECTIVE: To assess the clinical efficacy of fucoidan-assisted standard quadruple therapy (SQT) in Helicobacter pylori (H. pylori) eradication and the improvement of gut microbiota.<br><br>METHODS: An open-label randomized controlled trial was conducted at the Affiliated Hospital of Qingdao University in Shandong Province, China. Ninety patients who tested positive for H. pylori were randomized to the standard quadruple therapy (SQT) group (SQ), SQT&#x2009;+&#x2009;fucoidan combination group (SF), and fucoidan&#x2009;+&#x2009;sequential SQT group (FS), respectively. Stool samples were collected for gut microbiota composition at baseline and after treatment.<br><br>RESULTS: After H. pylori eradication, the relative abundances of most conditional pathogens in the SQ decreased, while those of several beneficial bacteria increased or decreased (P&#x2009;<&#x2009;0.05). In FS, the abundances of most beneficial bacteria increased gradually from baseline to week 12, while those of the conditional pathogens decreased (P&#x2009;<&#x2009;0.05). The abundance of Bifidobacterium had a decreasing trend in SQ, but remained unchanged in SF and increased in FS (P&#x2009;<&#x2009;0.05). The abundances of most beneficial bacteria were significantly higher in FS than in SQ and SF (P&#x2009;<&#x2009;0.05). Addition of fucoidan enhanced symptom improvement during H. pylori eradication compared with SQT alone.<br><br>CONCLUSIONS: Fucoidan considerably improved gut dysbiosis during SQT for H. pylori eradication. Gut microbiota can be maintained by the addition of fucoidan before eradication therapy with SQT rather than by concomitant addition with therapy. Fucoidan-assisted SQT could relieve gastrointestinal symptoms during H. pylori eradication.}, }
@article {pmid37678799, year = {2023}, author = {Patel, RK and Rahman, S and Schwantes, IR and Bartlett, A and Eil, R and Farsad, K and Fowler, K and Goodyear, SM and Hansen, L and Kardosh, A and Nabavizadeh, N and Rocha, FG and Tsikitis, VL and Wong, MH and Mayo, SC}, title = {Updated Management of Colorectal Cancer Liver Metastases: Scientific Advances Driving Modern Therapeutic Innovations.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcmgh.2023.08.012}, pmid = {37678799}, issn = {2352-345X}, abstract = {Colorectal cancer is the 2[nd] leading cause of cancer-related deaths in the United States and accounts for an estimated 1 million deaths annually worldwide. The liver is the most common site of metastatic spread from colorectal cancer, significantly driving both morbidity and mortality. While remarkable advances have been made in recent years in the management for patients with colorectal cancer liver metastases, significant challenges remain in early detection, prevention of progression and recurrence, and in the development of more effective therapeutics. In 2017, our group held a multidisciplinary state-of-the science symposium, in order to discuss the rapidly evolving clinical and scientific advances in the field of colorectal liver metastases, including novel early detection and prognostic liquid biomarkers, identification of high-risk cohorts, advances in tumor-immune therapy, and different regional and systemic therapeutic strategies. Since that time, there has been scientific discoveries translating into therapeutic innovations addressing the current management challenges. These innovations are currently reshaping the treatment paradigms and spurring further scientific discovery. Herein, we present an updated discussion of both the scientific and clinical advances and future directions in the management of colorectal liver metastases, including adoptive T-cell therapies, novel blood-based biomarkers, and the role of the tumor microbiome. Additionally, we provide a comprehensive overview detailing the role of modern multidisciplinary clinical approaches used in the management of patients with colorectal liver metastases, including considerations towards specific molecular tumor profiles identified on next generation sequencing, as well as quality of life implications for these innovative treatments.}, }
@article {pmid37678747, year = {2023}, author = {Liu, Q and Zheng, L and Wang, Y and Huang, Z and Zhu, J and Fang, M and Xie, L and Ding, C and Gu, Y and Xu, D and Jin, H and Yang, J and Zhang, X and Shen, H}, title = {Primary choledocholithiasis occurrence and recurrence is synergetcally modulated by the bile microbiome and metabolome alternations.}, journal = {Life sciences}, volume = {}, number = {}, pages = {122073}, doi = {10.1016/j.lfs.2023.122073}, pmid = {37678747}, issn = {1879-0631}, abstract = {AIMS: Primary choledocholithiasis is a common digestive disease with high morbidity and relapse. However, the compositions and functions of the bile microbial ecosystem and the pathogenesis of microfloral regulation of host metabolism resulting in stone formation are poorly understood.<br><br>MAIN METHODS: Biliary samples collected from patients with acute cholangitis induced by benign biliary stricture (nonlithiasis group, n&#x202f;=&#x202f;17) and primary choledocholithiasis (lithiasis group, n&#x202f;=&#x202f;33) were subjected to multiomics analyses. Furthermore, clinicopathological features collected over a 24-month follow-up period were examined to evaluate the predictive value of candidate microbes.<br><br>KEY FINDINGS: Five alpha diversity indices of the bile microbiome were significantly decreased in the lithiasis group. Furthermore, we identified 49 differential bile flora between the two groups, and the relative abundances of 6 bacteria, Actinobacteria, Actinobacteriota, Staphylococcales, Micrococcales, Altererythrobacter and Carnobacteriaceae, were associated with primary choledocholithiasis relapse conditions. Multiomics analyses showed that specific changes in disease-related bacterial taxa were closely related to metabolite variation (low-molecular weight carboxylic acids, sterol liquid and acylcarnitine), which might reflect disease prognosis. According to microbiomic and metabolomic pathway analyses, we revealed that bacterial infections, microbiota-derived amino acid metabolites and secondary bile acid-related pathways were significantly enriched in the stone-formation group, suggesting a novel host-microbial metabolic mechanism of primary choledocholithiasis.<br><br>SIGNIFICANCE: Our study first indicates bile host-microbial dysbiosis modulates the abnormal accumulation of metabolites might further disrupt calcium homeostasis and generate insoluble saponification. Additionally, we determined the predictive value of Actinomycetes phylum reduction for recurrence in primary common bile duct stone patients.}, }
@article {pmid37678377, year = {2023}, author = {Baker, KA and Poole, C}, title = {Current and Emerging Applications of Fecal Microbiota Transplantation.}, journal = {The American journal of nursing}, volume = {Published Ahead of Print}, number = {}, pages = {}, doi = {10.1097/01.NAJ.0000978920.88346.77}, pmid = {37678377}, issn = {1538-7488}, abstract = {Fecal microbiota transplantation (FMT) is a life-changing treatment for people with recurrent Clostridioides difficile infection (rCDI). Frequently acquired in the hospital, CDI can cause serious gastrointestinal symptoms, including persistent watery diarrhea, abdominal pain, and severe dehydration. Antibiotics, the primary treatment, can unfortunately disrupt the gut microbiome and lead to antimicrobial resistance. FMT involves introducing stool from a healthy donor into the affected recipient to strengthen their compromised microbiome. Individuals receiving this treatment have reported remarkable improvement in clinical outcomes and quality of life. In addition to a discussion of rCDI within the context of the gastrointestinal microbiome, this article provides an overview of the FMT procedure, discusses nursing management of individuals undergoing FMT, and highlights emerging applications beyond rCDI. A case scenario is also provided to illustrate a typical trajectory for a patient undergoing FMT.}, }
@article {pmid37678191, year = {2023}, author = {Hagen, SJ}, title = {Pathophysiology updates: gastroduodenal injury and repair mechanisms.}, journal = {Current opinion in gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1097/MOG.0000000000000973}, pmid = {37678191}, issn = {1531-7056}, abstract = {PURPOSE OF REVIEW: Although the mucosal barrier serves as a primary interface between the environment and host, little is known about the repair of acute, superficial lesions or deeper, persistent lesions that if not healed, can be the site of increased permeability to luminal antigens, inflammation, and/or neoplasia development.<br><br>RECENT FINDINGS: Recent studies on acute superficial lesions have focused on calcium signaling and focal adhesion kinase, which regulate cell migration and controlled matrix adhesion during restitution. Microfluidic organ-on-a-chip and gut-on-a-chip models continued in development to support reductionist studies of epithelial-bacterial and/or epithelial-immune cell interactions during mucosal barrier disruption. In fact, these models may allow personalized medicine studies in the future using patient-derived cells to evaluate injury and repair mechanisms. Work done in the past year evaluated the safety and efficacy of acid blocking drugs on ulcer healing, with new animal studies providing evidence that each drug affects the microbiome in a different way that can be correlated with its efficacy in ulcer healing. Lastly, work to understand the way in which mature epithelial cells or committed stem cells dedifferentiate, reprogram, proliferate, and then regenerate the gastroduodenal mucosa after injury was a major focus of studies in the past year.<br><br>SUMMARY: Recent studies highlight novel mechanisms that promote restitution and mucosal regeneration after injury of the gastroduodenal mucosa.}, }
@article {pmid37677136, year = {2023}, author = {Sulaiman, I and Wu, BG and Chung, M and Isaacs, B and Tsay, JJ and Holub, M and Barnett, CR and Kwok, B and Kugler, MC and Natalini, JG and Singh, S and Li, Y and Schluger, R and Carpenito, J and Collazo, D and Perez, L and Kyeremateng, Y and Chang, M and Campbell, CD and Hansbro, PM and Oppenheimer, BW and Berger, KI and Goldring, RM and Koralov, SB and Weiden, MD and Xiao, R and D'Armiento, J and Clemente, JC and Ghedin, E and Segal, LN}, title = {Lower Airway Dysbiosis Augments Lung Inflammatory Injury in Mild-to-Moderate COPD.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1164/rccm.202210-1865OC}, pmid = {37677136}, issn = {1535-4970}, abstract = {RATIONALE: Chronic obstructive pulmonary disease (COPD) is associated with high morbidity, mortality and health care costs. Cigarette smoke is a causative factor, however not all heavy smokers develop COPD. Microbial colonization and infections are contributing factors to disease progression in advance stages.<br><br>OBJECTIVE: Here we investigated whether lower airway dysbiosis occurs in mild-to-moderate COPD and analyzed possible mechanistic contributions to COPD pathogenesis.<br><br>METHODS: We recruited 57 patients with >10 pack year smoking history: 26 had physiological evidence of COPD, 31 had normal lung function (smoker controls). Bronchoscopy sampled the upper airways (UA), lower airways (BAL) and environmental background (BKG). Samples were analyzed by 16S rRNA gene sequencing, whole genome, RNA metatranscriptome and host RNA transcriptome. A preclinical mouse model was used to evaluate the contributions of cigarette smoke and dysbiosis on lower airway inflammatory injury.<br><br>MEASUREMENTS/MAIN RESULTS: Compared with smoker controls, microbiome analyses showed that the lower airways of subjects with COPD were enriched with common oral commensals. The lower airway host transcriptomics demonstrated differences in markers of inflammation and tumorigenesis such as upregulation of IL-17, IL-6, ERK/MAPK, PI3K, MUC1 and MUC4 in mild-to-moderate COPD. Finally, in a pre-clinical murine model exposed to cigarette smoke, lower airway dysbiosis with common oral commensals augments the inflammatory injury revealing transcriptomic signatures similar to those observed in human COPD subjects.<br><br>CONCLUSIONS: Lower airway dysbiosis in the setting of smoke exposure contributes to inflammatory injury early in COPD. Targeting the lower airway microbiome in combination with smoking cessation may be of potential therapeutic relevance.}, }
@article {pmid37676767, year = {2023}, author = {Schmit, KJ and Garcia, P and Sciortino, A and Aho, VTE and Pardo Rodriguez, B and Thomas, MH and Gérardy, JJ and Bastero Acha, I and Halder, R and Cialini, C and Heurtaux, T and Ostahi, I and Busi, SB and Grandmougin, L and Lowndes, T and Singh, Y and Martens, EC and Mittelbronn, M and Buttini, M and Wilmes, P}, title = {Fiber deprivation and microbiome-borne curli shift gut bacterial populations and accelerate disease in a mouse model of Parkinson's disease.}, journal = {Cell reports}, volume = {42}, number = {9}, pages = {113071}, doi = {10.1016/j.celrep.2023.113071}, pmid = {37676767}, issn = {2211-1247}, abstract = {Parkinson's disease (PD) is a neurological disorder characterized by motor dysfunction, dopaminergic neuron loss, and alpha-synuclein (αSyn) inclusions. Many PD risk factors are known, but those affecting disease progression are not. Lifestyle and microbial dysbiosis are candidates in this context. Diet-driven gut dysbiosis and reduced barrier function may increase exposure of enteric neurons to toxins. Here, we study whether fiber deprivation and exposure to bacterial curli, a protein cross-seeding with αSyn, individually or together, exacerbate disease in the enteric and central nervous systems of a transgenic PD mouse model. We analyze the gut microbiome, motor behavior, and gastrointestinal and brain pathologies. We find that diet and bacterial curli alter the microbiome and exacerbate motor performance, as well as intestinal and brain pathologies, but to different extents. Our results shed important insights on how diet and microbiome-borne insults modulate PD progression via the gut-brain axis and have implications for lifestyle management of PD.}, }
@article {pmid37676387, year = {2022}, author = {Mehmood, MA and Fu, Y and Zhao, H and Cheng, J and Xie, J and Jiang, D}, title = {Enrichment of bacteria involved in the nitrogen cycle and plant growth promotion in soil by sclerotia of rice sheath blight fungus.}, journal = {Stress biology}, volume = {2}, number = {1}, pages = {32}, pmid = {37676387}, issn = {2731-0450}, support = {//China Agriculture Research System of MOF and MARA/ ; }, abstract = {Rice sheath blight pathogen, Rhizoctonia solani, produces numerous sclerotia to overwinter. As a rich source of nutrients in the soil, sclerotia may lead to the change of soil microbiota. For this purpose, we amended the sclerotia of R. solani in soil and analyzed the changes in bacterial microbiota within the soil at different time points. At the phyla level, Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chloroflexi and Firmicutes showed varied abundance in the amended soil samples compared to those in the control. An increased abundance of ammonia-oxidizing bacterium (AOB) Nitrosospira and Nitrite oxidizing bacteria (NOB) i.e., Nitrospira was observed, where the latter is reportedly involved in the nitrifier denitrification. Moreover, Thiobacillus, Gemmatimonas, Anaeromyxobacter and Geobacter, the vital players in denitrification, N2O reduction and reductive nitrogen transformation, respectively, depicted enhanced abundance in R. solani sclerotia-amended samples. Furthermore, asymbiotic nitrogen-fixing bacteria, notably, Azotobacter as well as Microvirga and Phenylobacterium with nitrogen-fixing potential also enriched in the amended samples compared to the control. Plant growth promoting bacteria, such as Kribbella, Chitinophaga and Flavisolibacter also enriched in the sclerotia-amended soil. As per our knowledge, this study is of its kind where pathogenic fungal sclerotia activated microbes with a potential role in N transformation and provided clues about the ecological functions of R. solani sclerotia on the stimulation of bacterial genera involved in different processes of N-cycle within the soil in the absence of host plants.}, }
@article {pmid37675978, year = {2023}, author = {Shi, X and Zhang, Y and Shi, Y and Zhang, Q and Duan, H and Liu, J and Yang, B and Zhang, Y}, title = {Analysis of the alleviating effect of modified Huangqi Chifeng decoction on rats with focal segmental glomerulosclerosis based on gut microbiota and fecal metabolomics.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxad205}, pmid = {37675978}, issn = {1365-2672}, abstract = {AIMS: To investigate the reno-protective effects of modified Huangqi Chifeng decoction (MHCD) on focal segmental glomerulosclerosis (FSGS) rats, and the underlying mechanisms of systemic regulation of gut microbiota and metabolite profiles.<br><br>METHODS AND RESULTS: A rat FSGS model was established via unilateral nephrectomy plus doxorubicin injections. Rats were divided into sham, FSGS, and MHCD groups from which urine, blood, and histological tests were conducted. Fecal microbiotas were identified via 16S rRNA gene sequencing. Fecal metabolomics allowed for metabolic pathways analysis. Biochemical indices and pathological examination revealed that MHCD treatment improved the symptoms of FSGS, and corrected dysbiosis of gut microbiota, enriched the abundance of Bifidobacterium, Odoribacter, Christensella, Oscillospira, and reduced that of harmful bacteria such as Collinsella and Coprobacterilus at the genus level. Fecal metabolomic profiles revealed 152 different metabolites between the FSGS and sham groups, which are mainly enriched in signaling pathways like arachidonic acid, serotonergic synapse, and oxytocin. Besides, 93 differential metabolites between MHCD and FSGS groups were identified, which are mainly enriched in signaling pathways like steroid hormone biosynthesis, prostate cancer, and linoleic acid metabolism. Spearman's correlation analysis showed a correlation between differential fecal metabolites and enriched gut microbiota or serum biochemical parameters.<br><br>CONCLUSIONS: MHCD may exert a reno-protective effect by regulating the gut microbiome and metabolite profiles in FSGS rats.}, }
@article {pmid37675977, year = {2023}, author = {King, WL and Yates, CF and Cao, L and O'Rourke-Ibach, S and Fleishman, SM and Richards, SC and Centinari, M and Hafner, BD and Goebel, M and Bauerle, T and Kim, YM and Nicora, CD and Anderton, CR and Eissenstat, DM and Bell, TH}, title = {Functionally discrete fine roots differ in microbial assembly, microbial functional potential, and produced metabolites.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.14705}, pmid = {37675977}, issn = {1365-3040}, support = {//USDA National Institute of Food and Agriculture/ ; //DOE Biological and Environmental Research program/ ; //DOE Environmental Molecular Sciences Laboratory/ ; //NSF Centre for Research on Programmable Plant Systems/ ; }, abstract = {Traditionally, fine roots were grouped using arbitrary size categories, rarely capturing the heterogeneity in physiology, morphology and functionality among different fine root orders. Fine roots with different functional roles are rarely separated in microbiome-focused studies and may result in confounding microbial signals and host-filtering across different root microbiome compartments. Using a 26-year-old common garden, we sampled fine roots from four temperate tree species that varied in root morphology and sorted them into absorptive and transportive fine roots. The rhizoplane and rhizosphere were characterized using 16S rRNA gene and internal transcribed spacer region amplicon sequencing and shotgun metagenomics for the rhizoplane to identify potential microbial functions. Fine roots were subject to metabolomics to spatially characterize resource availability. Both fungi and bacteria differed according to root functional type. We observed additional differences between the bacterial rhizoplane and rhizosphere compartments for absorptive but not transportive fine roots. Rhizoplane bacteria, as well as the root metabolome and potential microbial functions, differed between absorptive and transportive fine roots, but not the rhizosphere bacteria. Functional differences were driven by sugar transport, peptidases and urea transport. Our data highlights the importance of root function when examining root-microbial relationships, emphasizing different host selective pressures imparted on different root microbiome compartments.}, }
@article {pmid37675926, year = {2023}, author = {Bautista, D and García, D and Dávila, L and Caro-Quintero, A and Cotes, AM and González, A and Zuluaga, AP}, title = {Studying the microbiome of suppressive soils against vascular wilt, caused by Fusarium oxysporum in cape gooseberry (Physalis peruviana).}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.13195}, pmid = {37675926}, issn = {1758-2229}, support = {687//Ministerio de Agricultura y Desarrollo Rural (Colombia)-MADR/ ; }, abstract = {Cape gooseberry (Physalis peruviana) is Colombia's second most exported fruit, with a market worth 37.8 million USD in 2021. Fusarium oxysporum f sp. physalis (Foph) is arguably the most devastating pathogen causing losses of up to 80%. Managing this disease is challenging due to pathogen resistance or the reduced efficacy of commercial fungicides and the production of resistant structures allowing pathogen survival in the soil for up to 30 years. Thus, new methods of control are necessary. Two cape gooseberry farms (organic vs. conventional) were detected free from Foph in Nariño. We hypothesize that the soil microbiome might have a suppressive effect against vascular wilt, caused by Foph. To test this, farm soils were propagated by adding 10% farm soil and 90% peat soil. Then, peat soil (control) and propagated soils were inoculated with Foph. A decrease of 65%-68% in disease incidence and a 70% in disease severity reduction was observed in seedlings grown in propagated soils compared to peat soil. We then used next-generation sequencing to study the soil microbiome to understand the possible mechanisms for disease suppression of propagated soils. We conclude that despite the high diversity of soil microbiomes, the relative abundance of some taxa might be a more important indicator of disease suppression than the presence of specific taxa.}, }
@article {pmid37675527, year = {2023}, author = {Che, YL and Xu, ZN and Wang, N and Ma, QZ and Zheng, ZY and Sun, YN and Wang, JT}, title = {[Analysis of nasal microbial characteristics in patients with allergic rhinitis and non-allergic rhinitis].}, journal = {Zhonghua er bi yan hou tou jing wai ke za zhi = Chinese journal of otorhinolaryngology head and neck surgery}, volume = {58}, number = {9}, pages = {885-891}, doi = {10.3760/cma.j.cn115330-20221012-00605}, pmid = {37675527}, issn = {1673-0860}, support = {LBH-Q21028//Heilongjiang Postdoctoral Scientific Research Developmental Fund/ ; }, mesh = {Female ; Male ; Humans ; *Rhinitis ; *Rhinitis, Allergic ; }, abstract = {Objective: To investigate the characteristics of nasal flora and the pathogenic role of differential microbiome in patients with allergic rhinitis (AR) and non-allergic rhinitis (nAR). Methods: Thirty-five patients with AR who attended the rhinology outpatient clinic of the Second Hospital of Harbin Medical University from February to July 2022 were selected. A total of 35 nAR patients were selected as the test group, and 20 cases of healthy people with physical examination at the same period were selected as the control group, including 39 males and 51 females, aged 8 to 55 years. 16SrDNA High-throughput sequencing was used to analyze the relative abundance from nasal flora in the three groups of subjects. Alpha diversity index analysis was conducted with R software, and differences between groups were analyzed with LEfSe, Metastats, and t tests. At the same time, the role of microbiome and its relationship with environmental factors were analyzed with R software. Results: There was a significant difference in the bacterial composition of the samples from the three groups, with the relative abundance of Staphylococcus aureus (P=0.032) and Corynebacterium proinquum (P=0.032) within the AR group being significantly higher than that of the nAR group, and that of Lactobacillus murinus, Lactobacillus kunkeei, and Alcaligenes faecalis (P value was 0.016, 0.005, and 0.001, respectively) being significantly lower than that of the nAR group. The relative abundance of Ackermannia muciniphila within the nAR group was higher than that of the control group (P=0.009). Correlation analysis of environmental factors showed a negative correlation between Lactobacillus kunkeei and IgE (P=0.044), and a positive correlation between Lactobacillus murinus and age (P=0.019). AR and nAR random forest prediction models were constructed for the five genera, respectively, and the area under the curve (AUC) of the models of Streptococcus-SP-FF10, Pseudoalteromonas luteoviolacea, Pseudomonas parafulva, Acinetobacter ursingii, and Azotobacter chroococcum in the AR group was 100% (95%CI: 100% to 100%). The AUC for the Pseudomonas parafulva, Azotobacter chroococcum, Closoridium baratii, Turicibacter-SP-H121, and Streptococcus lutetiensis models in the nAR group was 98.4% (95%CI: 94.9% to 100%). Conclusions: The distribution of nasal flora in AR patients, nAR patients and healthy subjects is significantly different, and the changes of bacterial flora abundance are significantly related to the occurrence of AR and nAR. Combined detection of microbiota has the potential to diagnose AR and nAR patients.}, }
@article {pmid37675481, year = {2023}, author = {Wood, CM and Wang, J and Jung, EH and Pelster, B}, title = {The physiological consequences of a very large natural meal in a voracious marine fish, the staghorn sculpin (Leptocottus armatus).}, journal = {The Journal of experimental biology}, volume = {}, number = {}, pages = {}, doi = {10.1242/jeb.246034}, pmid = {37675481}, issn = {1477-9145}, support = {RG-PIN 2017-03843//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Little information exists on physiological consequences when wild fish eat natural food. Staghorn sculpins at 10°-13°C voluntarily consumed 15.8% of their body weight in anchovies. Gastric clearance was slow with>60% of the meal retained in the stomach at 48h, and not complete until 84h. At 14-24h post-feeding, pH was depressed by 3 units and [Cl-] elevated 2-fold in gastric chyme, reflecting HCl secretion, while in all sections of the intestine, pH declined by 1 pH unit but [Cl-] remained unchanged. PCO2 and [total ammonia] were greatly elevated throughout the tract, whereas PNH3 and [HCO3-] were depressed. Intestinal HCO3- secretion rates, measured in gut sacs in vitro, were also lower in fed fish. Whole animal O2 consumption rate was elevated approximately 2-fold for 72h post-feeding, reflecting "specific dynamic action", whereas ammonia and urea-N excretion rates were elevated about 5-fold. Arterial blood exhibited a modest "alkaline tide" for about 48h, but there was negligible excretion of metabolic base to the external seawater. PaCO2 and PaO2 remained unchanged. Plasma [total amino acids] and [total lipids] were elevated about 1.5-fold for at least 48h, whereas small increases in plasma [total ammonia], PNH3, and [urea-N] were quickly attenuated. Plasma [glucose] remained unchanged. We conclude that despite the very large meal, slow processing with high efficiency minimizes internal physiological disturbances. This differs greatly from the picture provided by previous studies on aquacultured species using synthetic diets and/or force-feeding. Questions remain about the role of the gastro-intestinal microbiome in nitrogen and acid-base metabolism.}, }
@article {pmid37675425, year = {2023}, author = {Cui, Z and Wu, Y and Zhang, QH and Wang, SG and He, Y and Huang, DS}, title = {MV-CVIB: a microbiome-based multi-view convolutional variational information bottleneck for predicting metastatic colorectal cancer.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1238199}, pmid = {37675425}, issn = {1664-302X}, abstract = {INTRODUCTION: Imbalances in gut microbes have been implied in many human diseases, including colorectal cancer (CRC), inflammatory bowel disease, type 2 diabetes, obesity, autism, and Alzheimer's disease. Compared with other human diseases, CRC is a gastrointestinal malignancy with high mortality and a high probability of metastasis. However, current studies mainly focus on the prediction of colorectal cancer while neglecting the more serious malignancy of metastatic colorectal cancer (mCRC). In addition, high dimensionality and small samples lead to the complexity of gut microbial data, which increases the difficulty of traditional machine learning models.<br><br>METHODS: To address these challenges, we collected and processed 16S rRNA data and calculated abundance data from patients with non-metastatic colorectal cancer (non-mCRC) and mCRC. Different from the traditional health-disease classification strategy, we adopted a novel disease-disease classification strategy and proposed a microbiome-based multi-view convolutional variational information bottleneck (MV-CVIB).<br><br>RESULTS: The experimental results show that MV-CVIB can effectively predict mCRC. This model can achieve AUC values above 0.9 compared to other state-of-the-art models. Not only that, MV-CVIB also achieved satisfactory predictive performance on multiple published CRC gut microbiome datasets.<br><br>DISCUSSION: Finally, multiple gut microbiota analyses were used to elucidate communities and differences between mCRC and non-mCRC, and the metastatic properties of CRC were assessed by patient age and microbiota expression.}, }
@article {pmid37675282, year = {2023}, author = {Fonseca, F and Fuentes, J}, title = {Editorial: Microbiome dynamics as biomarkers of welfare status in aquatic species.}, journal = {Frontiers in physiology}, volume = {14}, number = {}, pages = {1276351}, doi = {10.3389/fphys.2023.1276351}, pmid = {37675282}, issn = {1664-042X}, }
@article {pmid37675244, year = {2023}, author = {Makgabo, SM and Brayton, KA and Oosthuizen, MC and Collins, NE}, title = {Unravelling the diversity of Anaplasma species circulating in selected African wildlife hosts by targeted 16S microbiome analysis.}, journal = {Current research in microbial sciences}, volume = {5}, number = {}, pages = {100198}, pmid = {37675244}, issn = {2666-5174}, abstract = {Organisms in the genus Anaplasma are obligate intracellular alphaproteobacteria. Bovine anaplasmosis, predominantly caused by Anaplasma marginale, is the most prevalent tick-borne disease (TBD) of cattle worldwide. Other Anaplasma species are known to cause disease; these include A. ovis, A. platys in dogs, A. capra in goats and humans, and A. phagocytophilum in humans. The rapid advancement of next-generation sequencing technologies has led to the discovery of many novel sequences ascribed to the genus Anaplasma, with over 20 putative new species being proposed since the last formal organization of the genus. Most 16S rRNA gene surveys for Anaplasma were conducted on cattle and to a lesser extent on rodents, dogs, and ticks. Little is known about the occurrence, diversity, or impact of Anaplasma species circulating in wildlife species. Therefore, we conducted a 16S rRNA gene survey with the goal of identifying Anaplasma species in a variety of wildlife species in the Kruger National Park and neighbouring game reserves, using an unbiased 16S rRNA gene microbiome approach. An Anaplasma/Ehrlichia-group specific quantitative real-time PCR (qPCR) assay revealed the presence of Anaplasma and/or Ehrlichia species in 70.0% (21/30) of African buffalo, 86.7% (26/30) of impala, 36.7% (11/30) of greater kudu, 3.2% (1/31) of African wild dog, 40.6% (13/32) of Burchell's zebra, 43.3% (13/30) of warthog, 22.6% (7/31) of spotted hyena, 40.0% (12/30) of leopard, 17.6% (6/34) of lion, 16.7% (5/30) of African elephant and 8.6% (3/35) of white rhinoceros samples. Microbiome sequencing data from the qPCR positive samples revealed four 16S rRNA sequences identical to previously published Anaplasma sequences, as well as nine novel Anaplasma 16S genotypes. Our results reveal a greater diversity of putative Anaplasma species circulating in wildlife than currently classified within the genus. Our findings highlight a potential expansion of the Anaplasma host range and the need for more genetic information from other important genes or genome sequencing of putative novel species for correct classification and further assessment of their occurrence in wildlife, livestock and companion animals.}, }
@article {pmid37674988, year = {2022}, author = {Miao, J and Sise, ME and Herrmann, SM}, title = {Immune checkpoint inhibitor related nephrotoxicity: Advances in clinicopathologic features, noninvasive approaches, and therapeutic strategy and rechallenge.}, journal = {Frontiers in nephrology}, volume = {2}, number = {}, pages = {1017921}, pmid = {37674988}, issn = {2813-0626}, abstract = {Immune checkpoint inhibitors (ICIs) are used increasingly to treat more than 17 cancers and have shown promising therapeutic results. However, ICI use can result in a variety of immune-related adverse events (IRAEs) which can occur in any organ, including the kidneys. Acute kidney injury (AKI) is the most common nephrotoxicity, classically related to acute interstitial nephritis. Much more diverse patterns and presentations of ICI-related kidney injury can occur, and have implications for diagnostic and therapeutic management approaches. In this review, we summarize the recently approved ICIs for cancer, the incidence and risk factors for nephrotoxicity, our current understanding of the pathophysiological mechanisms and the key clinicopathological features of ICI-related AKI, and therapeutic strategies. We also explore important knowledge that require further investigation, such as the risks/benefits of ICI rechallenge in patients who recover from an episode of ICI-related AKI, and the application of liquid biopsy and microbiome to identify noninvasive biomarkers to diagnose and predict kidney injury and guide ICI therapy.}, }
@article {pmid37674900, year = {2023}, author = {Moon, JH and Roh, DH and Kwack, KH and Lee, JH}, title = {Bacterial single-cell transcriptomics: Recent technical advances and future applications in dentistry.}, journal = {The Japanese dental science review}, volume = {59}, number = {}, pages = {253-262}, pmid = {37674900}, issn = {1882-7616}, abstract = {Metagenomics and metatranscriptomics have enhanced our understanding of the oral microbiome and its impact on oral health. However, these approaches have inherent limitations in exploring individual cells and the heterogeneity within mixed microbial communities, which restricts our current understanding to bulk cells and species-level information. Fortunately, recent technical advances have enabled the application of single-cell RNA sequencing (scRNA-seq) for studying bacteria, shedding light on cell-to-cell diversity and interactions between host-bacterial cells at the single-cell level. Here, we address the technical barriers in capturing RNA from single bacterial cells and highlight pioneering studies from the past decade. We also discuss recent achievements in host-bacterial dual transcriptional profiling at the single-cell level. Bacterial scRNA-seq provides advantages in various research fields, including the investigation of phenotypic heterogeneity within genetically identical bacteria, identification of rare cell types, detection of antibiotic-resistant or persistent cells, analysis of individual gene expression patterns and metabolic activities, and characterization of specific microbe-host interactions. Integrating single-cell techniques with bulk approaches is essential to gain a comprehensive understanding of oral diseases and develop targeted and personalized treatment in dentistry. The reviewed pioneering studies are expected to inspire future research on the oral microbiome at the single-cell level.}, }
@article {pmid37675014, year = {2022}, author = {Chávez-Iñiguez, JS and Villegas-Gutiérrez, LY and Gallardo-González, AM}, title = {Acute Kidney Injury and Intestinal Dysbiosis.}, journal = {Frontiers in nephrology}, volume = {2}, number = {}, pages = {916151}, pmid = {37675014}, issn = {2813-0626}, abstract = {Within the multiple communication pathways of the intestine-kidney axis, one of the most important pathways is the interaction between the commensals of the intestinal microbiome, through the production of short-chain fatty acids, and the segments of the nephron. These interactions maintain a perfect environmental balance. During AKI, there are negative repercussions in all organs, and the systemic interconnection is related in part to the intense inflammation and the uremic environment that this syndrome generates. For example, in the intestine, the microbiome is severely affected, with a decrease in benign bacteria that promote anti-inflammatory effects and an increase in negative, pro-inflammatory bacteria. This scenario of intestinal dysbiosis widens the inflammatory loop that favors worsening kidney function and the probability of dying. It is possible that the manipulation of the intestinal microbiome with probiotics, prebiotics and symbiotics is a reasonable therapeutic goal for AKI.}, }
@article {pmid37676341, year = {2022}, author = {Singh, SK and Wu, X and Shao, C and Zhang, H}, title = {Microbial enhancement of plant nutrient acquisition.}, journal = {Stress biology}, volume = {2}, number = {1}, pages = {3}, pmid = {37676341}, issn = {2731-0450}, abstract = {Nutrient availability is a determining factor for crop yield and quality. While fertilization is a major approach for improving plant nutrition, its efficacy can be limited and the production and application of fertilizers frequently bring problems to the environment. A large number of soil microbes are capable of enhancing plant nutrient acquisition and thereby offer environmentally benign solutions to meet the requirements of plant nutrition. Herein we provide summations of how beneficial microbes enhance plant acquisition of macronutrients and micronutrients. We also review recent studies on nutrition-dependent plant-microbe interactions, which highlight the plant's initiative in establishing or deterring the plant-microbe association. By dissecting complex signaling interactions between microbes within the root microbiome, a greater understanding of microbe-enhanced plant nutrition under specific biotic and abiotic stresses will be possible.}, }
@article {pmid37676535, year = {2021}, author = {Lin, J and Xu, L and Yang, J and Wang, Z and Shen, X}, title = {Beyond dueling: roles of the type VI secretion system in microbiome modulation, pathogenesis and stress resistance.}, journal = {Stress biology}, volume = {1}, number = {1}, pages = {11}, pmid = {37676535}, issn = {2731-0450}, support = {31725003//National Natural Science Foundation of China/ ; 32070103, 31860012//National Natural Science Foundation of China/ ; 31800113//National Natural Science Foundation of China/ ; 2018M631201//Postdoctoral Research Foundation of China/ ; 2018BSHTDZZ20//Shaanxi Province Postdoctoral Science Foundation/ ; 2018YFA0901200//national key r&amp;d program of china/ ; }, abstract = {Bacteria inhabit diverse and dynamic environments, where nutrients may be limited and toxic chemicals can be prevalent. To adapt to these stressful conditions, bacteria have evolved specialized protein secretion systems, such as the type VI secretion system (T6SS) to facilitate their survival. As a molecular syringe, the T6SS expels various effectors into neighboring bacterial cells, eukaryotic cells, or the extracellular environment. These effectors improve the competitive fitness and environmental adaption of bacterial cells. Although primarily recognized as antibacterial weapons, recent studies have demonstrated that T6SSs have functions beyond interspecies competition. Here, we summarize recent research on the role of T6SSs in microbiome modulation, pathogenesis, and stress resistance.}, }
@article {pmid37674721, year = {2023}, author = {Rodriguez, CI and Isobe, K and Martiny, JBH}, title = {Short-term dietary fiber interventions produce consistent gut microbiome responses across studies.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-3283675/v1}, pmid = {37674721}, abstract = {Background The composition of the human gut microbiome varies tremendously among individuals, making the effects of dietary or treatment interventions difficult to detect and characterize. The consumption of fiber is important for gut health, yet the specific effects of increased fiber intake on the gut microbiome vary across studies. The variation in study outcomes might be due to inter-individual (or inter-population) variation or to the details of the interventions including the types of fiber, length of study, size of cohort, and molecular approaches. Thus, to identify consistent fiber-induced responses in the gut microbiome of healthy individuals, we re-analyzed 16S rRNA sequencing data from 21 dietary fiber interventions from 12 human studies, which included 2564 fecal samples from 538 subjects across all interventions. Results Short-term increases in dietary fiber consumption resulted in highly consistent gut microbiome responses across studies. Increased fiber consumption explained an average of 1.5% of compositional variation (versus 82% of variation attributed to the individual), reduced alpha diversity, and resulted in phylogenetically conserved responses in relative abundances among bacterial taxa. Additionally, we identified bacterial clades, at approximately the genus level, that were highly consistent in their response (increasing or decreasing in their relative abundance) to dietary fiber interventions across the studies. Conclusions Our study is an example of the power of synthesizing and reanalyzing microbiome data from many intervention studies. Despite high inter-individual variation of the composition of the human gut microbiome, dietary fiber interventions cause a consistent response both in the degree of change as well as the particular taxa that respond to increased fiber.}, }
@article {pmid37674718, year = {2023}, author = {Wang, Q and Wang, BY and Pratap, S and Xie, H}, title = {Oral microbiome associated with differential ratios of Porphyromonas gingivalis and Streptococcus cristatus.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-3266326/v1}, pmid = {37674718}, abstract = {Background Periodontitis has been recently defined as a dysbiotic disease resulting from imbalanced oral microbiota. The transition of microbial communities from commensal to periodontitis-associated ones likely requires colonization by specific pathogens, including Porphyromonas gingivalis . We previously reported an antagonistic relationship between Streptococcus cristatus and P. gingivalis and the role of S. cristatus in inhibition of the biofilm formation, invasion, and gingipain enzymatic activity of P. gingivalis . Given the importance of P. gingivalis as a keystone pathogen of polymicrobial communities, the determinants of P. gingivalis levels, its interaction with the core microbiota, and association with the pathogenic potential of the microbial communities need to be addressed. Results This present study intends to determine the role of S. cristatus in altering interactions of P. gingivalis with other oral bacteria in a complex context. We collected dental plaque samples from periodontitis patients and assigned them into two groups based on their ratios of S. cristatus and P. gingivalis . We then characterized microbial profiles of the dental plaque samples using shotgun metagenomic sequencing and subsequently compared oral microbial composition and functional capabilities between groups with high or low S. cristatus - P. gingivalis ratios. Taxonomic annotation showed significant differences in microbial compositions at both genus and species levels between the two groups. Notably, a higher microbial composition diversity was observed in the samples with low S. cristatus - P. gingivalis ratios. The antibiotic resistance gene profiles of the two groups are also distinct, with significantly increased diversity and abundance of antibiotic resistance genes in the dental plaque samples with low S. cristatus - P. gingivalis ratios, which likely lead to elevated virulence potential. Conclusions Overall, our work highlights the importance of S. cristatus - P. gingivalis ratios in influencing the virulence of the oral microbiome. Approaches to enhance S. cristatus - P. gingivalis ratios in oral microbial communities will be attractive for revising the dysbiotic oral microbiome.}, }
@article {pmid37674578, year = {2023}, author = {Hou, Y and Zhang, M and Jiang, Q and Yang, Y and Liu, J and Yuan, K and Sun, Z and Liu, X}, title = {Microbial signatures of neonatal bacterial meningitis from multiple body sites.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1169101}, pmid = {37674578}, issn = {2235-2988}, abstract = {As a common central nervous system infection in newborns, neonatal bacterial meningitis (NBM) can seriously affect their health and growth. However, although metagenomic approaches are being applied in clinical diagnostic practice, there are some limitations for whole metagenome sequencing and amplicon sequencing in handling low microbial biomass samples. Through a newly developed ultra-sensitive metagenomic sequencing method named 2bRAD-M, we investigated the microbial signatures of central nervous system infections in neonates admitted to the neonatal intensive care unit. Particularly, we recruited a total of 23 neonates suspected of having NBM and collected their blood, cerebrospinal fluid, and skin samples for 2bRAD-M sequencing. Then we developed a novel decontamination method (Reads Level Decontamination, RLD) for 2bRAD-M by which we efficiently denoised the sequencing data and found some potential biomarkers that have significantly different relative abundance between 12 patients that were diagnosed as NBM and 11 Non-NBM based on their cerebrospinal fluid (CSF) examination results. Specifically, we discovered 11 and 8 potential biomarkers for NBM in blood and CSF separately and further identified 16 and 35 microbial species that highly correlated with the physiological indicators in blood and CSF. Our study not only provide microbiological evidence to aid in the diagnosis of NBM but also demonstrated the application of an ultra-sensitive metagenomic sequencing method in pathogenesis study.}, }
@article {pmid37674497, year = {2023}, author = {El-Matary, W and Carroll, MW and Deslandres, C and Griffiths, AM and Kuenzig, ME and Mack, DR and Wine, E and Weinstein, J and Geist, R and Davis, T and Chan, J and Khan, R and Matthews, P and Kaplan, GG and Windsor, JW and Bernstein, CN and Bitton, A and Coward, S and Jones, JL and Lee, K and Murthy, SK and Targownik, LE and Peña-Sánchez, JN and Rohatinsky, N and Ghandeharian, S and Im, JHB and Goddard, Q and Gorospe, J and Verdugo, J and Morin, SA and Morganstein, T and Banning, L and Benchimol, EI}, title = {The 2023 Impact of Inflammatory Bowel Disease in Canada: Special Populations-Children and Adolescents with IBD.}, journal = {Journal of the Canadian Association of Gastroenterology}, volume = {6}, number = {Suppl 2}, pages = {S35-S44}, pmid = {37674497}, issn = {2515-2092}, abstract = {Rates of inflammatory bowel disease (IBD) in Canadian children and adolescents are among the highest in the world, and the incidence is rising most rapidly in children under five years of age. These young children may have either a typical form of IBD with multi-factorial aetiology, or they may have a monogenic form. Despite the growing number of children in Canada living with this important chronic disease, there are few available medical therapies approved by Health Canada due to the omission of children from most clinical trials of newly developed biologics. As a result, off-label use of medications is common, and physicians have learned to use existing therapies more effectively. In addition, most Canadian children are treated in multidisciplinary, specialty clinics by physicians with extra training or experience in IBD, as well as specialist nurses, dietitians, mental health care providers and other allied health professionals. This specialized clinic approach has facilitated cutting edge research, led by Canadian clinicians and scientists, to understand the causes of IBD, the optimal use of therapies, and the best ways to treat children from a biopsychosocial perspective. Canadians are engaged in work to understand the monogenic causes of IBD; the interaction between genes, the environment, and the microbiome; and how to address the mental health concerns and medical needs of adolescents and young adults transitioning from paediatric to adult care.}, }
@article {pmid37674314, year = {2023}, author = {Pixley, KV and Cairns, JE and Lopez-Ridaura, S and Ojiewo, CO and Dawud, MA and Drabo, I and Mindaye, T and Nebie, B and Asea, G and Das, B and Daudi, H and Desmae, H and Batieno, BJ and Boukar, O and Mukankusi, CTM and Nkalubo, ST and Hearne, SJ and Dhugga, KS and Gandhi, H and Snapp, S and Zepeda-Villarreal, EA}, title = {Redesigning crop varieties to win the race between climate change and food security.}, journal = {Molecular plant}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molp.2023.09.003}, pmid = {37674314}, issn = {1752-9867}, abstract = {Climate change poses daunting challenges to agricultural production and food security. Rising temperatures, shifting weather patterns, and more frequent extreme events have already demonstrated their effects on local, regional, and global agricultural systems. Crop varieties that withstand climate-related stresses and are suitable for cultivation in innovative cropping systems will be crucial to maximize risk avoidance, productivity, and profitability under climate-changed environments. We surveyed 588 expert stakeholders to predict current and novel traits that may be essential for future pearl millet, sorghum, maize, groundnut, cowpea, and common bean varieties, particularly in sub-Saharan Africa. We then review the current progress and prospects for breeding three prioritized future-essential traits for each of these crops. Experts predict that most current breeding priorities will remain important, but that rates of genetic gain must increase to keep pace with climate challenges and consumer demands. Importantly, the predicted future-essential traits include innovative breeding targets that must also be prioritized; for example, 1) optimized rhizosphere microbiome, with benefits for P, N, and water use efficiency, 2) optimized performance across or in specific cropping systems, 3) lower nighttime respiration, 4) improved stover quality, and 5) increased early vigor. We describe cutting-edge tools and approaches to discover, validate, and incorporate novel genetic diversity from exotic germplasm into breeding populations with unprecedented precision, accuracy, and speed, concluding that the greatest challenge to developing crop varieties to win the race between climate change and food security might be our innovativeness in defining and boldness to breed for the traits of tomorrow.}, }
@article {pmid37674277, year = {2023}, author = {Mato, EG and Montaño-Barrientos, BJ and Rivas-Mundiña, B and Aneiros, IV and López, LS and Posse, JL and Lamas, LM}, title = {Anti-caries Streptococcus spp.: A potential preventive tool for special needs patients.}, journal = {Special care in dentistry : official publication of the American Association of Hospital Dentists, the Academy of Dentistry for the Handicapped, and the American Society for Geriatric Dentistry}, volume = {}, number = {}, pages = {}, doi = {10.1111/scd.12920}, pmid = {37674277}, issn = {1754-4505}, abstract = {INTRODUCTION: Probiotics are living microorganisms that act on the host-microbiome interface to restore the microbiota's physiological homeostasis. Numerous probiotics have been marketed with inhibitory activity against Streptococcus mutans and consequently with a potential anti-caries effect, mainly of the genera Lactobacillus and Bifidobacterium, whose main disadvantage is their limited ability to settle in the oral cavity.<br><br>METHODS: This narrative review describes the main Streptococcus spp. with probiotic anti-Streptococcus mutans activity, whose substantivity is greater than that of Lactobacillus spp. and consequently with anti-caries potentiality. We performed a literature review in the PubMed, Science Direct and Google Scholar databases of articles published in English (without time restriction) related to caries and probiotics.<br><br>RESULTS: The potential identified anti-caries probiotics included Streptococcus spp. A12, Streptococcus oralis (AJ3), Streptococcus oligofermentans, Streptococcus salivarius (K12, M18, JH, LAB813, 24SMB), Streptococcus spp. with arginolytic activity (S. sanguinis, S. gordonii, S. ratti, S. parasanguinis, S. intermedius, S. australis, and S. cristatus), Streptococcus rattus (JH145), Streptococcus dentisani and Streptococcus downii.<br><br>CONCLUSIONS: The possibility of using these Streptococcus spp. as probiotics that inhibit the growth of dental plaque and the development of carious lesions represents a potential tool of particular interest for individuals with physical or intellectual disabilities that impede the routine and effective application of mechanical dental plaque removal techniques.}, }
@article {pmid37674159, year = {2023}, author = {Bruno, A and Sandionigi, A and Panio, A and Rimoldi, S and Orizio, F and Agostinetto, G and Hasan, I and Gasco, L and Terova, G and Labra, M}, title = {Aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with Tenebrio molitor novel diets.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {248}, pmid = {37674159}, issn = {1471-2180}, abstract = {BACKGROUND: Sustainable aquaculture relies on multiple factors, including water quality, fish diets, and farmed fish. Replacing fishmeal (FM) with alternative protein sources is key for improving sustainability in aquaculture and promoting fish health. Indeed, great research efforts have been made to evaluate novel feed formulations, focusing especially on the effects on the fish gut microbiome. Few studies have explored host-environment interactions. In the present study, we evaluated the influence of novel insect-based (Tenebrio molitor) fish diets on the microbiome at the water-fish interface in an engineered rainbow trout (Oncorhynchus mykiss) farming ecosystem. Using 16S rRNA gene metabarcoding, we comprehensively analyzed the microbiomes of water, tank biofilm, fish intestinal mucus, fish cutis, and feed samples.<br><br>RESULTS: Core microbiome analysis revealed the presence of a highly reduced core shared by all sample sources, constituted by Aeromonas spp., in both the control and novel feed test groups. Network analysis showed that samples were clustered based on the sample source, with no significant differences related to the feed formulation tested. Thus, the different diets did not seem to affect the environment (water and tank biofilm) and fish (cutis and intestinal mucus) microbiomes. To disentangle the contribution of feed at a finer scale, we performed a differential abundance analysis and observed differential enrichment/impoverishment in specific taxa, comparing the samples belonging to the control diet group and the insect-based diet group.<br><br>CONCLUSIONS: Omic exploration of the water-fish interface exposes patterns that are otherwise undetected. These data demonstrate a link between the environment and fish and show that subtle but significant differences are caused by feed composition. Thus, the research presented here is a step towards positively influencing the aquaculture environment and its microbiome.}, }
@article {pmid37674095, year = {2023}, author = {Bourceau, P and Geier, B and Suerdieck, V and Bien, T and Soltwisch, J and Dreisewerd, K and Liebeke, M}, title = {Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling.}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, pmid = {37674095}, issn = {1750-2799}, support = {LT0015/2022-L//Human Frontier Science Program (HFSP)/ ; DR 416/12-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; O976/41//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CRC TRR332 (Z1)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DR 416/12-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; O976/41//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CRC TRR332 (Z1)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SO976/5-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Label-free molecular imaging techniques such as matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) enable the direct and simultaneous mapping of hundreds of different metabolites in thin sections of biological tissues. However, in host-microbe interactions it remains challenging to localize microbes and to assign metabolites to the host versus members of the microbiome. We therefore developed a correlative imaging approach combining MALDI-MSI with fluorescence in situ hybridization (FISH) on the same section to identify and localize microbial cells. Here, we detail metaFISH as a robust and easy method for assigning the spatial distribution of metabolites to microbiome members based on imaging of nucleic acid probes, down to single-cell resolution. We describe the steps required for tissue preparation, on-tissue hybridization, fluorescence microscopy, data integration into a correlative image dataset, matrix application and MSI data acquisition. Using metaFISH, we map hundreds of metabolites and several microbial species to the micrometer scale on a single tissue section. For example, intra- and extracellular bacteria, host cells and their associated metabolites can be localized in animal tissues, revealing their complex metabolic interactions. We explain how we identify low-abundance bacterial infection sites as regions of interest for high-resolution MSI analysis, guiding the user to a trade-off between metabolite signal intensities and fluorescence signals. MetaFISH is suitable for a broad range of users from environmental microbiologists to clinical scientists. The protocol requires ~2 work days.}, }
@article {pmid37674059, year = {2023}, author = {Tian, Y and Liu, Y and Uwaremwe, C and Zhao, X and Yue, L and Zhou, Q and Wang, Y and Tran, LP and Li, W and Chen, G and Sha, Y and Wang, R}, title = {Characterization of three new plant growth-promoting microbes and effects of the interkingdom interactions on plant growth and disease prevention.}, journal = {Plant cell reports}, volume = {}, number = {}, pages = {}, pmid = {37674059}, issn = {1432-203X}, support = {21ZD4NA019//Science and Technology Planning Project of Gansu Province, major special project/ ; 2022BBF02031//Research and Development Projects of Ningxia Hui Autonomous Region/ ; }, abstract = {The novel interkingdom PGPM consortia enhanced the ability of plant growth promotion and disease resistance, which would be beneficial to improve plant growth in sustainable agriculture through engineering microbiome. Plant growth-promoting microbes (PGPMs) play important roles in promoting plant growth and bio-controlling of pathogens. Much information reveals that the plant growth-promoting ability of individual PGPM affects plant growth. However, the effects of the PGPM consortia properties on plant growth remain largely unexplored. Here, we characterized three new PGPM strains including Rhodotorula graminis JJ10.1 (termed as J), Pseudomonas psychrotolerans YY7 (termed as Y) and P. chlororaphis T8 (termed as T), and assessed their effects in combination with Bacillus amyloliquefaciens FZB42 (termed as F) on plant growth promotion and disease prevention in Arabidopsis thaliana and tomato (Solanum lycopersicum) plants by investigating morphological changes, whole-genome sequencing and plant growth promoting (PGP) characterization. Results revealed that the three new strains R. graminis JJ10.1, P. psychrotolerans YY7 and P. chlororaphis T8 had the potential for being combined with B. amyloliquefaciens FZB42 to form interkingdom PGPM consortia. The combinations of R. graminis JJ10.1, B. amyloliquefaciens FZB42, and P. psychrotolerans YY7, i. e. JF and JYF, exhibited the strongest ability of synergetic biofilm production. Furthermore, the growth-promotion abilities of the consortia were significantly enhanced compared with those of individual strains under both inoculation and volatile organic compounds (VOCs) treatment. Importantly, the consortia showed stronger abilities of in planta disease prevention than individual strains. Findings of our study may provide future guidance for engineering the minimal microbiome communities to improve plant growth and/or disease resistance in sustainable agriculture.}, }
@article {pmid37674038, year = {2023}, author = {Amaral, AL and Lwaleed, BA and Andrade, SA}, title = {Electronic nicotine delivery systems (ENDS): a strategy for smoking cessation or a new risk factor for oral health?.}, journal = {Evidence-based dentistry}, volume = {}, number = {}, pages = {}, pmid = {37674038}, issn = {1476-5446}, abstract = {DATA SOURCES: A search was conducted in PubMed and Cochrane Library databases for articles published in English between January 2012 and October 2022.<br><br>STUDY SELECTION: Articles were selected using both the term "electronic nicotine delivery system" (ENDS), as per the Medical Subject Heading (MeSH), in conjunction with specific oral domains. In vitro studies, animal models, unregistered clinical trials, and articles with conflicts of interest were excluded.<br><br>DATA EXTRACTION AND SYNTHESIS: Clinical and public health studies comparing ENDS users, smokers, and non-smokers in the context of oral-related diseases were included. Results from duplicate articles were not considered.<br><br>RESULTS: The study indicates a potential carcinogenic effect due to cytogenotoxicity from intrinsic components of ENDS. However, this does not establish ENDS as an independent risk factor for oral cancer. ENDS use may alter the oral microbiome, leading to increased biofilm adhesion and potential associations with caries, periodontal disease, and peri-implantitis. The wide variety of flavors available in the ENDS market is a significant factor influencing initiation and long-term use by young people.<br><br>CONCLUSIONS: ENDS users are susceptible to periodontal disease, caries, soft tissue injuries, and changes in tooth and prosthesis coloration. The chemical components in ENDS can induce cellular changes associated with a potential risk of oral cancer. However, more long-term studies are required to fully understand the impact of ENDS use on oral health.}, }
@article {pmid37674014, year = {2023}, author = {Cornish, CM and Bergholz, P and Schmidt, K and Sweetman, J}, title = {How Benthic Sediment Microbial Communities Respond to Glyphosate and Its Metabolite: a Microcosm Experiment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37674014}, issn = {1432-184X}, abstract = {Glyphosate is the most commonly used agricultural herbicide in the world. In aquatic ecosystems, glyphosate often adsorbs to benthic substrates or is metabolized and degraded by microorganisms. The effects of glyphosate on microbial communities vary widely as microorganisms respond differently to exposure. To help understand the impacts of glyphosate on the sediment microbiome, we conducted a microcosm experiment examining the responses of benthic sediment microbial communities to herbicide treatments. Sediments from a prairie pothole wetland were collected, and 16S rRNA gene sequencing was used to analyze community composition 2-h and 14-days after a single treatment of low (0.07 ppm), medium (0.7 ppm), or high (7 ppm) glyphosate, aminomethylphosphonic acid (glyphosate metabolite), or a glyphosate-based commercial formula. We found no significant differences in microbial community composition across treatments, concentration levels, or day of sampling. These findings suggest that microbial species in the Prairie Pothole Region of North America may be tolerant to glyphosate exposure.}, }
@article {pmid37674003, year = {2023}, author = {Choi, KJ and Yoon, MY and Kim, JE and Yoon, SS}, title = {Gut commensal Kineothrix alysoides mitigates liver dysfunction by restoring lipid metabolism and gut microbial balance.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14668}, pmid = {37674003}, issn = {2045-2322}, support = {NRF-2022M3A9F3017506//the National Research Foundation (NRF) of Korea/ ; HI14C1324//the Korea Health Technology R&amp;D Project through the Korea Health Industry Development Institute (KHIDI)/ ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD), previously known as Non-Alcoholic Fatty Liver Disease, is a widespread liver condition characterized by excessive fat buildup in hepatocytes without significant alcohol consumption. Manipulation of the gut microbiome has been considered to prevent and improve the occurrence and progression of MASLD, particularly through the gut-liver axis. This study aimed to investigate the correlation between the gut microbiome and liver function and determine whether the gut microbiome can ameliorate MASLD. We comparatively analyzed the gut microbiome composition between mice fed normal chow and those fed a high-fat diet and observed that the abundance of Kineothrix alysoides decreased in the high-fat group. Further analysis showed that treatment with K. alysoides in the high-fat diet group led to decreased weight loss, and MASLD attenuation. Importantly, K. alysoides treatment attenuated MASLD in mice fed a high-fat, high-fructose diet (HFHF), which can cause advanced liver damage. Furthermore, administration of K. alysoides altered the gut microbial composition in the HFHF diet group and improved MASLD. Overall, these findings demonstrate the potential of K. alysoides in restoring gut health and facilitating lipid metabolism to prevent and treat MASLD.}, }
@article {pmid37673976, year = {2023}, author = {Kingwell, K}, title = {Microbiome screening platform finds drugs for bugs.}, journal = {Nature reviews. Drug discovery}, volume = {}, number = {}, pages = {}, pmid = {37673976}, issn = {1474-1784}, }
@article {pmid37673969, year = {2023}, author = {Petersen, C and Hamerich, IK and Adair, KL and Griem-Krey, H and Torres Oliva, M and Hoeppner, MP and Bohannan, BJM and Schulenburg, H}, title = {Host and microbiome jointly contribute to environmental adaptation.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37673969}, issn = {1751-7370}, support = {CRC 1182, A1.1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CRC 1182, INF//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Fellowship//Max-Planck-Gesellschaft (Max Planck Society)/ ; Humboldt Research Award//Alexander von Humboldt-Stiftung (Alexander von Humboldt Foundation)/ ; }, abstract = {Most animals and plants have associated microorganisms, collectively referred to as their microbiomes, which can provide essential functions. Given their importance, host-associated microbiomes have the potential to contribute substantially to adaptation of the host-microbiome assemblage (the "metaorganism"). Microbiomes may be especially important for rapid adaptation to novel environments because microbiomes can change more rapidly than host genomes. However, it is not well understood how hosts and microbiomes jointly contribute to metaorganism adaptation. We developed a model system with which to disentangle the contributions of hosts and microbiomes to metaorganism adaptation. We established replicate mesocosms containing the nematode Caenorhabditis elegans co-cultured with microorganisms in a novel complex environment (laboratory compost). After approximately 30 nematode generations (100 days), we harvested worm populations and associated microbiomes, and subjected them to a common garden experiment designed to unravel the impacts of microbiome composition and host genetics on metaorganism adaptation. We observed that adaptation took different trajectories in different mesocosm lines, with some increasing in fitness and others decreasing, and that interactions between host and microbiome played an important role in these contrasting evolutionary paths. We chose two exemplary mesocosms (one with a fitness increase and one with a decrease) for detailed study. For each example, we identified specific changes in both microbiome composition (for both bacteria and fungi) and nematode gene expression associated with each change in fitness. Our study provides experimental evidence that adaptation to a novel environment can be jointly influenced by host and microbiome.}, }
@article {pmid37673852, year = {2023}, author = {Joshi, M and Hiremath, P and John, J and Ranadive, N and Nandakumar, K and Mudgal, J}, title = {Modulatory role of vitamins A, B3, C, D, and E on skin health, immunity, microbiome, and diseases.}, journal = {Pharmacological reports : PR}, volume = {}, number = {}, pages = {}, pmid = {37673852}, issn = {2299-5684}, abstract = {Disruption of the skin barrier and immunity has been associated with several skin diseases, namely atopic dermatitis (AD), psoriasis, and acne. Resident and non-resident immune cells and the barrier system of the skin are integral to innate immunity. Recent advances in understanding skin microbiota have opened the scope of further understanding the various communications between these microbiota and skin immune cells. Vitamins, being one of the important micronutrients, have been reported to exert antioxidant, anti-inflammatory, and anti-microbial effects. The immunomodulatory action of vitamins can halt the progression of skin diseases, and thus, understanding the immuno-pharmacology of these vitamins, especially for skin diseases can pave the way for their therapeutic potential. At the same time, molecular and cellular markers modulated with these vitamins and their derivatives need to be explored. The present review is focused on significant vitamins (vitamins A, B3, C, D, and E) consumed as nutritional supplements to discuss the outcomes and scope of studies related to skin immunity, health, and diseases.}, }
@article {pmid37673331, year = {2023}, author = {Carson, MD and Westwater, C and Novince, CM}, title = {Adolescence and the Microbiome: Implications for Healthy Growth and Maturation.}, journal = {The American journal of pathology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajpath.2023.07.004}, pmid = {37673331}, issn = {1525-2191}, abstract = {The gut microbiota was initially thought to develop into a stable, adult-like profile during early postnatal life. The formation of the gut microbiota during early life has been shown to contribute to healthy growth and has lifelong implications for host health. Adolescence, the developmental period between childhood and adulthood, is a critical window for healthy growth and maturation. The composition of the gut microbiota in adolescents is distinct from that of children and adults, which supports the premise that the gut microbiota continues to develop during adolescence toward an adult-like profile. Research has begun to shift its focus from understanding the gut microbiome at the extremes of the lifespan to evaluating the importance of the gut microbiome during adolescence and the role it plays in healthy development. This article provides an overview of adolescent development, host-microbiota interactions, and experimental models used to discern gut microbiota effects on health and disease. The role of the gut microbiota is reviewed as it relates to adolescent: i) brain development, cognition, and behavior; ii) metabolism and adiposity, and iii) skeletal growth and bone mass accrual. Future directions are addressed including omics investigations defining mechanisms through which the gut microbiota influences adolescent development. Further, we discuss advancing non-invasive interventions targeting the adolescent gut microbiota that could be employed to support healthy growth and maturation.}, }
@article {pmid37673213, year = {2023}, author = {Lehman, P and Ghimire, S and Price, JD and Ramer-Tait, AE and Mangalam, A}, title = {Diet-microbiome-immune interplay in multiple sclerosis: Understanding the impact of phytoestrogen metabolizing gut bacteria.}, journal = {European journal of immunology}, volume = {}, number = {}, pages = {e2250236}, doi = {10.1002/eji.202250236}, pmid = {37673213}, issn = {1521-4141}, abstract = {Multiple sclerosis (MS) is a chronic and progressive autoimmune disease of the central nervous system (CNS), with both genetic and environmental factors contributing to the pathobiology of the disease. While HLA genes have emerged as the strongest genetic factor linked to MS, consensus on the environmental risk factors is lacking. Recently, the gut microbiota has garnered increasing attention as a potential environmental factor in MS, as mounting evidence suggests that individuals with MS exhibit microbial dysbiosis (changes in the gut microbiome). Thus, there has been a strong emphasis on understanding the role of the gut microbiome in the pathobiology of MS, specifically, factors regulating the gut microbiota and the mechanism(s) through which gut microbes may contribute to MS. Among all factors, diet has emerged to have the strongest influence on the composition and function of gut microbiota. As MS patients lack gut bacteria capable of metabolizing dietary phytoestrogen, we will specifically discuss the role of a phytoestrogen diet and phytoestrogen metabolizing gut bacteria in the pathobiology of MS. A better understanding of these mechanisms will help to harness the enormous potential of the gut microbiota as potential therapeutics to treat MS and other autoimmune diseases. This article is protected by copyright. All rights reserved.}, }
@article {pmid37673134, year = {2023}, author = {Gomes, N and Ferreira-Sa, L and Alves, N and Dallago, B and Moraes, A and Carvalho, JL and Nitz, N and Hagström, L and Braz, S and Machado, ER and Gurgel-Gonçalves, R and Hecht, M}, title = {Uncovering the effects of Giardia duodenalis on the balance of DNA viruses and bacteria in children's gut microbiota.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {107018}, doi = {10.1016/j.actatropica.2023.107018}, pmid = {37673134}, issn = {1873-6254}, abstract = {The neglected parasitosis giardiasis is one of the most common intestinal infections worldwide, affecting mainly infants and young children. Giardia duodenalis may disturb the local microbiome, leading to intestinal ecosystem disorders, and altering different processes in the host, such as the immune response. Nevertheless, the alterations promoted by G. duodenalis on the human gut microbiome have not been thoroughly investigated. Here, we characterized the gut microbiota of G. duodenalis-infected children and determine the main alterations promoted by the parasite. To do so, fecal samples of 26 infected and four uninfected children aged 2 to 6 years old were processed for High Efficiency Microarray analysis, in order to describe their bacterial and viral profiles. Then, we quantified the total bacterial population by qPCR and assessed fecal calprotectin levels, which are closely related with gut inflammation. A total of 286 bacteria's species and 17 viruses' strains were identified. Our results revealed no statistically significant differences between G. duodenalis positive and negative groups in the taxa's phyla and families. However, bacterial species diversity was increased in children infected with G. duodenalis (p < 0.05), while the total number of bacteria was decreased (p < 0.05). Considering the virome analysis, 17 different strains were identified, 88% being bacteriophages. The correlation analysis revealed an important disruption in the balance of DNA virus and bacteria within the intestinal microbiota of Giardia-positive children. Our findings constitute the first description of the gut virome of Giardia-infected children and suggest that G. duodenalis infection exerts a modulatory effect on the gut microbiome, promoting local inflammation and altering the equilibrium of the parasite-microbiota-host triad. This highlights the importance of considering polymicrobial associations and understanding the broader context of giardiasis. Overall, our study provides new insights into the complex interactions between intestinal parasites and the microbiota, which may have implications for the development of novel therapeutic interventions in the future.}, }
@article {pmid37673131, year = {2023}, author = {Saha, P and Panda, S and Holkar, A and Vashishth, R and Rana, SS and Arumugam, MP and Ashraf, GM and Haque, S and Ahmad, F}, title = {Neuroprotection by agmatine: Possible involvement of the gut microbiome?.}, journal = {Ageing research reviews}, volume = {}, number = {}, pages = {102056}, doi = {10.1016/j.arr.2023.102056}, pmid = {37673131}, issn = {1872-9649}, abstract = {Agmatine, an endogenous polyamine derived from L-arginine, elicits tremendous multimodal neuromodulant properties. Alterations in agmatinergic signalling are closely linked to the pathogeneses of several brain disorders. Importantly, exogenous agmatine has been shown to act as a potent neuroprotectant in varied pathologies, including brain ageing and associated comorbidities. The antioxidant, anxiolytic, analgesic, antidepressant and memory-enhancing activities of agmatine may derive from its ability to regulate several cellular pathways; including cell metabolism, survival and differentiation, nitric oxide signalling, protein translation, oxidative homeostasis and neurotransmitter signalling. This review briefly discusses mammalian metabolism of agmatine and then proceeds to summarize our current understanding of the neuromodulation and neuroprotection mediated by agmatine. Further, the emerging exciting bidirectional links between agmatine and the resident gut microbiome and their implications for brain pathophysiology and ageing are also discussed.}, }
@article {pmid37673036, year = {2023}, author = {Ni, Y and Qian, L and Siliceo, SL and Long, X and Nychas, E and Liu, Y and Ismaiah, MJ and Leung, H and Zhang, L and Gao, Q and Wu, Q and Zhang, Y and Jia, X and Liu, S and Yuan, R and Zhou, L and Wang, X and Li, Q and Zhao, Y and El-Nezami, H and Xu, A and Xu, G and Li, H and Panagiotou, G and Jia, W}, title = {Resistant starch decreases intrahepatic triglycerides in patients with NAFLD via gut microbiome alterations.}, journal = {Cell metabolism}, volume = {35}, number = {9}, pages = {1530-1547.e8}, doi = {10.1016/j.cmet.2023.08.002}, pmid = {37673036}, issn = {1932-7420}, abstract = {Non-alcoholic fatty liver disease (NAFLD) is a hepatic manifestation of metabolic dysfunction for which effective interventions are lacking. To investigate the effects of resistant starch (RS) as a microbiota-directed dietary supplement for NAFLD treatment, we coupled a 4-month randomized placebo-controlled clinical trial in individuals with NAFLD (ChiCTR-IOR-15007519) with metagenomics and metabolomics analysis. Relative to the control (n = 97), the RS intervention (n = 99) resulted in a 9.08% absolute reduction of intrahepatic triglyceride content (IHTC), which was 5.89% after adjusting for weight loss. Serum branched-chain amino acids (BCAAs) and gut microbial species, in particular Bacteroides stercoris, significantly correlated with IHTC and liver enzymes and were reduced by RS. Multi-omics integrative analyses revealed the interplay among gut microbiota changes, BCAA availability, and hepatic steatosis, with causality supported by fecal microbiota transplantation and monocolonization in mice. Thus, RS dietary supplementation might be a strategy for managing NAFLD by altering gut microbiota composition and functionality.}, }
@article {pmid37672729, year = {2023}, author = {Wierzbicka-Rucińska, A}, title = {Microbiome Relationship of gut microbiota and immunological response in obesity-related non-alcoholic fatty liver disease in children.}, journal = {Acta biochimica Polonica}, volume = {}, number = {}, pages = {}, doi = {10.18388/abp.2020_6573}, pmid = {37672729}, issn = {1734-154X}, abstract = {In the development of NAFLD plays an important role the intestinal microflora. Our aim was to characterize role microbiota in children. Distinctive gut microbiota composition was observed in children, characterized and short-chain fatty acid producing bacteria. For the treatment of NAFLD it is possible by therapeutic manipulations with prebiotics and probiotics to modulate the gut microbiota and maintain the integrity of the intestinal barrier are potential agents.}, }
@article {pmid37672536, year = {2023}, author = {Irvine, A and Huws, SA and Atkinson, LE and Mousley, A}, title = {Exploring the antimicrobial peptidome of nematodes through phylum-spanning in silico analyses highlights novel opportunities for pathogen control.}, journal = {PLoS neglected tropical diseases}, volume = {17}, number = {9}, pages = {e0011618}, doi = {10.1371/journal.pntd.0011618}, pmid = {37672536}, issn = {1935-2735}, abstract = {Antimicrobial Peptides (AMPs) are key constituents of the invertebrate innate immune system and provide critical protection against microbial threat. Nematodes display diverse life strategies where they are exposed to heterogenous, microbe rich, environments highlighting their need for an innate immune system. Within the Ecdysozoa, arthropod AMPs have been well characterised, however nematode-derived AMP knowledge is limited. In this study the distribution and abundance of putative AMP-encoding genes was examined in 134 nematode genomes providing the most comprehensive profile of AMP candidates within phylum Nematoda. Through genome and transcriptome analyses we reveal that phylum Nematoda is a rich source of putative AMP diversity and demonstrate (i) putative AMP group profiles that are influenced by nematode lifestyle where free-living nematodes appear to display enriched putative AMP profiles relative to parasitic species; (ii) major differences in the putative AMP profiles between nematode clades where Clade 9/V and 10/IV species possess expanded putative AMP repertoires; (iii) AMP groups with highly restricted profiles (e.g. Cecropins and Diapausins) and others [e.g. Nemapores and Glycine Rich Secreted Peptides (GRSPs)] which are more widely distributed; (iv) complexity in the distribution and abundance of CSαβ subgroup members; and (v) that putative AMPs are expressed in host-facing life stages and biofluids of key nematode parasites. These data indicate that phylum Nematoda displays diversity in putative AMPs and underscores the need for functional characterisation to reveal their role and importance to nematode biology and host-nematode-microbiome interactions.}, }
@article {pmid37672426, year = {2023}, author = {Prado, T and Magalhães, MGP and Moreira, DA and Brandão, ML and Fumian, TM and Ferreira, FC and Chame, M and Leomil, L and Degrave, WMS and Leite, JPG and Miagostovich, MP}, title = {Microbiome and virome on indoor surfaces of an Antarctic research ship.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {118}, number = {}, pages = {e230084}, pmid = {37672426}, issn = {1678-8060}, abstract = {BACKGROUND: Few studies have focused on microbial diversity in indoor environments of ships, as well as the role of the microbiome and its ecological interconnections. In this study, we investigated the microbiome and virome present on the internal surfaces of a polar ship in different stages (beginning, during, and at the end) of the Brazilian Antarctic expedition in order to evaluate abundance of microorganisms in different periods.<br><br>OBJECTIVES AND METHODS: We used shotgun metagenomic analysis on pooled samples from sampling surfaces in the ship's interior to track the microbial diversity.<br><br>FINDINGS: Considering the total fraction of the microbiome, the relative abundance of bacteria, eukaryotes, viruses, and archaea was 83.7%, 16.2%, 0.04%, and 0.002%, respectively. Proteobacteria was the most abundant bacterial phyla, followed by Firmicutes, Actinobacteria, and Bacteroidetes. Concerning the virome, the greatest richness of viral species was identified during the middle of the trip, including ten viral families after de novo assembly: Autographiviridae, Chrysoviridae, Genomoviridae, Herelleviridae, Myoviridae, Partitiviridae, Podoviridae, Potyviridae, Siphoviridae, and Virgaviridae.<br><br>MAIN CONCLUSIONS: This study contributed to the knowledge of microbial diversity in naval transportation facilities, and variations in the abundance of microorganisms probably occurred due to factors such as the number of passengers and activities on the ship.}, }
@article {pmid37672357, year = {2023}, author = {Sitkin, S and Pokrotnieks, J}, title = {Targeted Probiotics Against Bacterial-Fungal Biofilms: A New Concept Seems to Bring Us Closer to Microbiome-modulating Therapy for Inflammatory Bowel Disease.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izad209}, pmid = {37672357}, issn = {1536-4844}, }
@article {pmid37672354, year = {2023}, author = {Di Martino, L}, title = {Reply: "Targeted Probiotics Against Bacterial-Fungal Biofilms: A New Concept Seems to Bring Us Closer to Microbiome-Modulating Therapy for Inflammatory Bowel Disease".}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izad206}, pmid = {37672354}, issn = {1536-4844}, }
@article {pmid37672084, year = {2023}, author = {Bang, C and Heinzel, S}, title = {[Relationships between microbiome and neurodegeneration].}, journal = {Der Nervenarzt}, volume = {}, number = {}, pages = {}, pmid = {37672084}, issn = {1433-0407}, abstract = {BACKGROUND: Neurodegenerative diseases are often associated with changes in the (gut) microbiome.<br><br>OBJECTIVE: Based on studies in Parkinson's disease (PD) and Alzheimer's disease (AD), an overview of the current evidence of microbial changes and their possible role in the development of these diseases is given.<br><br>METHODS: Analysis, summary, and evaluation of the current literature on (gut) microbiome and neurodegeneration.<br><br>RESULTS: Numerous studies have shown dysbiotic changes in the gut microbiome of PD and AD patients compared to healthy individuals, some of which might occur even in the prodromal phase. Specifically, these patients show a&#xa0;reduction in bacteria involved in the synthesis of short-chain fatty acids. These microbial alterations have been associated with systemic inflammation and a&#xa0;compromised integrity of the intestinal barrier and blood-brain barrier. Bacterial molecules such as lipopolysaccharides may play an important role in these changes. Additionally, the bacterial protein curli, found on the surface of e.g., Escherichia coli, has been shown in vitro and in animal models to promote the misfolding of &#x3b1;-synuclein, thus suggesting a&#xa0;crucial pathomechanism. Moreover, certain oral bacteria appear to be more prevalent in AD patients and may contribute to the pathogenesis of AD.<br><br>CONCLUSION: Neurodegenerative diseases are associated with dysbiosis of the (gut) microbiome, which can have diverse systemic effects; however, it remains unclear whether this dysbiosis is a&#xa0;cause or a&#xa0;consequence of the diseases. Further investigation of this (prodromal) microbial imbalance could reveal new approaches for targeted therapeutic manipulation of the microbiome to modify and prevent these diseases.}, }
@article {pmid37671923, year = {2023}, author = {Rieg, T and Xue, J and Stevens, M and Thomas, L and White, JR and Dominguez Rieg, JA}, title = {Intravenous ferric carboxymaltose and ferric derisomaltose alter the intestinal microbiome in female iron-deficient anemic mice.}, journal = {Bioscience reports}, volume = {}, number = {}, pages = {}, doi = {10.1042/BSR20231217}, pmid = {37671923}, issn = {1573-4935}, abstract = {Iron deficiency anemia (IDA) is a leading global health concern affecting approximately 30% of the population. Treatment for IDA consists of replenishment of iron stores, either by oral or intravenous (IV) supplementation. There is a complex bidirectional interplay between the gut microbiota, the host's iron status, and dietary iron availability. Dietary iron deficiency and supplementation can influence the gut microbiome; however, the effect of IV iron on the gut microbiome is unknown. We studied how commonly used IV iron preparations, ferric carboxymaltose (FCM) and ferric derisomaltose (FDI), affected the gut microbiome in female iron-deficient anemic mice. At the phylum level, vehicle-treated mice showed an expansion in Verrucomicrobia, mostly because of the increased abundance of Akkermansia muciniphila, along with contraction in Firmicutes, resulting in a lower Firmicutes/Bacteroidetes ratio (indicator of dysbiosis). Treatment with either FCM or FDI restored the microbiome such that Firmicutes and Bacteroidetes were the dominant phyla. Interestingly, the phyla Proteobacteria and several members of Bacteroidetes (e.g., Alistipes) were expanded in mice treated with FCM compared to those treated with FDI. In contrast, several Clostridia class members were expanded in mice treated with FDI compared to FCM (e.g., Dorea spp., Eubacterium). Our data demonstrate that IV iron increases gut microbiome diversity independently of the iron preparation used; however, differences exist between FCM and FDI treatments. In conclusion, replenishing iron stores with IV iron preparations in clinical conditions, such as inflammatory bowel disease or chronic kidney disease, could affect gut microbiome composition and consequently contribute to an altered disease outcome.}, }
@article {pmid37671879, year = {2023}, author = {Vazquez-Munoz, R and Thompson, A and Sobue, T and Dongari-Bagtzoglou, A}, title = {A prebiotic diet modulates the oral microbiome composition and results in the attenuation of oropharyngeal candidiasis in mice.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0173423}, doi = {10.1128/spectrum.01734-23}, pmid = {37671879}, issn = {2165-0497}, abstract = {Oral bacteria can influence the ability of Candida albicans to cause oropharyngeal candidiasis (OPC). We recently reported that a Lactobacillus johnsonii-enriched oral microbiota reduced C. albicans virulence in an immunosuppressed OPC mouse model. As a follow-up, in this work, we aimed to enrich the resident oral Lactobacillus communities with a prebiotic diet to further assess their effect on the severity of OPC. We tested the effect of a prebiotic xylo-oligosaccharides (XOS)-enriched diet in the oral global bacterial composition and severity of OPC. We assessed changes in the oral microbiome composition via 16S-rRNA gene high-throughput sequencing, validated by qPCR. The impact of the prebiotic diet on Candida infection was assessed by quantifying changes in oral fungal and bacterial biomass and scoring tongue lesions. Contrary to expectations, oral Lactobacillus communities were not enriched by the XOS-supplemented diet. Yet, XOS modulated the oral microbiome composition, increasing Bifidobacterium abundance and reducing enterococci and staphylococci. In the OPC model, the XOS diet attenuated Candida virulence and bacterial dysbiosis, increasing lactobacilli and reducing enterococci on the oral mucosa. We conclude that XOS attenuates Candida virulence by promoting a bacterial microbiome structure more resilient to Candida infection. IMPORTANCE This is the first study on the effects of a prebiotic diet on the oral mucosal bacterial microbiome and an oropharyngeal candidiasis (OPC) mouse model. We found that xylo-oligosaccharides change the oral bacterial community composition and attenuate OPC. Our results contribute to the understanding of the impact of the oral bacterial communities on Candida virulence.}, }
@article {pmid37671803, year = {2023}, author = {Li, N and Tan, S and Wang, Y and Deng, J and Wang, N and Zhu, S and Tian, W and Xu, J and Wang, Q}, title = {Akkermansia muciniphila supplementation prevents cognitive impairment in sleep-deprived mice by modulating microglial engulfment of synapses.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2252764}, doi = {10.1080/19490976.2023.2252764}, pmid = {37671803}, issn = {1949-0984}, mesh = {Animals ; Mice ; Microglia ; Dysbiosis ; *Gastrointestinal Microbiome ; Sleep ; Sleep Deprivation ; Synapses ; *Cognitive Dysfunction ; Dietary Supplements ; }, abstract = {The microbiome-gut-brain axis plays a crucial role in many neurological diseases, including mild cognitive impairment. Sleep deprivation (SD) induces cognitive decline accompanied by alterations in the gut microbiota. However, the role of gut microbiota alterations in SD-induced cognitive dysfunction and the underlying mechanisms remain unclear. Here, we found that dysbiosis of the gut microbiota following pretreatment with broad-spectrum antibiotics worsens SD-induced cognitive impairment in mice. Fecal microbiota transplantation from SD mice to healthy mice induced cognitive impairment. Additionally, the abundance of Akkermansia muciniphila (A. muciniphila) in the mouse gut microbiota was significantly reduced after 7 days of SD. A. muciniphila pretreatment alleviated cognitive dysfunction and prevented synaptic reduction in the hippocampus in SD mice. A. muciniphila pretreatment inhibited extensive microglial activation and synaptic engulfment in the hippocampus of SD mice. Metabolomics analysis revealed that A. muciniphila pretreatment increased the serum acetate and butanoic acid levels in SD mice. Finally, pretreatment with short-chain fatty acids (SCFAs) inhibited microglial synaptic engulfment and prevented neuronal synaptic loss in SD mice and primary microglia-neuron co-culture following LPS stimulation. Together, our findings illustrate that gut dysbiosis plays an essential role in SD-induced cognitive impairment by activating microglial engulfment at synapses. A. muciniphila supplementation may be a novel preventative strategy for SD-induced cognitive dysfunction, by increasing SCFAs production and maintaining microglial homeostasis.}, }
@article {pmid37671363, year = {2023}, author = {Reyes, G and Andrade, B and Betancourt, I and Panchana, F and Solórzano, R and Preciado, C and Sorroza, L and Trujillo, LE and Bayot, B}, title = {Microbial signature profiles of Penaeus vannamei larvae in low-survival hatchery tanks affected by vibriosis.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15795}, pmid = {37671363}, issn = {2167-8359}, mesh = {Animals ; *Penaeidae ; *Vibrio Infections ; *Vibrionaceae ; *Alphaproteobacteria ; Bacteroidetes ; Larva ; Necrosis ; Syndrome ; }, abstract = {Vibriosis is caused by some pathogenic Vibrio and produces significant mortality in Pacific white shrimp Penaeus (Litopenaeus) vannamei larvae in commercial hatcheries. Acute hepatopancreatic necrosis disease (AHPND) is an emerging vibriosis affecting shrimp-producing countries worldwide. Zoea 2 syndrome is another type of vibriosis that affects the early stages of P. vannamei larvae. Although the pathogenesis of AHPND and zoea 2 syndrome is well known, there is scarce information about microbial composition and biomarkers of P.vannamei larvae affected by AHPND, and there is no study of the microbiome of larvae affected by zoea 2 syndrome. In this work, we characterized the microbiome of P. vannamei larvae collected from 12 commercial hatchery tanks by high-throughput sequencing. Seven tanks were affected by AHPND, and five tanks were affected by zoea 2 syndrome. Subsequently, all samples were selected for sequencing of the V3-V4 region of the16S rRNA gene. Similarity analysis using the beta diversity index revealed significant differences in the larval bacterial communities between disease conditions, particularly when Vibrio was analyzed. Linear discriminant analysis with effect size determined specific microbial signatures for AHPND and zoea 2 syndrome. Sneathiella, Cyclobacterium, Haliea, Lewinella, among other genera, were abundant in AHPND-affected larvae. Meanwhile, Vibrio, Spongiimonas, Meridianimaribacter, Tenacibaculum, among other genera, were significantly abundant in larvae affected by zoea 2 syndrome. The bacterial network at the phylum level for larvae collected from tanks affected by AHPND showed greater complexity and connectivity than in samples collected from tanks affected by zoea 2 syndrome. The bacterial connections inter Vibrio genera were higher in larvae from tanks affected by zoea 2 syndrome, also presenting other connections between the genera Vibrio and Catenococcus. The identification of specific biomarkers found in this study could be useful for understanding the microbial dynamics during different types of vibriosis.}, }
@article {pmid37671098, year = {2023}, author = {Yao, Y and Shen, Y}, title = {Cross-talk between gut microbiota and liver steatosis: Complications and therapeutic target.}, journal = {Open life sciences}, volume = {18}, number = {1}, pages = {20220699}, pmid = {37671098}, issn = {2391-5412}, abstract = {Liver steatosis is the most widespread chronic liver condition. Its global incidence is rising swiftly and is currently estimated to be 24%. Liver steatosis is strongly related with numerous metabolic syndrome characteristics, like obesity, insulin resistance, hyperlipidemia, and hypertension. The gastrointestinal tract contains about 100 trillion commensal organisms and more than 7,000 distinct bacterial strains. Fat deposition in the liver without secondary causes is known as liver steatosis. Dysregulation of the gut flora is one of the factors connected to the onset of fatty liver disease. Dietary choices may alter constitution of the microbiome and cause gut microbiome dysbiosis, particularly due to the intake of food high in fructose sugars, animal products, and saturated fats. Various gut bacteria cause nutrient metabolism in multiple ways, setting off different inflammatory cascades that encourage liver disease and pathways that help fat build up in the liver. Due to their relatively stable nature, genetic factors may not be responsible for the constant increase in liver steatosis incidence. Genetic factors set the stage for liver steatosis pathogenesis. This review will offer an overview of our present knowledge of the roles played by gut microbiota in regulating the development of liver steatosis, potential side effects, and potential treatment targets.}, }
@article {pmid37671072, year = {2023}, author = {Jain, S and Marotta, F and Haghshenas, L and Yadav, H}, title = {Treating Leaky Syndrome in the Over 65s: Progress and Challenges.}, journal = {Clinical interventions in aging}, volume = {18}, number = {}, pages = {1447-1451}, pmid = {37671072}, issn = {1178-1998}, mesh = {Humans ; *Aging ; Syndrome ; }, abstract = {As we age, our organ functions gradually decline. Circulating factors in the blood and the integrity of organ barriers can become dysfunctional, resulting in a condition known as leaky syndrome. This condition involves the unregulated exchange or leakage of components between organs. However, the triggers of leaky syndrome, as well as its role in aging-related disorders and illnesses, remain largely unknown. In this editorial, we discuss potential mechanisms that originate from the gut and resident microbes (microbiome) to contribute in leaky syndrome. Furthermore, we explore how the food we consume can impact the development of leaky syndrome, potentially influencing the biology of aging and challenges to diagnose the leaky gut condition accurately and clinically.}, }
@article {pmid37671025, year = {2023}, author = {Lan, J and Greter, G and Streckenbach, B and Wanner, B and Arnoldini, M and Zenobi, R and Slack, E}, title = {Non-invasive monitoring of microbiota and host metabolism using secondary electrospray ionization-mass spectrometry.}, journal = {Cell reports methods}, volume = {3}, number = {8}, pages = {100539}, pmid = {37671025}, issn = {2667-2375}, mesh = {Animals ; Mice ; Spectrometry, Mass, Electrospray Ionization ; *Microbiota ; *Gastrointestinal Microbiome ; Metabolome ; Atmosphere ; Mammals ; }, abstract = {The metabolic "handshake" between the microbiota and its mammalian host is a complex, dynamic process with major influences on health. Dissecting the interaction between microbial species and metabolites found in host tissues has been a challenge due to the requirement for invasive sampling. Here, we demonstrate that secondary electrospray ionization-mass spectrometry (SESI-MS) can be used to non-invasively monitor metabolic activity of the intestinal microbiome of a live, awake mouse. By comparing the headspace metabolome of individual gut bacterial culture with the "volatilome" (metabolites released to the atmosphere) of gnotobiotic mice, we demonstrate that the volatilome is characteristic of the dominant colonizing bacteria. Combining SESI-MS with feeding heavy-isotope-labeled microbiota-accessible sugars reveals the presence of microbial cross-feeding within the animal intestine. The microbiota is, therefore, a major contributor to the volatilome of a living animal, and it is possible to capture inter-species interaction within the gut microbiota using volatilome monitoring.}, }
@article {pmid37531269, year = {2023}, author = {Georjon, H and Tesson, F and Shomar, H and Bernheim, A}, title = {Genomic characterization of the antiviral arsenal of Actinobacteria.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {8}, pages = {}, pmid = {37531269}, issn = {1465-2080}, mesh = {*Actinobacteria/genetics ; Antiviral Agents/pharmacology/therapeutic use ; Bacteria ; Genomics ; }, abstract = {Phages are ubiquitous in nature, and bacteria with very different genomics, metabolisms, and lifestyles are subjected to their predation. Yet, the defence systems that allow bacteria to resist their phages have rarely been explored experimentally outside a very limited number of model organisms. Actinobacteria (Actinomycetota) are a phylum of GC-rich Gram-positive bacteria, which often produce an important diversity of secondary metabolites. Despite being ubiquitous in a wide range of environments, from soil to fresh and sea water but also the gut microbiome, relatively little is known about the anti-phage arsenal of Actinobacteria. In this work, we used DefenseFinder to systematically detect 131 anti-phage defence systems in 22803 fully sequenced prokaryotic genomes, among which are 2253 Actinobacteria of more than 700 species. We show that, like other bacteria, Actinobacteria encode many diverse anti-phage systems that are often encoded on mobile genetic elements. We further demonstrate that most detected defence systems are absent or rarer in Actinobacteria than in other bacteria, while a few rare systems are enriched (notably gp29-gp30 and Wadjet). We characterize the spatial distribution of anti-phage systems on Streptomyces chromosomes and show that some defence systems (e.g. RM systems) tend to be encoded in the core region, while others (e.g. Lamassu and Wadjet) are enriched towards the extremities. Overall, our results suggest that Actinobacteria might be a source of novel anti-phage systems and provide clues to characterize mechanistic aspects of known anti-phage systems.}, }
@article {pmid37670990, year = {2023}, author = {Pérez-Llano, Y and Yarzábal Rodríguez, LA and Martínez-Romero, E and Dobson, ADW and Gunde-Cimerman, N and Vasconcelos, V and Batista-García, RA}, title = {From friends to foes: fungi could be emerging marine sponge pathogens under global change scenarios.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1213340}, pmid = {37670990}, issn = {1664-302X}, }
@article {pmid37670983, year = {2023}, author = {Kolli, U and Roy, S}, title = {The role of the gut microbiome and microbial metabolism in mediating opioid-induced changes in the epigenome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1233194}, pmid = {37670983}, issn = {1664-302X}, abstract = {The current opioid pandemic is a major public health crisis in the United States, affecting millions of people and imposing significant health and socioeconomic burdens. Preclinical and clinical research over the past few decades has delineated certain molecular mechanisms and identified various genetic, epigenetic, and environmental factors responsible for the pathophysiology and comorbidities associated with opioid use. Opioid use-induced epigenetic modifications have been identified as one of the important factors that mediate genetic changes in brain regions that control reward and drug-seeking behavior and are also implicated in the development of tolerance. Recently, it has been shown that opioid use results in microbial dysbiosis, leading to gut barrier disruption, which drives systemic inflammation, impacting the perception of pain, the development of analgesic tolerance, and behavioral outcomes. In this review, we highlight the potential role of microbiota and microbial metabolites in mediating the epigenetic modifications induced by opioid use.}, }
@article {pmid37670872, year = {2023}, author = {Romano, I and Bodenhausen, N and Basch, G and Soares, M and Faist, H and Trognitz, F and Sessitsch, A and Doubell, M and Declerck, S and Symanczik, S}, title = {Impact of conservation tillage on wheat performance and its microbiome.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1211758}, pmid = {37670872}, issn = {1664-462X}, abstract = {Winter wheat is an important cereal consumed worldwide. However, current management practices involving chemical fertilizers, irrigation, and intensive tillage may have negative impacts on the environment. Conservation agriculture is often presented as a sustainable alternative to maintain wheat production, favoring the beneficial microbiome. Here, we evaluated the impact of different water regimes (rainfed and irrigated), fertilization levels (half and full fertilization), and tillage practices (occasional tillage and no-tillage) on wheat performance, microbial activity, and rhizosphere- and root-associated microbial communities of four winter wheat genotypes (Antequera, Allez-y, Apache, and Cellule) grown in a field experiment. Wheat performance (i.e., yield, plant nitrogen concentrations, and total nitrogen uptake) was mainly affected by irrigation, fertilization, and genotype, whereas microbial activity (i.e., protease and alkaline phosphatase activities) was affected by irrigation. Amplicon sequencing data revealed that habitat (rhizosphere vs. root) was the main factor shaping microbial communities and confirmed that the selection of endophytic microbial communities takes place thanks to specific plant-microbiome interactions. Among the experimental factors applied, the interaction of irrigation and tillage influenced rhizosphere- and root-associated microbiomes. The findings presented in this work make it possible to link agricultural practices to microbial communities, paving the way for better monitoring of these microorganisms in the context of agroecosystem sustainability.}, }
@article {pmid37670809, year = {2023}, author = {Kim, G and Lee, Y and You, JS and Hwang, W and Hwang, J and Kim, HY and Kim, J and Jo, A and Park, IH and Ali, M and Kim, J and Shin, JS and Kwon, HK and Kim, HJ and Yoon, SS}, title = {A Moonlighting Protein Secreted by a Nasal Microbiome Fortifies the Innate Host Defense Against Bacterial and Viral Infections.}, journal = {Immune network}, volume = {23}, number = {4}, pages = {e31}, pmid = {37670809}, issn = {1598-2629}, abstract = {Evidence suggests that the human respiratory tract, as with the gastrointestinal tract, has evolved to its current state in association with commensal microbes. However, little is known about how the airway microbiome affects the development of airway immune system. Here, we uncover a previously unidentified mode of interaction between host airway immunity and a unique strain (AIT01) of Staphylococcus epidermidis, a predominant species of the nasal microbiome. Intranasal administration of AIT01 increased the population of neutrophils and monocytes in mouse lungs. The recruitment of these immune cells resulted in the protection of the murine host against infection by Pseudomonas aeruginosa, a pathogenic bacterium. Interestingly, an AIT01-secreted protein identified as GAPDH, a well-known bacterial moonlighting protein, mediated this protective effect. Intranasal delivery of the purified GAPDH conferred significant resistance against other Gram-negative pathogens (Klebsiella pneumoniae and Acinetobacter baumannii) and influenza A virus. Our findings demonstrate the potential of a native nasal microbe and its secretory protein to enhance innate immune defense against airway infections. These results offer a promising preventive measure, particularly relevant in the context of global pandemics.}, }
@article {pmid37670792, year = {2023}, author = {Guilhot, R and Xuéreb, A and Lagmairi, A and Olazcuaga, L and Fellous, S}, title = {Microbiota acquisition and transmission in Drosophila flies.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107656}, pmid = {37670792}, issn = {2589-0042}, abstract = {Understanding the ecological and evolutionary dynamics of host-microbiota associations notably involves exploring how members of the microbiota assemble and whether they are transmitted along host generations. Here, we investigate the larval acquisition of facultative bacterial and yeast symbionts of Drosophila melanogaster and Drosophila suzukii in ecologically realistic setups. Fly mothers and fruit were major sources of symbionts. Microorganisms associated with adult males also contributed to larval microbiota, mostly in D. melanogaster. Yeasts acquired at the larval stage maintained through metamorphosis, adult life, and were transmitted to offspring. All these observations varied widely among microbial strains, suggesting they have different transmission strategies among fruits and insects. Our approach shows microbiota members of insects can be acquired from a diversity of sources and highlights the compound nature of microbiotas. Such microbial transmission events along generations should favor the evolution of mutualistic interactions and enable microbiota-mediated local adaptation of the insect host.}, }
@article {pmid37670791, year = {2023}, author = {Shibasaki, S and Mitri, S}, title = {A spatially structured mathematical model of the gut microbiome reveals factors that increase community stability.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107499}, pmid = {37670791}, issn = {2589-0042}, abstract = {Given the importance of gut microbial communities for human health, we may want to ensure their stability in terms of species composition and function. Here, we built a mathematical model of a simplified gut composed of two connected patches where species and metabolites can flow from an upstream patch, allowing upstream species to affect downstream species' growth. First, we found that communities in our model are more stable if they assemble through species invasion over time compared to combining a set of species from the start. Second, downstream communities are more stable when species invade the downstream patch less frequently than the upstream patch. Finally, upstream species that have positive effects on downstream species can further increase downstream community stability. Despite it being quite abstract, our model may inform future research on designing more stable microbial communities or increasing the stability of existing ones.}, }
@article {pmid37670337, year = {2023}, author = {Ballesteros-Ramírez, R and Pinilla, P and Sanchéz, J and Torregrosa, L and Aschner, P and Urueña, C and Fiorentino, S}, title = {Safety and efficacy of P2Et extract from Caesalpinia spinosa in breast cancer patients: study protocol for a randomized double blind phase II clinical trial (CS003-BC).}, journal = {BMC complementary medicine and therapies}, volume = {23}, number = {1}, pages = {309}, pmid = {37670337}, issn = {2662-7671}, support = {FP44842-221-2018//World Bank and Vicerrector&#xed;a de Investigaciones, Pontificia Universidad Javeriana/ ; FP44842-221-2018//World Bank and Vicerrector&#xed;a de Investigaciones, Pontificia Universidad Javeriana/ ; FP44842-221-2018//World Bank and Vicerrector&#xed;a de Investigaciones, Pontificia Universidad Javeriana/ ; FP44842-221-2018//World Bank and Vicerrector&#xed;a de Investigaciones, Pontificia Universidad Javeriana/ ; FP44842-221-2018//World Bank and Vicerrector&#xed;a de Investigaciones, Pontificia Universidad Javeriana/ ; FP44842-221-2018//World Bank and Vicerrector&#xed;a de Investigaciones, Pontificia Universidad Javeriana/ ; FP44842-221-2018//World Bank and Vicerrector&#xed;a de Investigaciones, Pontificia Universidad Javeriana/ ; }, abstract = {BACKGROUND: Chemotherapy in breast cancer is effective but can generate significant toxicity and lead to tumor resistance. Joint treatment with standardized plant extracts can be an alternative to improve the response and allow an effective activation of the antitumor immune response that favors recovery in the short and long term. The P2Et extract of Caesalpinia spinosa presents antitumor activity in cells and animal models of breast cancer, improves the tumor microenvironment, and induces activation of the specific immune response against the tumor and is synergistic when used together with anthracyclines, which makes it a good candidate for evaluation in patients.<br><br>METHODS: Conducted at a single center, this phase II study is a randomized, double-blind, placebo-controlled trial aimed at assessing the safety and efficacy of P2Et extract in patients diagnosed with stage II and III breast cancer, who are eligible for neoadjuvant treatment. The study aims to determine the safety profile at the previously established optimal biological dose from phase I trial while investigating various efficacy outcomes. These outcomes include improvements in quality of life, immunomodulation, metabolic profile, microbiome, as well as clinical indicators such as tumor reduction, disease-free survival, and pathological response, assessed at different stages of the treatment regimen.<br><br>DISCUSSION: Treatment with the P2Et extract in breast cancer patients is hypothesized to enhance overall well-being, positively influencing their quality of life, while also triggering an antitumor immune response and enhancing immune infiltration. These combined effects have the potential to contribute to improved long-term survival outcomes for patients receiving the phytomedicine alongside neoadjuvant chemotherapy treatment.<br><br>TRIAL REGISTRATION: This trial was registered in the US National Library of Medicine with identifier NCT05007444. First Registered August 16[th], 2021. Last Updated: August 9[th], 2022.}, }
@article {pmid37670315, year = {2023}, author = {Douglas, P}, title = {Does the Academy of Breastfeeding Medicine's Clinical Protocol #36 'The Mastitis Spectrum' promote overtreatment and risk worsened outcomes for breastfeeding families? Commentary.}, journal = {International breastfeeding journal}, volume = {18}, number = {1}, pages = {51}, pmid = {37670315}, issn = {1746-4358}, abstract = {BACKGROUND: In 2022 the Academy of Breastfeeding Medicine (ABM) published Clinical Protocol #36: The Mastitis Spectrum, which aims to update clinical approaches to management of benign lactation-related breast inflammation. The protocol has been timely because of the exponential increase in knowledge about the human milk microbiome over the past decade. This Commentary aims to continue respectful debate amongst clinicians and researchers within the Academy of Breastfeeding Medicine and more broadly, confident that we share a fundamental commitment to promote breastfeeding and support the well-being of lactating women, their infants and their families.<br><br>ANALYSIS: Although Clinical Protocol #36 offers advances, it does not fulfil the principles of best practice implementation science for translation of evidence into clinical guidelines. Clinical Protocol #36 inaccurately represents studies; misrepresents theoretical models as proven aetiologies; does not consistently attribute sources; does not reliably apply the SORT taxonomy; and relies upon single case reports. As a result, various recommendations in Clinical Protocol #36 lack an evidence-base or credible underlying theoretical model. This includes recommendations to use 'lymphatic drainage' massage, therapeutic ultrasound, and oral lecithin. Similarly, based on a contestable theoretical model which is presented as fact, Clinical Protocol #36 makes the recommendation to either reduce frequency of milk removal or to maintain current frequency of milk removal during an episode of breast inflammation. Although Clinical Protocol #36 limits this advice to cases of 'hyperlactation', the diagnosis 'hyperlactation' itself is undefinable. As a result, this recommendation may put breastfeeding women who present with breast inflammation at risk of worsened inflammation and decreased breast milk production.<br><br>CONCLUSION: Clinical Protocol #36 offers some advances in the management of breast inflammation. However, Clinical Protocol #36 also exposes clinicians to two international trends in healthcare which undermine health system sustainability: overdiagnosis, including by over-definition, which increases risk of overtreatment; and antibiotic over-use, which worsens the crisis of global antimicrobial resistance. Clinical Protocol #36 also recommends unnecessary or ineffective interventions which may be accessed by affluent patients within advanced economies but are difficult to access for the global majority. The Academy of Breastfeeding Medicine may benefit from a review of processes for development of Clinical Protocols.}, }
@article {pmid37670231, year = {2023}, author = {Guo, R and Zhang, W and Shen, W and Zhang, G and Xie, T and Li, L and Jinmei, J and Liu, Y and Kong, F and Guo, B and Li, B and Sun, Y and Liu, S}, title = {Analysis of gut microbiota in chinese donkey in different regions using metagenomic sequencing.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {524}, pmid = {37670231}, issn = {1471-2164}, support = {SDAIT-27//Donkey Innovation Team of Shandong Modern Agricultural Industry Technology System/ ; SD2019 XM 008//Major Agricultural Application Technology Innovation Projects of Shandong Province/ ; 225A6601D//Hebei Provincial science and Technology Planning Project/ ; 2022DZ01//Systematic Evaluation and Screening of donkey germplasm Resources in the Yellow River Basin/ ; 2021E02035//Autonomous region science and technology branch Xinjiang project/ ; ZR2022QC091//Shandong Province Natural Science Foundation/ ; 20210021//Experimental Technology Research Pro-gramme of Qingdao Agriculture University/ ; }, abstract = {BACKGROUND: Gut microbiota plays a significant role in host survival, health, and diseases; however, compared to other livestock, research on the gut microbiome of donkeys is limited.<br><br>RESULTS: In this study, a total of 30 donkey samples of rectal contents from six regions, including Shigatse, Changdu, Yunnan, Xinjiang, Qinghai, and Dezhou, were collected for metagenomic sequencing. The results of the species annotation revealed that the dominant phyla were Firmicutes and Bacteroidetes, and the dominant genera were Bacteroides, unclassified_o_Clostridiales (short for Clostridiales) and unclassified_f_Lachnospiraceae (short for Lachnospiraceae). The dominant phyla, genera and key discriminators were Bacteroidetes, Clostridiales and Bacteroidetes in Tibet donkeys (Shigatse); Firmicutes, Clostridiales and Clostridiales in Tibet donkeys (Changdu); Firmicutes, Fibrobacter and Tenericutes in Qinghai donkeys; Firmicutes, Clostridiales and Negativicutes in Yunnan donkeys; Firmicutes, Fibrobacter and Fibrobacteres in Xinjiang donkeys; Firmicutes, Clostridiales and Firmicutes in Dezhou donkeys. In the functional annotation, it was mainly enriched in the glycolysis and gluconeogenesis of carbohydrate metabolism, and the abundance was the highest in Dezhou donkeys. These results combined with altitude correlation analysis demonstrated that donkeys in the Dezhou region exhibited strong glucose-conversion ability, those in the Shigatse region exhibited strong glucose metabolism and utilization ability, those in the Changdu region exhibited a strong microbial metabolic function, and those in the Xinjiang region exhibited the strongest ability to decompose cellulose and hemicellulose.<br><br>CONCLUSION: According to published literature, this is the first study to construct a dataset with multi-regional donkey breeds. Our study revealed the differences in the composition and function of gut microbes in donkeys from different geographic regions and environmental settings and is valuable for donkey gut microbiome research.}, }
@article {pmid37670218, year = {2023}, author = {Shalileh, F and Gheibzadeh, MS and Lloyd, JR and Fietz, S and Shahbani Zahiri, H and Zolfaghari Emameh, R}, title = {Evolutionary analysis and quality assessment of ζ-carbonic anhydrase sequences from environmental microbiome.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jobm.202300323}, pmid = {37670218}, issn = {1521-4028}, support = {111210//South African Agency for Science and Technology Advancement/ ; 692//National Institute for Genetic Engineering and Biotechnology/ ; M/75137//Ministry of Science Research and Technology/ ; }, abstract = {Carbonic anhydrase (CA) is one of the most vital enzymes in living cells. This study has been performed due to the significance of this metalloenzyme for life and the novelty of some CA families like ζ-CA to evaluate evolutionary processes and quality check their sequences. In this study, bioinformatics methods revealed the presence of ζ-CA in some eukaryotic and prokaryotic microorganisms. Notably, it has not been previously reported in prokaryotes. The coexistence of β- and ζ-CAs in some microorganisms is also a novel finding as well. Also, our analysis identified several CA proteins with 6-14 amino acid intervals between histidine and cysteine in the second highly conserved motif, which can be classified as the novel ζ-CA subfamily members that emerged under the Zn deficiency of aquatic ecosystems and selection pressure in these environments. There is also a possibility that the achieved results are rooted in the contamination of samples from the environmental microbiome genome with genomes of diatom species and the occurrence of errors was observed in the DNA sequencing outcomes. Combining of all results from evolutionary analysis to quality control of ζ-CA DNA sequences is the incentive motivation to explore more the hidden aspects of ζ-CAs.}, }
@article {pmid37669144, year = {2023}, author = {Fassatoui, M and Saffarian, A and Mulet, C and Jamoussi, H and Gamoudi, A and Ben Halima, Y and Hechmi, M and Abdelhak, S and Abid, A and Sansonetti, PJ and Pedron, T and Kefi, R}, title = {Gut microbiota profile and the influence of nutritional status on bacterial distribution in diabetic and healthy Tunisian subjects.}, journal = {Bioscience reports}, volume = {}, number = {}, pages = {}, doi = {10.1042/BSR20220803}, pmid = {37669144}, issn = {1573-4935}, abstract = {Gut microbiota plays a key role in the regulation of metabolism and immunity. We investigated the profile of gut microbiota and the impact of dietary intake on gut bacterial distribution in diabetic and healthy Tunisian subjects, aiming to identify a dysbiotic condition, hence opening the way to restore eubiosis and facilitate return to health. In the present research, we enrolled 10 type 1 diabetic (T1D), 10 type 2 diabetic (T2D) patients and 13 healthy (H) subjects. Illumina Miseq technology was used to sequence V3-V4 hypervariable regions of bacterial 16SrRNA gene. Data was analyzed referring to QIIME 2 pipeline. RStudio software was used to explore the role of nutrition in gut bacterial distribution. At the phylum level, we identified an imbalanced gut microbiota composition in diabetic patients marked by a decrease in the proportion of Firmicutes and an increase in the abundance of Bacteroidetes compared with H subjects. We observed higher amounts of Fusobacteria and a decline in the levels of TM7 phyla in T1D patients compared with H subjects. However, we revealed a decrease in the proportions of Verrucomicrobia in T2D patients compared with H subjects. At the genus level, T2D subjects were more affected by gut microbiota alteration, showing a reduction in the relative abundance of Faecalibacterium, Akkermansia, Clostridium, Blautia and Oscillibacter, whereas T1D group shows a decrease in the proportion of Blautia. The gut bacteria distribution was mainly affected by fats and carbohydrates consumption. Gut microbiota composition was altered in Tunisian diabetic patients and affected by dietary habits.}, }
@article {pmid37668965, year = {2023}, author = {Guo, H and Liu, X and Chen, T and Wang, X and Zhang, X}, title = {Akkermansia muciniphila Improves Depressive-Like Symptoms by Modulating the Level of 5-HT Neurotransmitters in the Gut and Brain of Mice.}, journal = {Molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {37668965}, issn = {1559-1182}, support = {2021ZD0200700//the 2030 Plan Technology and Innovation of China/ ; 82271535//National Natural Science Foundation of China/ ; 2022RC1008//The Science and Technology Innovation Program of Hunan Province/ ; 2021JJ40894//Hunan Provincial Natural Science Foundation/ ; 2022JJ30882//Hunan Provincial Natural Science Foundation/ ; 202103090528//Scientific Research Project of Hunan Provincial Health Commission/ ; 202211004855//Scientific Research Project of Hunan Provincial Health Commission/ ; }, abstract = {Accumulating evidence has suggested that the gut microbiome plays an important role in depression. Akkermansia muciniphila (AKK), a next-generation probiotic, shows a beneficial effect on immune and metabolic homeostasis. The relative abundance of AKK was found negatively correlated with depressive symptoms in both clinical and pre-clinical studies. To evaluate the potential antidepressant effect of AKK and explore the possible mechanism, we used chronic alcohol exposure and chronic unpredictable mild stress (CUMS) to induce depressive-like behaviors in mice. We found that oral AKK administration significantly reduced the immobility time in the force swimming test (FST) and tail suspension test (TST) in the mice with chronic alcohol exposure and the CUMS mice. The sucrose preference in the mice receiving AKK was significantly increased in the sucrose preference test (SPT). More importantly, AKK implantation significantly increased the level of 5-HT in the gut and PFC of both the alcohol exposure mice and the CUMS mice. Furthermore, AKK had inhibited the expression of SERT in the gut but not in the brain for both NIAAA and the CUMS model mice. Interestingly, the expression of cFos in enteric nerves in the gut significantly decreased after AKK administration. In conclusion, our study demonstrated the antidepressant effect of AKK in mice exposed to alcohol exposure and CUMS, with the potential mechanism that AKK implantation might lead to an increased level of 5-HT and inhibited SERT expression in the gut, and might alter the gut-to-brain signal through suppression of enteric nerves activation.}, }
@article {pmid37668469, year = {2023}, author = {Mattoo, R and Mallikarjuna, S}, title = {Soil microbiome influences human health in the context of climate change.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2217/fmb-2023-0098}, pmid = {37668469}, issn = {1746-0921}, abstract = {Soil microbiomes continue to evolve and shape the human microbiota according to external anthropogenic and climate change effects. Ancient microbes are being exposed as a result of glacier melting, soil erosion and poor agricultural practices. Soil microbes subtly regulate greenhouse gas emissions and undergo profound alterations due to poor soil maintenance. This review highlights how the soil microbiome influences human digestion processes, mineral and vitamin production, mental health and mood stimulation. Although much about microbial functions remains unknown, increasing evidence suggests that beneficial soil microbes are vital for enhancing human tolerance to diseases and pathogens. Further research is essential to delineate the specific role of the soil microbiome in promoting human health, especially in light of the increasing anthropogenic pressures and changing climatic conditions.}, }
@article {pmid37668433, year = {2023}, author = {Huang, S and Bergonzi, C and Smith, S and Hicks, RE and Elias, MH}, title = {Field testing of an enzymatic quorum quencher coating additive to reduce biocorrosion of steel.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0517822}, doi = {10.1128/spectrum.05178-22}, pmid = {37668433}, issn = {2165-0497}, abstract = {Microbial colonization can be detrimental to the integrity of metal surfaces and lead to microbiologically influenced corrosion. Biocorrosion is a serious problem for aquatic and marine industries in the world and severely affects the maritime transportation industry by destroying port infrastructure and increasing fuel usage and the time and cost required for maintenance of transport vessels. Here, we evaluate the potential of a stable quorum quenching lactonase enzyme to reduce biocorrosion in the field. Over the course of 21 months, steel samples coated with lactonase-containing acrylic paint were submerged at two different sites and depths in the Duluth-Superior Harbor (Lake Superior, MN, USA) and benchmarked against controls, including the biological biocide surfactin. In this experiment, the lactonase treatment outperformed the surfactin biocide treatment and significantly reduced the number of corrosion tubercles (37%; P < 0.01) and the corroded surface area (39%; P < 0.01) as compared to the acrylic-coated control coupons. In an attempt to evaluate the effects of signal disruption of surface microbial communities and the reasons for lower corrosion levels, 16S rRNA sequencing was performed and community populations were analyzed. Interestingly, surface communities were similar between all treatments, and only minor changes could be observed. Among these changes, several groups, including sulfate-reducing bacteria (SRB), appeared to correlate with corrosion levels, and more specifically, SRB abundance levels were lower on lactonase-treated steel coupons. We surmise that these minute community changes may have large impacts on corrosion rates. Overall, these results highlight the potential use of stable quorum quenching lactonases as an eco-friendly antifouling coating additive. IMPORTANCE Biocorrosion severely affects the maritime transportation industry by destroying port infrastructure and increasing fuel usage and the time and cost required to maintain transport vessels. Current solutions are partly satisfactory, and the antifouling coating still largely depends on biocide-containing products that are harmful to the environment. The importance of microbial signaling in biofouling and biocorrosion is not elucidated. We here take advantage of a highly stable lactonase that can interfere with N-acyl homoserine lactone-based quorum sensing and remain active in a coating base. The observed results show that an enzyme-containing coating can reduce biocorrosion over 21 months in the field. It also reveals subtle changes in the abundance of surface microbes, including sulfate-reducing bacteria. This work may contribute to pave the way for strategies pertaining to surface microbiome changes to reduce biocorrosion.}, }
@article {pmid37668400, year = {2023}, author = {Du, H and Pan, J and Zhang, C and Yang, X and Wang, C and Lin, X and Li, J and Liu, W and Zhou, H and Yu, X and Mo, S and Zhang, G and Zhao, G and Qu, W and Jiang, C and Tian, Y and He, Z and Liu, Y and Li, M}, title = {Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0157723}, doi = {10.1128/spectrum.01577-23}, pmid = {37668400}, issn = {2165-0497}, abstract = {As an important coastal "blue carbon sink," mangrove ecosystems contain microbial communities with an as-yet-unknown high species diversity. Exploring the assemblage and structure of sediment microbial communities therein can aid in a better understanding of their ecosystem functioning, such as carbon sequestration and other biogeochemical cycles in mangrove wetlands. However, compared to other biomes, the study of mangrove sediment microbiomes is limited, especially in diverse mangrove ecosystems at a large spatial scale, which may harbor microbial communities with distinct compositions and functioning. Here, we analyzed 380 sediment samples from 13 and 8 representative mangrove ecosystems, respectively, in China and South America and compared their microbial features. Although the microbial community compositions exhibited strong distinctions, the community assemblage in the two locations followed analogous patterns: the assemblages of the entire community, abundant taxa, rare taxa, and generalists were predominantly driven by stochastic processes with significant distance-decay patterns, while the assembly of specialists was more likely related to the behaviors of other organisms in or surrounding the mangrove ecosystems. In addition, co-occurrence and topological network analysis of mangrove sediment microbiomes underlined the dominance of sulfate-reducing prokaryotes in both the regions. Moreover, we found that more than 70% of the keystone and hub taxa were sulfate-reducing prokaryotes, implying their important roles in maintaining the linkage and stability of the mangrove sediment microbial communities. This study fills a gap in the large-scale analysis of microbiome features covering distantly located and diverse mangrove ecosystems. Here, we propose a suggestion to the Mangrove Microbiome Initiative that 16S rRNA sequencing protocols should be standardized with a unified primer to facilitate the global-scale analysis of mangrove microbiomes and further comparisons with the reference data sets from other biomes.IMPORTANCEMangrove wetlands are important ecosystems possessing valuable ecological functions for carbon storage, species diversity maintenance, and coastline stabilization. These functions are greatly driven or supported by microorganisms that make essential contributions to biogeochemical cycles in mangrove ecosystems. The mechanisms governing the microbial community assembly, structure, and functions are vital to microbial ecology but remain unclear. Moreover, studying these mechanisms of mangrove microbiomes at a large spatial scale can provide a more comprehensive insight into their universal features and can help untangle microbial interaction patterns and microbiome functions. In this study, we compared the mangrove microbiomes in a large spatial range and found that the assembly patterns and key functional guilds of the Chinese and South American mangrove microbiomes were analogous. The entire communities exhibited significant distance-decay patterns and were strongly governed by stochastic processes, while the assemblage of specialists may be merely associated with the behaviors of the organisms in mangrove ecosystems. Furthermore, our results highlight the dominance of sulfate-reducing prokaryotes in mangrove microbiomes and their key roles in maintaining the stability of community structure and functions.}, }
@article {pmid37668195, year = {2023}, author = {Zheng, Q and Hu, Y and Kosina, SM and Van Goethem, MW and Tringe, SG and Bowen, BP and Northen, TR}, title = {Conservation of beneficial microbes between the rhizosphere and the cyanosphere.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19225}, pmid = {37668195}, issn = {1469-8137}, support = {DE-SC0021369//Office of Science, Office of Biological and Environmental Research, US Department of Energy/ ; DE-AC02-05CH11231//the Office of Science Early Career Research Program, Office of Biological and Environmental Research, of the US Department of Energy/ ; }, abstract = {Biocrusts are phototroph-driven communities inhabiting arid soil surfaces. Like plants, most photoautotrophs (largely cyanobacteria) in biocrusts are thought to exchange fixed carbon for essential nutrients like nitrogen with cyanosphere bacteria. Here, we aim to compare beneficial interactions in rhizosphere and cyanosphere environments, including finding growth-promoting strains for hosts from both environments. To examine this, we performed a retrospective analysis of 16S rRNA gene sequencing datasets, host-microbe co-culture experiments between biocrust communities/biocrust isolates and a model grass (Brachypodium distachyon) or a dominant biocrust cyanobacterium (Microcoleus vaginatus), and metabolomic analysis. All 18 microbial phyla in the cyanosphere were also present in the rhizosphere, with additional 17 phyla uniquely found in the rhizosphere. The biocrust microbes promoted the growth of the model grass, and three biocrust isolates (Bosea sp._L1B56, Pseudarthrobacter sp._L1D14 and Pseudarthrobacter picheli_L1D33) significantly promoted the growth of both hosts. Moreover, pantothenic acid was produced by Pseudarthrobacter sp._L1D14 when grown on B. distachyon exudates, and supplementation of plant growth medium with this metabolite increased B. distachyon biomass by over 60%. These findings suggest that cyanobacteria and other diverse photoautotrophic hosts can be a source for new plant growth-promoting microbes and metabolites.}, }
@article {pmid37667968, year = {2023}, author = {Yau, YK and Su, Q and Xu, Z and Tang, W and Ching, JYL and Mak, JWY and Cheung, CP and Fung, M and Ip, M and Chan, PKS and Wu, JCY and Chan, FKL and Ng, SC}, title = {Randomised clinical trial: Faecal microbiota transplantation for irritable bowel syndrome with diarrhoea.}, journal = {Alimentary pharmacology &amp; therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1111/apt.17703}, pmid = {37667968}, issn = {1365-2036}, support = {//Health and Medical Research Fund, the Food and Health Bureau/ ; }, abstract = {BACKGROUND: Faecal microbiota transplantation (FMT) has been shown to improve symptoms in a proportion of patients with irritable bowel syndrome (IBS).<br><br>AIM: We performed a randomised trial to assess the efficacy of FMT in patients with IBS.<br><br>METHODS: We randomised 56 patients with diarrhoea-predominant IBS 1:1 to FMT or placebo via the duodenal route at baseline and week 4. The primary outcome was > 50 points decrease in IBS severity scoring system (IBS-SSS) score at week 12. Secondary outcomes were improvement in bloating and change in gut microbiota at week 12. After 12-week follow-up, those in the placebo group were assigned to receive open-label FMT.<br><br>RESULTS: At week 12, 57.1% in the FMT group and 46.4% in the placebo group achieved the primary endpoint (p&#x2009;=&#x2009;0.42). More patients receiving FMT than placebo had improvement in bloating (72% vs 30%; p&#x2009;=&#x2009;0.005). In an open-label extension, 65.2% and 82.4% of patients achieved, respectively, the primary endpoint and improvement in bloating. Faecal microbiome of patients in the FMT group showed a reduction in bacteria like Ruminococcus gnavus and enrichment of bacteria such as Lawsonibacter at week 12, while no change in the placebo group. Functional analyses showed that the hydrogen sulphide-producing pathway decreased in patients who had FMT (p&#x2009;<&#x2009;0.05) accompanied by a reduction in contributing bacteria. There were no serious adverse events related to FMT.<br><br>CONCLUSION: FMT performed twice at an interval of four weeks did not significantly reduce IBS-SSS score. However, more patients had improvement in abdominal bloating, which was associated with a reduction in hydrogen sulphide-producing bacteria. (ClinicalTrials.gov NCT03125564).}, }
@article {pmid37667688, year = {2023}, author = {Feuerstadt, P and Oneto, C and Tillotson, G and Van Hise, NW}, title = {Patient Perception of Route of Rectal Administration of Live Biotherapeutic Product for Recurrent Clostridioides difficile Infection.}, journal = {Patient preference and adherence}, volume = {17}, number = {}, pages = {2153-2159}, pmid = {37667688}, issn = {1177-889X}, abstract = {INTRODUCTION: CDI is a recurrent disease that is treated with antibiotics, but patients commonly experience repeat infections with significant impacts on hospital budgets and patient health quality. Standard of care management includes the antibiotics, vancomycin and fidaxomicin, which frequently provide clinical response, but do not avoid recurrence of Clostridioides difficile infection (rCDI). These recurrent infections occur due to dysbiosis of the colonic microbiota. One adjunctive therapeutic approach is to restore the deficient gastrointestinal flora using fecal microbiota transplantation (FMT) or live biotherapeutic products (LBP) when given after standard of care antimicrobials, which have been successful in reducing repeat infections with success rates up to 88%. FMT or LBP can be given by various routes.<br><br>METHODS: Two groups of subjects aged &#x2265;18 years with at least one previous CDI episode within the previous 36 months completed self-administered online surveys to assess the acceptability of an LBP administered rectally. Group 1 consisted of LBP-recipients who had received RBL (REBYOTA) rectally as part of the Phase III PUNCH CD3 clinical trial. Group 2 consisted of LBP-na&#xef;ve subjects who volunteered to participate and had experienced CDI within the prior 36 months but had no history of receiving FMT or LBP therapy.<br><br>RESULTS: LBP-recipients considered rectal administration easy (96%) and quick (94%), while 98% of respondents considered the lack of need for bowel preparation appealing. Most LBP-recipients (96%) wished they had earlier access to RBL. Most LBP-na&#xef;ve subjects (87%) were likely or somewhat likely to consider a rectally administered treatment and 80% preferred a treatment option that does not require bowel preparation. Many of these subjects (76%) expressed interest in finding out about new treatment options for rCDI.<br><br>DISCUSSION: LBP-recipients and LBP-na&#xef;ve subjects alike felt that rectal delivery of microbiome therapy is not only acceptable but highly interesting as a treatment avenue.}, }
@article {pmid37667515, year = {2023}, author = {Baker, JL}, title = {Illuminating the oral microbiome and its host interactions: recent Advancements in omics and bioinformatics technologies in the context of oral microbiome research.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuad051}, pmid = {37667515}, issn = {1574-6976}, abstract = {The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a comprehensive perspective of the current state-of-the-art tools available to perform genomics, metagenomics, phylogenomics, pangenomics, transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics analysis on (all) microbiomes, and then provides examples of how the techniques have been applied to research of the oral microbiome, specifically. Key findings of these studies and remaining challenges for the field are highlighted. Although the methods discussed here are placed in the context of their contributions to oral microbiome research specifically, they are pertinent to the study of any microbiome, and the intended audience of this includes researchers would simply like to get an introduction to microbial omics and/or an update on the latest omics methods. Continued research of the oral microbiota using omics approaches is crucial and will lead to dramatic improvements in human health, longevity, and quality of life.}, }
@article {pmid37667052, year = {2023}, author = {Proal, AD and VanElzakker, MB and Aleman, S and Bach, K and Boribong, BP and Buggert, M and Cherry, S and Chertow, DS and Davies, HE and Dupont, CL and Deeks, SG and Eimer, W and Ely, EW and Fasano, A and Freire, M and Geng, LN and Griffin, DE and Henrich, TJ and Iwasaki, A and Izquierdo-Garcia, D and Locci, M and Mehandru, S and Painter, MM and Peluso, MJ and Pretorius, E and Price, DA and Putrino, D and Scheuermann, RH and Tan, GS and Tanzi, RE and VanBrocklin, HF and Yonker, LM and Wherry, EJ}, title = {SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC).}, journal = {Nature immunology}, volume = {}, number = {}, pages = {}, pmid = {37667052}, issn = {1529-2916}, abstract = {Millions of people are suffering from Long COVID or post-acute sequelae of COVID-19 (PASC). Several biological factors have emerged as potential drivers of PASC pathology. Some individuals with PASC may not fully clear the coronavirus SARS-CoV-2 after acute infection. Instead, replicating virus and/or viral RNA-potentially capable of being translated to produce viral proteins-persist in tissue as a 'reservoir'. This reservoir could modulate host immune responses or release viral proteins into the circulation. Here we review studies that have identified SARS-CoV-2 RNA/protein or immune responses indicative of a SARS-CoV-2 reservoir in PASC samples. Mechanisms by which a SARS-CoV-2 reservoir may contribute to PASC pathology, including coagulation, microbiome and neuroimmune abnormalities, are delineated. We identify research priorities to guide the further study of a SARS-CoV-2 reservoir in PASC, with the goal that clinical trials of antivirals or other therapeutics with potential to clear a SARS-CoV-2 reservoir are accelerated.}, }
@article {pmid37666952, year = {2023}, author = {Sugiyama, Y and Yamamoto, K and Honda, T and Kato, A and Muto, H and Yokoyama, S and Ito, T and Imai, N and Ishizu, Y and Nakamura, M and Asano, T and Enomoto, A and Zaitsu, K and Ishigami, M and Fujishiro, M and Kawashima, H}, title = {Impact of elobixibat on liver tumors, microbiome, and bile acid levels in a mouse model of nonalcoholic steatohepatitis.}, journal = {Hepatology international}, volume = {}, number = {}, pages = {}, pmid = {37666952}, issn = {1936-0541}, support = {21K15970//Grant-in-Aid for Young Scientists/ ; 20K08382//Grant-in-Aid for Scientific Research(C)/ ; }, abstract = {BACKGROUND: Elevated bile acid levels have been associated with liver tumors in fatty liver. Ileal bile acid transporter inhibitors may inhibit bile acid absorption in the distal ileum and increase bile acid levels in the colon, potentially decreasing the serum and hepatic bile acid levels. This study aimed to investigate the impact of these factors on liver tumor.<br><br>METHODS: C57BL/6J mice received a one-time intraperitoneal injection of 25-mg/kg diethylnitrosamine. They were fed a choline-deficient high-fat diet for 20&#xa0;weeks starting from 8&#xa0;weeks of age, with or without elobixibat (EA Pharma, Tokyo, Japan).<br><br>RESULTS: Both groups showed liver fat accumulation and fibrosis, with no significant differences between the two groups. However, mice with elobixibat showed fewer liver tumors. The total serum bile acid levels, including free, tauro-conjugated, glyco-conjugated, and tauro-&#x3b1;/&#x3b2;-muricholic acids in the liver, were noticeably reduced following elobixibat treatment. The proportion of gram-positive bacteria in feces was significantly lower in the group treated with elobixibat (5.4%) than in the group without elobixibat (33.7%).<br><br>CONCLUSION: Elobixibat suppressed tumor growth by inhibiting bile acid reabsorption, and decreasing total bile acid and primary bile acid levels in the serum and liver. Additionally, the presence of bile acids in the colon may have led to a significant reduction in the proportion of gram-positive bacteria, potentially resulting in decreased secondary bile acid synthesis.}, }
@article {pmid37666816, year = {2023}, author = {Shoer, S and Shilo, S and Godneva, A and Ben-Yacov, O and Rein, M and Wolf, BC and Lotan-Pompan, M and Bar, N and Weiss, EI and Houri-Haddad, Y and Pilpel, Y and Weinberger, A and Segal, E}, title = {Impact of dietary interventions on pre-diabetic oral and gut microbiome, metabolites and cytokines.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5384}, pmid = {37666816}, issn = {2041-1723}, mesh = {Humans ; Cytokines ; *Gastrointestinal Microbiome ; *Hyperglycemia ; *Microbiota ; *Prediabetic State ; }, abstract = {Diabetes and associated comorbidities are a global health threat on the rise. We conducted a six-month dietary intervention in pre-diabetic individuals (NCT03222791), to mitigate the hyperglycemia and enhance metabolic health. The current work explores early diabetes markers in the 200 individuals who completed the trial. We find 166 of 2,803 measured features, including oral and gut microbial species and pathways, serum metabolites and cytokines, show significant change in response to a personalized postprandial glucose-targeting diet or the standard of care Mediterranean diet. These changes include established markers of hyperglycemia as well as novel features that can now be investigated as potential therapeutic targets. Our results indicate the microbiome mediates the effect of diet on glycemic, metabolic and immune measurements, with gut microbiome compositional change explaining 12.25% of serum metabolites variance. Although the gut microbiome displays greater compositional changes compared to the oral microbiome, the oral microbiome demonstrates more changes at the genetic level, with trends dependent on environmental richness and species prevalence in the population. In conclusion, our study shows dietary interventions can affect the microbiome, cardiometabolic profile and immune response of the host, and that these factors are well associated with each other, and can be harnessed for new therapeutic modalities.}, }
@article {pmid37666790, year = {2023}, author = {Robles-Rodríguez, C and Muley, VY and González-Dávalos, ML and Shimada, A and Varela-Echavarría, A and Mora, O}, title = {Microbial colonization dynamics of the postnatal digestive tract of Bos indicus calves.}, journal = {Animal science journal = Nihon chikusan Gakkaiho}, volume = {94}, number = {1}, pages = {e13872}, doi = {10.1111/asj.13872}, pmid = {37666790}, issn = {1740-0929}, support = {IN211518//PAPIIT-UNAM/ ; }, abstract = {The rumen and the jejunum of calves have distinct functional roles; the former is in the storage and fermentation of feed, and the latter is in transporting digesta to the ileum. It is unknown how nutrition changes the evolution of the microbiome of these organs after birth. We sequenced and characterized the entire microbiome of the rumen and the jejunum from Bos indicus calves of the Mexican Tropics to study their dynamics at Days 0, 7, 28, and 42 after birth. Operational taxonomic units (OTUs) belonging to 185 and 222 genera from 15 phylum were observed in the organs, respectively. The most abundant OTUs were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. We observed that proteobacterial species were outcompeted after the first week of life by Bacteroidetes and Firmicutes in the rumen and the jejunum, respectively. Moreover, Prevotella species were found to predominate in the rumen (36% of total OTUs), while the jejunum microbiome is composed of small proportions of several genera. Presumably, their high relative abundance assists in specialized functions and is more likely in fermentation since they are anaerobes. In summary, the rumen and the jejunum microbiomes were outcompeted by new microbiomes in a dynamic process that begins at birth.}, }
@article {pmid37666340, year = {2023}, author = {Xia, R and Cheng, J and Chen, Z and Zhang, Z and Zhou, X and Zhou, J}, title = {Co-NC@Co-NP hierarchical nanoforest steering charge exchange efficiency at biotic-abiotic interface for microbial electrochemical carbon reduction.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {166793}, doi = {10.1016/j.scitotenv.2023.166793}, pmid = {37666340}, issn = {1879-1026}, abstract = {Converting anthropogenic carbon dioxide (CO2) to value-added products using bio-electrochemical conversions represents a promising strategy for producing sustainable fuel. However, the reaction kinetics are hindered by insufficient attachment of microorganisms and limited charge extraction at the bioinorganic interface. A hierarchical nanoforest with doped cobalt‑nitrogen-doped carbon covering cobalt nanoparticle (Co-NC@Co-NP) was integrated with a CO2-to-CH4 conversion microbiome for methane production to address these shortcomings. In-situ nanoforests were developed on the nanosheet by chemical vapor deposition with Co nanoparticles catalyzed. The bio-nanowire-like carbon nanotubes enhanced the electrostatic force for microbe enrichment via the tip effect, providing a maximum of 3.6-fold electron-receiving microbes to utilize reducing equivalents. The Co-NC@Co-NP enhanced the direct electron transfer between microbes and electrodes, reducing the adoption of energy barriers for heme-like proteins. Thus, the optimized electron transfer pathway improved selectivity by a factor of 2.0 compared to the pristine nanosheet biohybrid. Furthermore, the adjusted microbial community structure provided sufficient methanogenesis genes to match the strong electron flow, achieving maximal methane production rates (311.1 mmol/m[2]/day at -0.9 V vs. Ag/AgCl), 8.62 times higher than those of the counterpart nanosheet biohybrid (36.06 mmol/m[2]/day). This work demonstrates a comprehensive assessment of biotic-abiotic energy transfer, which may serve as a guiding principle for designing efficient bio-electrochemical systems.}, }
@article {pmid37666133, year = {2023}, author = {Ahmed, B and Gahlot, P and Balasundaram, G and Tyagi, VK and Banu J, R and Vivekanand, V and Kazmi, AA}, title = {Semi-continuous anaerobic co-digestion of thermal and thermal-alkali processed organic fraction of municipal solid waste: Methane yield, energy analysis, anaerobic microbiome.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118907}, doi = {10.1016/j.jenvman.2023.118907}, pmid = {37666133}, issn = {1095-8630}, abstract = {The semi-continuous anaerobic co-digestion (AcoD) of thermal and thermal-alkali pretreated organic fraction of municipal solid waste (OFMSW) and sewage sludge (SS) was studied under varying hydraulic retention times (HRT) and organic loading rates (OLR Three semi-continuous digesters were operated under control (non-pre-treated), thermally pretreated (125 °C), and thermal-alkali pretreated (125°C-3g/L NaOH) conditions at variable OLRs at 2.5, 4.0, 5.1, and 7.6 kgVS/m[3].d and corresponding HRTs of 30, 20, 15, and 10 days. The 10 and 43% higher methane yield (0.445 m[3]/kgVS) and 11 and 57% higher VS removal (52%) was achieved for thermal-alkali pretreated digester at 5.1 kgVS/m[3].d OLR over thermally pretreated (0.408 m[3]/kgVS, 45% VS removal) and control digesters (0.310 m[3]/kgVS, 33% VS removal), respectively. Thermal and thermal-alkali digesters failed on increasing the OLR to 7.6 kgVS/m[3].d, whereas the control digester becomes upset at 5.1 kgVS/m[3].d OLR. The metagenomic study revealed that Firmicutes, Bacteroidetes, Chloroflexi, Euryarchaeota, Proteobacteria, and Actinobacteria were the predominant bacterial population, whereas Methanosarcina and Methanothrix dominated the archaeal community. Energy balance analysis revealed that thermal alkali pretreatment showed the highest positive energy balance of 114.6 MJ/ton with an energy ratio of 1.25 compared with thermally pretreated (81.5 MJ/ton) and control samples (-46.9 MJ/ton). This work pave the way for scaleup of both thermal and thermal-alkali pre-treatment at 125 °C to realize the techno-economic and energy potential of the process.}, }
@article {pmid37666106, year = {2023}, author = {Zheng, Y and Fateh, B and Xu, G}, title = {Effects of methomyl on the intestinal microbiome and hepatic transcriptome of tilapia, and the modifying effects of mint co-culture.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {263}, number = {}, pages = {106675}, doi = {10.1016/j.aquatox.2023.106675}, pmid = {37666106}, issn = {1879-1514}, abstract = {Methomyl (MET) is an oxime carbamate insecticide that can contaminate aquatic systems resulting in toxicological effects. It can harm some fish species possibly through the anti-oxidative, phagosome pathway. Mint is one of the most widely herbal plants exhibiting antioxidant activities. In this study, we investigated the impact of MET on the antioxidant system of Oreochromis niloticus in presence of mint as a floating bed. Results revealed that the superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase, and glutathione S-transferase significantly decreased and the GSH content significantly increased in the intestine. The hepatic peroxisome proliferator-activated receptor (PPAR) signalling pathway, carbon metabolism, renal phosphoinositide 3-kinase (PI3K)-Akt, mitogen-activated protein kinase (MAPK) signalling pathway, and phagosomes were significantly affected. Upon long-term exposure, circadian rhythm and phagosomes were enriched in the liver and kidney. However, mint increased the enriched pathways of Toll-like receptor, PPAR, p53, NF-kappa B, MAPK, oestrogen, and B cell receptor signalling pathways. MET with different concentrations destroyed the balance of gut microbiota, mint decreased Verrucomicrobia and Akkermansia for the maintenance resulted from MET. Cetobacterium had a positive impact on total nitrogen (TN), chemical oxygen demand (CODMn), and glutathione reductase (GR), while Akkermansia had a positive impact on feed conversion ratio (FCR), SOD and CAT, and the abundance of both decreased due to MET exposure. High mint density removed more concentrations of nitrogen and phosphorus in the tilapia cultivation wastewater. Therefore, planting with mint can alleviate the toxicological effects produced by MET, shape the intestinal microbiota, and strengthen the connection between water quality and the metabolic parameters.}, }
@article {pmid37666023, year = {2023}, author = {Ekanem, E and Ngene, NC and Moodley, J and Konje, J}, title = {Prevention of surgical site infection and sepsis in pregnant obese women.}, journal = {Best practice &amp; research. Clinical obstetrics &amp; gynaecology}, volume = {91}, number = {}, pages = {102406}, doi = {10.1016/j.bpobgyn.2023.102406}, pmid = {37666023}, issn = {1532-1932}, abstract = {Obesity is a major determinant of health outcomes and is on the increase in women worldwide. It predisposes to surgical site infection (SSI). Risk factors for the SSI include extremes of age, smoking, comorbidities such as hypertension and diabetes, inappropriate vertical abdominal and or uterine wall incisions, increased operating time, subcutaneous layer of 3 cm or more, and unnecessary use of subcutaneous drain. Most bacteria that cause SSIs are human commensals. Common organisms responsible for SSI include Staphylococcus aureus and coliforms such as Proteus mirabilis, and Escherichia coli. A surgeon's gloves post caesarean section in the obese has a preponderance of Firmicutes and Bacteroidetes, which increases SSI risk. The interaction of skin commensals and vaginal microbiome at the surgical incision site increases the risk of SSI in the obese compared to non-obese. Minimizing the risk of SSI involves modification of risk factors, timely treatment of SSI to prevent sepsis and compliance with the recommended care bundles.}, }
@article {pmid37665554, year = {2023}, author = {Park, KH and Oh, SY and Cho, Y and Seo, CW and Kim, JS and Yoo, S and Lim, J and Kim, CS and Lim, YW}, title = {Mycorrhizal Fungal Diversity Associated with Six Understudied Ectomycorrhizal Trees in the Republic of Korea.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {}, number = {}, pages = {}, pmid = {37665554}, issn = {1976-3794}, support = {KNA1-1-25, 19-2//Korea National Arboretum/ ; }, abstract = {Mycorrhizal fungi are key components of forest ecosystems and play essential roles in host health. The host specificity of mycorrhizal fungi is variable and the mycorrhizal fungi composition for the dominant tree species is largely known but remains unknown for the less common tree species. In this study, we collected soil samples from the roots of six understudied ectomycorrhizal tree species from a preserved natural park in the Republic of Korea over four seasons to investigate the host specificity of mycorrhizal fungi in multiple tree species, considering the abiotic factors. We evaluated the mycorrhizal fungal composition in each tree species using a metabarcoding approach. Our results revealed that each host tree species harbored unique mycorrhizal communities, despite close localization. Most mycorrhizal taxa belonged to ectomycorrhizal fungi, but a small proportion of ericoid mycorrhizal fungi and arbuscular mycorrhizal fungi were also detected. While common mycorrhizal fungi were shared between the plant species at the genus or higher taxonomic level, we found high host specificity at the species/OTU (operational taxonomic unit) level. Moreover, the effects of the seasons and soil properties on the mycorrhizal communities differed by tree species. Our results indicate that mycorrhizal fungi feature host-specificity at lower taxonomic levels.}, }
@article {pmid37665552, year = {2023}, author = {Liu, NH and Liu, HQ and Zheng, JY and Zhu, ML and Wu, LH and Pan, HF and He, XX}, title = {Fresh Washed Microbiota Transplantation Alters Gut Microbiota Metabolites to Ameliorate Sleeping Disorder Symptom of Autistic Children.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {}, number = {}, pages = {}, pmid = {37665552}, issn = {1976-3794}, support = {ZYYCXTD-C-202208//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; 2022B1212010012//Guangdong Provincial Key Laboratory of TCM Pathgenesis and Prescriptions of Heart and Spleen Diseases/ ; 2020B1111100011//Special Project for Research and Development in Key areas of Guangdong Province/ ; 2018A030313639//Natural Science Foundation of Guangdong Province/ ; 2019A1515010125//Natural Science Foundation of Guangdong Province/ ; 2023A1515010751//Natural Science Foundation of Guangdong Province/ ; 2019-GDXK-0013//Guangdong Key Discipline Research Project of Department of Education of Guangdong Province/ ; 2020KZDZX1132//COVID-19 Epidemic Prevention and Control Special Research Project of Department of Education of Guangdong Province/ ; 202201010134//Basic and Applied Basic Research Project of Guangzhou Basic Research Program/ ; 2021xk36//Discipline Collaborative Innovation Team of Guangzhou University of Traditional Chinese Medicine/ ; }, abstract = {Accumulating studies have raised concerns about gut dysbiosis associating autism spectrum disorder (ASD) and its related symptoms. However, the effect of gut microbiota modification on the Chinese ASD population and its underlying mechanism were still elusive. Herein, we enrolled 24 ASD children to perform the first course of fresh washed microbiota transplantation (WMT), 18 patients decided to participate the second course, 13 of which stayed to participate the third course, and there were 8 patients at the fourth course. Then we evaluated the effects of fresh WMT on these patients and their related symptoms. Our results found that the sleeping disorder symptom was positively interrelated to ASD, fresh WMT significantly alleviated ASD and its sleeping disorder and constipation symptoms. In addition, WMT stably and continuously downregulated Bacteroides/Flavonifractor/Parasutterella while upregulated Prevotella_9 to decrease toxic metabolic production and improve detoxification by regulating glycolysis/myo-inositol/D-glucuronide/D-glucarate degradation, L-1,2-propanediol degradation, fatty acid β-oxidation. Thus, our results suggested that fresh WMT moderated gut microbiome to improve the behavioral and sleeping disorder symptoms of ASD via decrease toxic metabolic production and improve detoxification. Which thus provides a promising gut ecological strategy for ASD children and its related symptoms treatments.}, }
@article {pmid37665249, year = {2023}, author = {Hugon, AM and Deblois, CL and Simmons, HA and Mejia, A and Schotzo, ML and Czuprynski, CJ and Suen, G and Golos, TG}, title = {Listeria monocytogenes infection in pregnant macaques alters the maternal gut microbiome.}, journal = {Biology of reproduction}, volume = {}, number = {}, pages = {}, doi = {10.1093/biolre/ioad104}, pmid = {37665249}, issn = {1529-7268}, abstract = {OBJECTIVES: The bacterium Listeria monocytogenes (Lm) is associated with adverse pregnancy outcomes. Infection occurs through consumption of contaminated food that is disseminated to the maternal-fetal interface. The influence on the gastrointestinal microbiome during Lm infection remains unexplored in pregnancy. The objective of this study was to determine the impact of listeriosis on the gut microbiota of pregnant macaques.<br><br>METHODS: A nonhuman primate model of listeriosis in pregnancy has been previously described [1, 2]. Both pregnant and nonpregnant cynomolgus macaques were inoculated with L. monocytogenes and bacteremia and fecal shedding were monitored for 14&#xa0;days. Nonpregnant animal tissues were collected at necropsy to determine bacterial burden, and fecal samples from both pregnant and nonpregnant animals were evaluated by 16S rRNA next-generation sequencing.<br><br>RESULTS: Unlike pregnant macaques, nonpregnant macaques did not exhibit bacteremia, fecal shedding, or tissue colonization by Lm. Dispersion of Lm during pregnancy was associated with a significant decrease in alpha-diversity of the host gut microbiome, compared to nonpregnant counterparts. The combined effects of pregnancy and listeriosis were associated with a significant loss in microbial richness, although there were increases in some genera and decreases in others. Conclusions; Although pregnancy alone is not associated with gut microbiome disruption, we observed dysbiosis with listeriosis during pregnancy. The macaque model may provide an understanding of the roles that pregnancy and the gut microbiota play in the ability of Lm to establish intestinal infection and disseminate throughout the host, thereby contributing to adverse pregnancy outcomes and risk to the developing fetus.}, }
@article {pmid37665023, year = {2023}, author = {Browning, BD and Kirkland, AE and Green, R and Engevik, M and Alekseyenko, AV and Leggio, L and Tomko, RL and Squeglia, LM}, title = {The adolescent and young adult microbiome and its association with substance use: a scoping review.}, journal = {Alcohol and alcoholism (Oxford, Oxfordshire)}, volume = {}, number = {}, pages = {}, doi = {10.1093/alcalc/agad055}, pmid = {37665023}, issn = {1464-3502}, support = {F31AA030920//NIH Intramural Research Program/ ; }, abstract = {AIMS: The microbiome is a critical factor in health throughout human development. The aims of this scoping review are to (i) elucidate the differences between the youth (post-natal day 21-65 for rodents, 2-7 years for non-human primates, and 10-25 years for humans) microbiome with other life stages and (ii) identify youth-specific microbial changes associated with substance use.<br><br>METHODS: Peer-reviewed studies published up to May 2023 were identified in PubMed and SCOPUS and included gut and oral microbiome studies from rodents, non-human primates, and humans (N&#x2009;=&#x2009;1733). Twenty-six articles were determined eligible based on inclusion criteria (aim 1: n&#x2009;=&#x2009;19, aim 2: n&#x2009;=&#x2009;7).<br><br>RESULTS: The adolescent and young adult oral and gut microbiomes are distinct compared to other life stages, within both non-human and human models. While there is limited research in this area, the microbiome appears to be vulnerable to substance use exposure earlier in life, including substances commonly initiated and escalated during adolescence and young adulthood (i.e. alcohol, cannabis, and tobacco).<br><br>CONCLUSIONS: Studies across the lifespan indicate that adolescence and young adulthood are distinct periods of development, where the microbiome is sensitive to exposures, including substance use. There is a need for more studies focused on the adolescent and young adult microbiome and substance use, as well as focused on the oral microbiome during this developmental period. Understanding the gut and oral microbiome during adolescence and young adulthood may provide insight into the pathophysiology of substance use disorders.}, }
@article {pmid37665015, year = {2023}, author = {Sinjab, K and Sawant, S and Ou, A and Fenno, JC and Wang, HL and Kumar, P}, title = {Impact of surface characteristics on the peri-implant microbiome in health and disease.}, journal = {Journal of periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1002/JPER.23-0205}, pmid = {37665015}, issn = {1943-3670}, abstract = {BACKGROUND: Because little is known about the impact of implant surface modifications on the peri-implant microbiome, we aimed to examine peri-implant communities in various surface types in order to better understand the impact of these surfaces on the development of peri-implantitis (PI).<br><br>METHODS: One hundred and six systemically healthy individuals with anodized (AN), hydroxyapatite-coated (HA), or sandblasted acid-etched (SLA) implants that were >6 months in function were recruited and categorized into health (H) or PI. Peri-implant biofilm was analyzed using 16S rRNA gene sequencing and compared between health/disease and HA/SLA/AN using community-level and taxa-level metrics.<br><br>RESULTS: Healthy implants did not demonstrate significant differences in clustering, alpha- or beta-diversity based on surface modification. AN and HA surfaces displayed significant differences between health and PI (p&#xa0;<&#xa0;0.05); however, such a clustering was not evident with SLA (p&#xa0;>&#xa0;0.05). AN and HA surfaces also differed in the magnitude and diversity of differences between health and PI. Six species belonging to the genera Shuttleworthia, Scardovia, and Prevotella demonstrated lower abundances in AN implants with PI, and 18 species belonging to the genera Fretibacterium, Tannerella, Treponema, and Fusobacterium were elevated, while in HA implants with PI, 20 species belonging to the genera Streptococcus, Lactobacillus, Veillonella, Rothia, and family Ruminococcaceae were depleted and Peptostreptococcaceae, Atopobiaceae, Veillonellaceae, Porphyromonadaceae, Desulfobulbaceae, and order Synergistales were enriched.<br><br>CONCLUSIONS: Within the limitations of this study, we demonstrate that implant surface can differentially modify the disease-associated microbiome, suggesting that surface topography must be considered in the multi-factorial etiology of peri-implant diseases.}, }
@article {pmid37664974, year = {2023}, author = {Rolf, S and Joshua, C and Riccardo, S and Juergen, VH}, title = {Sunscreens can preserve human skin microbiome upon erythemal UV exposure.}, journal = {International journal of cosmetic science}, volume = {}, number = {}, pages = {}, doi = {10.1111/ics.12910}, pmid = {37664974}, issn = {1468-2494}, abstract = {OBJECTIVE: Ultraviolet radiation (UVR) is a known environmental key factor for premature skin aging. Only few scientific evidence is available to support the effects of UVR on the skin microbiome. This in vivo pilot study aimed to evaluate the impact on the skin microbiome upon erythemal UV exposure and the protection of UV-exposed skin microbiome by UV filters.<br><br>METHODS: Ten female volunteers were treated with an SPF 20 sunscreen and placebo formulation (without UV filters) on their upper middle backs and irradiated with an erythemal dose (2 MED) by a solar simulator. Skin swabbing samples from four zones (i.e., unexposed, exposed, sunscreen- and placebo-treated on exposed skin) were collected for the microbiome analysis before and 2 hours after UV exposure, respectively, and processed via shallow 16S rRNA Amplicon and Shotgun Metagenomic sequencing. An in vitro UV method was developed to confirm the protection of isolated bacterial strains by single UV filters and combinations.<br><br>RESULTS: Alpha diversity was impacted by significant inter-individual differences and by treatment rather than by irradiation. Cutibacterium acnes was found to be most abundant and a confounding factor for diversity. On a species level Lactobacillus crispatus was negatively associated with UVR and placebo treatment, whereas there was a positive association with the sunscreen treatment. The sunscreen treatment also favored an interaction network with central Micrococcus genus. The in vitro results showed that both single UV filters and combinations had specific effects on the survival rates of L. crispatus, C. acnes, and S. epidermidis.<br><br>CONCLUSION: We identified potential microorganisms and bacterial interactions that were associated with an SPF 20 sunscreen treatment. The specific protection of L. crispatus as a key player in the UV-exposed skin microbiome and reduction of C. acnes population by UV filters might lead to new cosmetic concepts for photoprotection.}, }
@article {pmid37664966, year = {2023}, author = {Liesegang, A and Burger, B and de Vries de Heekelingen, T and Schroeter-Vogt, C and Hatt, JM and Kowalewski, MP and Clauss, M}, title = {Rabbits (Oryctolagus cuniculus) increase caecal calcium absorption at increasing dietary calcium levels.}, journal = {Journal of animal physiology and animal nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpn.13880}, pmid = {37664966}, issn = {1439-0396}, support = {Project Nr. ZH/2006//Vetsuisse Grant for Clinical Research of the University of Zurich/ ; }, abstract = {Hindgut fermenting herbivores from different vertebrate taxa, including tortoises, and among mammals some afrotheria, perissodactyla incl. equids, several rodents as well as lagomorphs absorb more calcium (Ca) from the digesta than they require, and excrete the surplus via urine. Both proximate and ultimate causes are elusive. It was suggested that this mechanism might ensure phosphorus availability for the hindgut microbiome by removing potentially complex-building Ca from the digesta. Here we use Ussing chamber experiments to show that rabbits (Oryctolagus cuniculus) maintained on four different diets (six animals/diet) increase active Ca absorption at increasing Ca levels. This contradicts the common assumption that at higher dietary levels, where passive uptake should be more prevalent, active transport can relax and hence supports the deliberate removal hypothesis. In the rabbits, this absorption was distinctively higher in the caecum than in the duodenum, which is unexpected in mammals. Additional quantification of the presence of two proteins involved in active Ca absorption (calbindin-D9K CB; vitamin D receptor, VDR) showed higher presence with higher dietary Ca. However, their detailed distribution across the intestinal tract and the diet groups suggests that other factors not investigated in this study must play major roles in Ca absorption in rabbits. Investigating strategies of herbivores to mitigate potential negative effects of Ca in the digesta on microbial activity and growth might represent a promising area of future research.}, }
@article {pmid37664937, year = {2023}, author = {Dübüş, EN and Lamminpää, I and Nannini, G and Niccolai, E}, title = {Nourishing Immunity and Combatting Neuroinflammation: The Power of Immunonutrition and The Microbiome.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {28}, number = {8}, pages = {178}, doi = {10.31083/j.fbl2808178}, pmid = {37664937}, issn = {2768-6698}, mesh = {Humans ; Immunonutrition Diet ; Neuroinflammatory Diseases ; *Microbiota ; *Gastrointestinal Microbiome ; Inflammation ; }, abstract = {The gut-microbiome-brain axis plays a crucial role in the control of systemic metabolism and homeostasis. Recent research has shown that dietary habits and nutrients can affect immune system and inflammatory status by influencing various factors, including microbiome composition, microbial products release, gastrointestinal signaling molecules, and neurotransmitters. In addition, the gut microbiome affects the brain by altering levels of key brain transmitters, circulating cytokines, and short-chain fatty acids that can cross the blood-brain barrier. Immunonutrition, a newly born discipline, examines the relationship between diet, nutritional status, the immune system, inflammation, infection, injury, and healing. This review explores the relationship between nutrition and the immune system, focusing on immunonutrition and immunonutrients, the connections between nutrition, immunity, and the microbiome, microbiota-gut-brain communication, and potential nutritional interventions to improve neurological disorders. The manuscript provides a comprehensive overview of the complex interplay between nutrition and the immune system, highlighting the many ways in which our diets can impact our health and wellbeing, particularly in the context of neuroinflammatory and neurodegenerative conditions.}, }
@article {pmid37664629, year = {2023}, author = {Simon, LM and Flocco, C and Burkart, F and Methner, A and Henke, D and Rauer, L and Müller, CL and Vogel, J and Quaisser, C and Overmann, J and Simon, S}, title = {Microbial fingerprints reveal interaction between museum objects, curators, and visitors.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107578}, pmid = {37664629}, issn = {2589-0042}, abstract = {Microbial communities reside at the interface between humans and their environment. Whether the microbiome can be leveraged to gain information on human interaction with museum objects is unclear. To investigate this, we selected objects from the Museum für Naturkunde and the Pergamonmuseum in Berlin, Germany, varying in material and size. Using swabs, we collected 126 samples from natural and cultural heritage objects, which were analyzed through 16S rRNA sequencing. By comparing the microbial composition of touched and untouched objects, we identified a microbial signature associated with human skin microbes. Applying this signature to cultural heritage objects, we identified areas with varying degrees of exposure to human contact on the Ishtar gate and Sam'al gate lions. Furthermore, we differentiated objects touched by two different individuals. Our findings demonstrate that the microbiome of museum objects provides insights into the level of human contact, crucial for conservation, heritage science, and potentially provenance research.}, }
@article {pmid37664615, year = {2023}, author = {Xu, Y and Wang, F and Mi, K and Wang, X and Wang, D and Zhao, Q and Wang, J and Liu, Z and Zhang, Q and Liu, Y and Zhang, X and Liu, X}, title = {Biglycan regulated colorectal cancer progress by modulating enteric neuron-derived IL-10 and abundance of Bacteroides thetaiotaomicron.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107515}, pmid = {37664615}, issn = {2589-0042}, abstract = {Biglycan (BGN) is a proteoglycan with branch chains and highly expressed in enteric neurons in the tumor tissue of colorectal cancer (CRC), which is negatively associated with survival rates in patients with CRC. However, how the proteoglycan promotes the progress of CRC through interacting with bacteria and regulating the immune response of enteric neurons remains largely unknown. In the present study, we found that biglycan deficiency changed tumor distribution in a colitis-associated colon cancer model. Furthermore, we revealed that BGN deficiency inhibits tumor growth in an allograft tumor model and the migration of cancer cell by upregulating interleukin-10 expression in enteric neurons. Significantly, we demonstrated that biglycan deficiency enriched the abundance of Bacteroides thetaiotaomicron through competing with it for chondroitin sulfate to inhibit CRC progress. Our work provided new insights into the interaction between host proteoglycan and gut microbiota as well as the role of enteric neurons in the tumor microenvironment.}, }
@article {pmid37664431, year = {2023}, author = {Bakonyi, P and Kolonics, A and Aczel, D and Zhou, L and Mozaffaritabar, S and Molnár, K and László, L and Kutasi, B and Tanisawa, K and Park, J and Gu, Y and Pinho, RA and Radak, Z}, title = {Voluntary exercise does not increase gastrointestinal motility but increases spatial memory, intestinal eNOS, Akt levels, and Bifidobacteria abundance in the microbiome.}, journal = {Frontiers in physiology}, volume = {14}, number = {}, pages = {1173636}, pmid = {37664431}, issn = {1664-042X}, abstract = {The interaction between the gut and brain is a great puzzle since it is mediated by very complex mechanisms. Therefore, the possible interactions of the brain-exercise-intestine-microbiome axis were investigated in a control (C, N = 6) and voluntarily exercised (VE, N = 8) middle-aged rats. The endurance capacity was assessed by VO2max on the treadmill, spatial memory by the Morris maze test, gastrointestinal motility by EMG, the microbiome by 16S RNA gene amplicon sequencing, caveolae by electron microscopy, and biochemical assays were used to measure protein levels and production of reactive oxygen species (ROS). Eight weeks of voluntary running increased VO2max, and spatial memory was assessed by the Morris maze test but did not significantly change the motility of the gastrointestinal tract or production of ROS in the intestine. The protein kinase B (Akt) and endothelial nitric oxide synthase (eNOS) protein levels significantly increased in the intestine, while peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1α), mitochondrial transcription factor A (TFAM), nuclear respiratory factor 1 (NFR1), SIRT1, SIRT3, nicotinamide phosphoribosyl transferase (NAMPT), and nuclear factor κB (NF-κB) did not change. On the other hand, voluntary exercise increased the number of caveolae in the smooth muscles of the intestine and relative abundance of Bifidobacteria in the microbiome, which correlated with the Akt levels in the intestine. Voluntary exercise has systemic effects and the relationship between intestinal Akt and the microbiome of the gastrointestinal tract could be an important adaptive response.}, }
@article {pmid37664383, year = {2023}, author = {Mahmoud, A and Begg, M and Tarhuni, M and N Fotso, M and Gonzalez, NA and Sanivarapu, RR and Osman, U and Latha Kumar, A and Sadagopan, A and Alfonso, M}, title = {Inflammatory Bowel Sugar Disease: A Pause From New Pharmacological Agents and an Embrace of Natural Therapy.}, journal = {Cureus}, volume = {15}, number = {8}, pages = {e42786}, pmid = {37664383}, issn = {2168-8184}, abstract = {Inflammatory bowel diseases (IBDs), including Crohn's disease and ulcerative colitis, are immune-mediated chronic inflammatory diseases that target the gastrointestinal tract and other distant organs. The incidence of IBDs has been rising and is more prevailing in Western communities. The etiology has been vague, but different theories include environmental factors that elicit an uncontrolled immune response, which damages internal organs. Treatment of either Crohn's disease or ulcerative colitis has witnessed significant advances; however, pharmacological drugs' side effects limit their use. Research about microbiota and its influence on IBDs has gained fame, and multiple studies correlate microbiota diversity positively with IBD treatment. Many factors contribute to the microbiota's health, including different diets, antibiotics, prebiotics, probiotics, synbiotics, and postbiotics. Specific immune responses lie behind the pathogenesis of IBDs and microbiota dysbiosis, and different studies have postulated new ways to control this abnormal response. Physical activity, sun exposure, efficient sleep, intermittent fasting, and supplementation of probiotics and vitamins are natural ways that help modulate this immune response, do not cost money as IBD pharmacological drugs, and do not come with deleterious side effects that are sometimes more harmful than IBDs. Our article proposes a comprehensive natural approach that can benefit IBD patients enormously. This approach does not replace the medications currently used in treating IBDs. The suggested approach can be used in combination with medications and might aid in reducing the doses of those medications.}, }
@article {pmid37664266, year = {2023}, author = {Choudhuri, G and Shah, S and Kulkarni, A and Jagtap, N and Gaonkar, P and Desai, A and Adhav, C}, title = {Non-alcoholic Steatohepatitis in Asians: Current Perspectives and Future Directions.}, journal = {Cureus}, volume = {15}, number = {8}, pages = {e42852}, pmid = {37664266}, issn = {2168-8184}, abstract = {Non-alcoholic steatohepatitis (NASH) is a subset of non-alcoholic fatty liver disease (NAFLD), which, apart from excess fat in the liver, may be characterised by some level of inflammatory infiltration and fibrogenesis, occasionally progressing to liver cirrhosis or hepatocellular carcinoma (HCC). The objective of the current review is to elucidate the rising prevalence, the role of microbiome and genetics in pathogenesis, diagnostic challenges, and novel treatment alternatives for NASH. Newer diagnostic techniques are being developed since using liver biopsy in a larger population is not a reasonable option and is primarily restricted to clinical research, at least in developing countries. Besides these technical challenges, another important factor leading to deviation from guideline practice is the lack of health insurance coverage in countries like India. It leads to reluctance on the part of physicians and patients to delay required tests to curb out-of-pocket expenditure. There is no cure for NASH, with liver transplantation remaining the last option for those who progress to end-stage liver disease (ESLD) or are detected with early-stage HCC. Thus, lifestyle modification remains the only viable option for many, but compliance and long-term adherence remain major challenges. In obese individuals, bariatric surgery and weight reduction have shown favourable results. In patients with less severe obesity, endoscopic bariatric metabolic therapies (EBMT) are rapidly emerging as less invasive therapies. However, access and acceptability remain poor for these weight reduction methods. Therefore, intense research is being conducted for potential newer drug classes with several agents currently in phase II or III of clinical development. Some of these have demonstrated promising results, such as a reduction in hepatic fat content, and attenuation of fibrosis with an acceptable tolerability profile in phase II studies. The developments in the management of NASH have been fairly encouraging. Further well-designed long-term prospective studies should be undertaken to generate evidence with definitive results.}, }
@article {pmid37664112, year = {2023}, author = {Deng, X and Chen, X and Luo, Y and Que, J and Chen, L}, title = {Intratumor microbiome derived glycolysis-lactate signatures depicts immune heterogeneity in lung adenocarcinoma by integration of microbiomic, transcriptomic, proteomic and single-cell data.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1202454}, pmid = {37664112}, issn = {1664-302X}, abstract = {INTRODUCTION: Microbiome plays roles in lung adenocarcinoma (LUAD) development and anti-tumor treatment efficacy. Aberrant glycolysis in tumor might promote lactate production that alter tumor microenvironment, affecting microbiome, cancer cells and immune cells. We aimed to construct intratumor microbiome score to predict prognosis of LUAD patients and thoroughly investigate glycolysis and lactate signature's association with LUAD immune cell infiltration.<br><br>METHODS: The Cancer Genome Atlas-LUAD (TCGA-LUAD) microbiome data was downloaded from cBioPortal and analyzed to examine its association with overall survival to create a prognostic scoring model. Gene Set Enrichment Analysis (GSEA) was used to find each group's major mechanisms involved. Our study then investigated the glycolysis and lactate pattern in LUAD patients based on 19 genes, which were correlated with the tumor microenvironment (TME) phenotypes and immunotherapy outcomes. We developed a glycolysis-lactate risk score and signature to accurately predict TME phenotypes, prognosis, and response to immunotherapy.<br><br>RESULTS: Using the univariate Cox regression analysis, the abundance of 38 genera were identified with prognostic values and a lung-resident microbial score (LMS) was then developed from the TCGA-LUAD-microbiome dataset. Glycolysis hallmark pathway was significantly enriched in high-LMS group and three distinct glycolysis-lactate patterns were generated. Patients in Cluster1 exhibited unfavorable outcomes and might be insensitive to immunotherapy. Glycolysis-lactate score was constructed for predicting prognosis with high accuracy and validated in external cohorts. Gene signature was developed and this signature was elevated in epithelial cells especially in tumor mass on single-cell level. Finally, we found that the glycolysis-lactate signature levels were consistent with the malignancy of histological subtypes.<br><br>DISCUSSION: Our study demonstrated that an 18-microbe prognostic score and a 19-gene glycolysis-lactate signature for predicting prognosis of LUAD patients. Our LMS, glycolysis-lactate score and glycolysis-lactate signature have potential roles in precision therapy of LUAD patients.}, }
@article {pmid37664075, year = {2023}, author = {Hoskinson, C and Jiang, RY and Stiemsma, LT}, title = {Elucidating the roles of the mammary and gut microbiomes in breast cancer development.}, journal = {Frontiers in oncology}, volume = {13}, number = {}, pages = {1198259}, pmid = {37664075}, issn = {2234-943X}, abstract = {The mammary microbiome is a newly characterized bacterial niche that might offer biological insight into the development of breast cancer. Together with in-depth analysis of the gut microbiome in breast cancer, current evidence using next-generation sequencing and metabolic profiling suggests compositional and functional shifts in microbial consortia are associated with breast cancer. In this review, we discuss the fundamental studies that have progressed this important area of research, focusing on the roles of both the mammary tissue microbiome and the gut microbiome. From the literature, we identified the following major conclusions, (I) There are unique breast and gut microbial signatures (both compositional and functional) that are associated with breast cancer, (II) breast and gut microbiome compositional and breast functional dysbiosis represent potential early events of breast tumor development, (III) specific breast and gut microbes confer host immune responses that can combat breast tumor development and progression, and (IV) chemotherapies alter the microbiome and thus maintenance of a eubiotic microbiome may be key in breast cancer treatment. As the field expectantly advances, it is necessary for the role of the microbiome to continue to be elucidated using multi-omic approaches and translational animal models in order to improve predictive, preventive, and therapeutic strategies for breast cancer.}, }
@article {pmid37663945, year = {2023}, author = {Fan, JQ and Zhao, WF and Lu, QW and Zha, FR and Lv, LB and Ye, GL and Gao, HL}, title = {Fecal microbial biomarkers combined with multi-target stool DNA test improve diagnostic accuracy for colorectal cancer.}, journal = {World journal of gastrointestinal oncology}, volume = {15}, number = {8}, pages = {1424-1435}, pmid = {37663945}, issn = {1948-5204}, abstract = {BACKGROUND: Colorectal cancer (CRC) is a major global health burden. The current diagnostic tests have shortcomings of being invasive and low accuracy.<br><br>AIM: To explore the combination of intestinal microbiome composition and multi-target stool DNA (MT-sDNA) test in the diagnosis of CRC.<br><br>METHODS: We assessed the performance of the MT-sDNA test based on a hospital clinical trial. The intestinal microbiota was tested using 16S rRNA gene sequencing. This case-control study enrolled 54 CRC patients and 51 healthy controls. We identified biomarkers of bacterial structure, analyzed the relationship between different tumor markers and the relative abundance of related flora components, and distinguished CRC patients from healthy subjects by the linear discriminant analysis effect size, redundancy analysis, and random forest analysis.<br><br>RESULTS: MT-sDNA was associated with Bacteroides. MT-sDNA and carcinoembryonic antigen (CEA) were positively correlated with the existence of Parabacteroides, and alpha-fetoprotein (AFP) was positively associated with Faecalibacterium and Megamonas. In the random forest model, the existence of Streptococcus, Escherichia, Chitinophaga, Parasutterella, Lachnospira, and Romboutsia can distinguish CRC from health controls. The diagnostic accuracy of MT-sDNA combined with the six genera and CEA in the diagnosis of CRC was 97.1%, with a sensitivity and specificity of 98.1% and 92.3%, respectively.<br><br>CONCLUSION: There is a positive correlation of MT-sDNA, CEA, and AFP with intestinal microbiome. Eight biomarkers including six genera of gut microbiota, MT-sDNA, and CEA showed a prominent sensitivity and specificity for CRC prediction, which could be used as a non-invasive method for improving the diagnostic accuracy for this malignancy.}, }
@article {pmid37663937, year = {2023}, author = {Dan, WY and Zhou, GZ and Peng, LH and Pan, F}, title = {Update and latest advances in mechanisms and management of colitis-associated colorectal cancer.}, journal = {World journal of gastrointestinal oncology}, volume = {15}, number = {8}, pages = {1317-1331}, pmid = {37663937}, issn = {1948-5204}, abstract = {Colitis-associated colorectal cancer (CAC) is defined as a specific cluster of colorectal cancers that develop as a result of prolonged colitis in patients with inflammatory bowel disease (IBD). Patients with IBD, including ulcerative colitis and Crohn's disease, are known to have an increased risk of developing CAC. Although the incidence of CAC has significantly decreased over the past few decades, individuals with CAC have increased mortality compared to individuals with sporadic colorectal cancer, and the incidence of CAC increases with duration. Chronic inflammation is generally recognized as a major contributor to the pathogenesis of CAC. CAC has been shown to progress from colitis to dysplasia and finally to carcinoma. Accumulating evidence suggests that multiple immune-mediated pathways, DNA damage pathways, and pathogens are involved in the pathogenesis of CAC. Over the past decade, there has been an increasing effort to develop clinical approaches that could help improve outcomes for CAC patients. Colonoscopic surveillance plays an important role in reducing the risk of advanced and interval cancers. It is generally recommended that CAC patients undergo endoscopic removal or colectomy. This review summarizes the current understanding of CAC, particularly its epidemiology, mechanisms, and management. It focuses on the mechanisms that contribute to the development of CAC, covering advances in genomics, immunology, and the microbiome; presents evidence for management strategies, including endoscopy and colectomy; and discusses new strategies to interfere with the process and development of CAC. These scientific findings will pave the way for the management of CAC in the near future.}, }
@article {pmid37663891, year = {2023}, author = {Pathare, NN and Fayet-Moore, F and Fogarty, JA and Jacka, FN and Strandwitz, P and Strangman, GE and Donoviel, DB}, title = {Nourishing the brain on deep space missions: nutritional psychiatry in promoting resilience.}, journal = {Frontiers in neural circuits}, volume = {17}, number = {}, pages = {1170395}, pmid = {37663891}, issn = {1662-5110}, mesh = {Brain ; Mental Health ; *Psychiatry ; *Space Flight ; }, abstract = {The grueling psychological demands of a journey into deep space coupled with ever-increasing distances away from home pose a unique problem: how can we best take advantage of the benefits of fresh foods in a place that has none? Here, we consider the biggest challenges associated with our current spaceflight food system, highlight the importance of supporting optimal brain health on missions into deep space, and discuss evidence about food components that impact brain health. We propose a future f