@article {pmid36409379,
year = {2022},
author = {Vishwakarma, A and Srivastava, A and Mishra, S and Verma, D},
title = {Taxonomic and functional profiling of Indian smokeless tobacco bacteriome uncovers several bacterial-derived risks to human health.},
journal = {World journal of microbiology & biotechnology},
volume = {39},
number = {1},
pages = {20},
pmid = {36409379},
issn = {1573-0972},
support = {F 30.442/2018/BSR//University Grants Commission/ ; },
abstract = {Smokeless tobacco (ST) consumption keeps human oral health at high risk which is one of the major reasons for oral tumorigenesis. The chemical constituents of the ST products have been well discussed; however, the inhabitant microbial diversity of the ST products is less explored especially from south Asian regions. Therefore, the present investigation discusses the bacteriome-based analysis of indigenous tobacco products. The study relies on 16S amplicon-based bacteriome analysis of Indian smokeless tobacco (ST) products using a metagenomic approach. A total of 59,15,143 high-quality reads were assigned to 34 phyla, 82 classes, 176 orders, 256 families, 356 genera, and 154 species using the SILVA database. Of the phyla (> 1%), Firmicutes dominate among the Indian smokeless tobacco followed by Proteobacteria, Bacteroidetes, and Actinobacteria (> 1%). Whereas, at the genera level (> 1%), Lysinibacillus, Dickeya, Terribacillus, and Bacillus dominate. The comparative analysis between the loose tobacco (LT) and commercial tobacco (CT) groups showed no significant difference at the phyla level, however, only three genera (Bacillus, Aerococcus, and Halomonas) were identified as significantly different between the groups. It indicates that CT and LT tobacco share similar bacterial diversity and poses equal health risks to human oral health. The phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt 2.0) based analysis uncovered several genes involved in nitrate/nitrite reduction, biofilm formation, and pro-inflammation that find roles in oral pathogenesis including oral cancer. The strong correlation analysis of these genes with several pathogenic bacteria suggests that tobacco products pose a high bacterial-derived risk to human health. The study paves the way to understand the bacterial diversity of Indian smokeless tobacco products and their putative functions with respect to human oral health. The study grabs attention to the bacterial diversity of the smokeless tobacco products from a country where tobacco consumers are rampantly prevalent however oral health is of least concern.},
}
@article {pmid36409330,
year = {2022},
author = {Hissong, R and Evans, KR and Evans, CR},
title = {Compound Identification Strategies in Mass Spectrometry-Based Metabolomics and Pharmacometabolomics.},
journal = {Handbook of experimental pharmacology},
volume = {},
number = {},
pages = {},
pmid = {36409330},
issn = {0171-2004},
abstract = {The metabolome is composed of a vast array of molecules, including endogenous metabolites and lipids, diet- and microbiome-derived substances, pharmaceuticals and supplements, and exposome chemicals. Correct identification of compounds from this diversity of classes is essential to derive biologically relevant insights from metabolomics data. In this chapter, we aim to provide a practical overview of compound identification strategies for mass spectrometry-based metabolomics, with a particular eye toward pharmacologically-relevant studies. First, we describe routine compound identification strategies applicable to targeted metabolomics. Next, we discuss both experimental (data acquisition-focused) and computational (software-focused) strategies used to identify unknown compounds in untargeted metabolomics data. We then discuss the importance of, and methods for, assessing and reporting the level of confidence of compound identifications. Throughout the chapter, we discuss how these steps can be implemented using today's technology, but also highlight research underway to further improve accuracy and certainty of compound identification. For readers interested in interpreting metabolomics data already collected, this chapter will supply important context regarding the origin of the metabolite names assigned to features in the data and help them assess the certainty of the identifications. For those planning new data acquisition, the chapter supplies guidance for designing experiments and selecting analysis methods to enable accurate compound identification, and it will point the reader toward best-practice data analysis and reporting strategies to allow sound biological and pharmacological interpretation.},
}
@article {pmid36409161,
year = {2022},
author = {Jalodia, R and Kolli, U and Braniff, RG and Tao, J and Abu, YF and Chupikova, I and Moidunny, S and Ramakrishnan, S and Roy, S},
title = {Morphine mediated neutrophil infiltration in intestinal tissue play essential role in histological damage and microbial dysbiosis.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2143225},
doi = {10.1080/19490976.2022.2143225},
pmid = {36409161},
issn = {1949-0984},
abstract = {The gut microbial ecosystem exhibits a complex bidirectional communication with the host and is one of the key contributing factors in determining mucosal immune homeostasis or an inflammatory state. Opioid use has been established to induce gut microbial dysbiosis consistent with increased intestinal tissue inflammation. In this study, we investigated the role of infiltrated immune cells in morphine-induced intestinal tissue damage and gut microbial dysbiosis in mice. Results reveal a significant increase in chemokine expression in intestinal tissues followed by increased neutrophil infiltration post morphine treatment which is direct consequence of a dysbiotic microbiome since the effect is attenuated in antibiotics treated animals and in germ-free mice. Neutrophil neutralization using anti-Ly6G monoclonal antibody showed a significant decrease in tissue damage and an increase in tight junction protein organization. 16S rRNA sequencing on intestinal samples highlighted the role of infiltrated neutrophils in modulating microbial community structure by providing a growth benefit for pathogenic bacteria, such as Enterococcus, and simultaneously causing a significant depletion of commensal bacteria, such as Lactobacillus. Taken together, we provide the first direct evidence that neutrophil infiltration contributes to morphine-induced intestinal tissue damage and gut microbial dysbiosis. Our findings implicate that inhibition of neutrophil infiltration may provide therapeutic benefits against gastrointestinal dysfunctions associated with opioid use.},
}
@article {pmid36409145,
year = {2022},
author = {Wang, W and Jiang, S and Xu, C and Tang, L and Liang, Y and Zhao, Y and Zhu, G},
title = {Transcriptome and Gut Microbiota Profiling Analysis of ANIT-Induced Cholestasis and the Effects of Da-Huang-Xiao-Shi Decoction Intervention.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0324222},
doi = {10.1128/spectrum.03242-22},
pmid = {36409145},
issn = {2165-0497},
abstract = {Cholestasis is characterized by bile acid (BA) circulation disorders, which is usually related to damage of hepatocyte barrier function. Currently, patients with cholestasis face several obstacles in seeking diagnosis and therapy. Da-Huang-Xiao-Shi decoction (DHXSD) is an ancient classic formula that has been used clinically for cholestasis treatment. Nevertheless, the underlying biological activities and therapeutic mechanisms remain unclear. In this study, an alpha-naphthylisothiocyanate (ANIT)-induced cholestasis rat model was established to examine the anticholestatic effects of DHXSD using histopathological and molecular analyses. Transcriptomic analysis combined with 16S rRNA gene sequencing analysis was systematically applied to study the mechanism of action of DHXSD. Simultaneously, the effect of DHXSD on gut microbiota, short-chain fatty acids (SCFAs), and intestinal barrier function were evaluated based on the ANIT-induced cholestasis model in rats. The results showed that DHXSD effectively attenuated ANIT-induced cholestasis by reducing liver function indicators (alanine transaminase [ALT], P < 0.05; alkaline phosphatase [ALP], P < 0.05; total bile acid [TBA], P < 0.01; γ-glutamyl transpeptidase [GGT], P < 0.001) and levels of hepatotoxicity-related enzymes (P < 0.05), thus improving the recovery of histopathological injuries, and regulating levels of inflammatory cytokines (P < 0.05). In addition, 16S rRNA gene sequencing analysis combined with intestinal barrier function analysis revealed that the DHXSD significantly ameliorated ANIT-induced gut microbiota dysbiosis. Significantly altered genes in the model and treatment groups were screened using transcriptomic analysis. Sixty-eight genes and four microbial genera were simultaneously altered with opposing trends in variation after ANIT and DHXSD treatments. We built a framework for predicting targets and host-microbe interaction mechanisms, as well as identifying alternative treatment for cholestasis, which should be validated further for clinical application. In conclusion, DHXSD appears to be a promising agent for protection against liver injury. IMPORTANCE Cholestasis is a serious manifestation of liver diseases resulting in liver injury, fibrosis, and liver failure with limited therapies. To date, only ursodeoxycholic acid (UDCA) has been approved by the U.S. Food and Drug Administration for the treatment of cholestasis. However, approximately one-third of patients with cholestasis are unresponsive to UDCA. Therefore, it is urgent to search for appropriate therapeutic agents for restoring stoppage status of the bile components to treat cholestasis. In this study, we investigated how the microbiome and transcriptome data sets correlated with each other to clarify the role of microbiome alterations in host metabolism. In combination, this research offers potential molecular biomarkers that should be validated for more accurate diagnosis of cholestasis and the clinical utilisation of gut microbiota as a target for treatment.},
}
@article {pmid36409130,
year = {2022},
author = {Lane, S and Hilliam, Y and Bomberger, JM},
title = {Microbial and Immune Regulation of the Gut-Lung Axis during Viral-Bacterial Coinfection.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0029522},
doi = {10.1128/jb.00295-22},
pmid = {36409130},
issn = {1098-5530},
abstract = {Viral-bacterial coinfections of the respiratory tract have long been associated with worsened disease outcomes. Clinical and basic research studies demonstrate that these infections are driven via complex interactions between the infecting pathogens, microbiome, and host immune response, although how these interactions contribute to disease progression is still not fully understood. Research over the last decade shows that the gut has a significant role in mediating respiratory outcomes, in a phenomenon known as the "gut-lung axis." Emerging literature demonstrates that acute respiratory viruses can modulate the gut-lung axis, suggesting that dysregulation of gut-lung cross talk may be a contributing factor during respiratory coinfection. This review will summarize the current literature regarding modulation of the gut-lung axis during acute respiratory infection, with a focus on the role of the microbiome, secondary infections, and the host immune response.},
}
@article {pmid36409096,
year = {2022},
author = {Dillon, KP and Krumins, V and Deshpande, A and Kerkhof, LJ and Mainelis, G and Fennell, DE},
title = {Characterization and DNA Stable-Isotope Probing of Methanotrophic Bioaerosols.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0342122},
doi = {10.1128/spectrum.03421-22},
pmid = {36409096},
issn = {2165-0497},
abstract = {The growth and activity of bacteria have been extensively studied in nearly every environment on Earth, but there have been limited studies focusing on the air. Suspended bacteria (outside of water droplets) may stay in the atmosphere for time frames that could allow for growth on volatile compounds, including the potent greenhouse gas methane. We investigated the ability of aerosolized methanotrophic bacteria to grow on methane in the airborne state in rotating gas-phase bioreactors. The physical half-life of the aerial bacterium-sized particles was 3 days. To assess the potential for airborne growth, gas-phase bioreactors containing the aerosolized cultures were amended with 1,500 ppmv [13]CH4 or [12]CH4. Three of seven experiments demonstrated [13]C incorporation into DNA, indicating growth in air. Bacteria associated with the genera Methylocystis and Methylocaldum were detected in [13]C-DNA fractions, thus indicating that they were synthesizing new DNA, suggesting growth in air. We conclude that methanotrophs outside of water droplets in the air can potentially grow under certain conditions. Based on our data, humidity seems to be a major limitation to bacterial growth in air. Furthermore, low biomass levels can pose problems for detecting [13]C-DNA synthesis in our experimental system. IMPORTANCE Currently, the cellular activities of bacteria in the airborne state outside of water droplets have not been heavily studied. Evidence suggests that these airborne bacteria produce ribosomes and metabolize gaseous compounds. Despite having a potentially important impact on atmospheric chemistry, the ability of bacteria in the air to metabolize substrates such as methane is not well understood. Demonstrating that bacteria in the air can metabolize and grow on substrates will expand knowledge about the potential activities and functions of the atmospheric microbiome. This study provides evidence for DNA synthesis and, ultimately, growth of airborne methanotrophs.},
}
@article {pmid36409086,
year = {2022},
author = {Spoto, M and Riera Puma, JP and Fleming, E and Guan, C and Ondouah Nzutchi, Y and Kim, D and Oh, J},
title = {Large-Scale CRISPRi and Transcriptomics of Staphylococcus epidermidis Identify Genetic Factors Implicated in Lifestyle Versatility.},
journal = {mBio},
volume = {},
number = {},
pages = {e0263222},
doi = {10.1128/mbio.02632-22},
pmid = {36409086},
issn = {2150-7511},
abstract = {Staphylococcus epidermidis is a ubiquitous human commensal skin bacterium that is also one of the most prevalent nosocomial pathogens. The genetic factors underlying this remarkable lifestyle plasticity are incompletely understood, mainly due to the difficulties of genetic manipulation, precluding high-throughput functional profiling of this species. To probe the versatility of S. epidermidis to survive across a diversity of environmental conditions, we developed a large-scale CRISPR interference (CRISPRi) screen complemented by transcriptional profiling (RNA sequencing) across 24 diverse conditions and piloted a droplet-based CRISPRi approach to enhance throughput and sensitivity. We identified putative essential genes, importantly revealing amino acid metabolism as crucial to survival across diverse environments, and demonstrated the importance of trace metal uptake for survival under multiple stress conditions. We identified pathways significantly enriched and repressed across our range of stress and nutrient-limited conditions, demonstrating the considerable plasticity of S. epidermidis in responding to environmental stressors. Additionally, we postulate a mechanism by which nitrogen metabolism is linked to lifestyle versatility in response to hyperosmotic challenges, such as those encountered on human skin. Finally, we examined the survival of S. epidermidis under acid stress and hypothesize a role for cell wall modification as a vital component of the survival response under acidic conditions. Taken together, this study integrates large-scale CRISPRi and transcriptomics data across multiple environments to provide insights into a keystone member of the human skin microbiome. Our results additionally provide a valuable benchmarking analysis for CRISPRi screens and are a rich resource for other staphylococcal researchers. IMPORTANCE Staphylococcus epidermidis is a bacteria that broadly inhabits healthy human skin, yet it is also a common cause of skin infections and bloodstream infections associated with implanted medical devices. Because human skin has many different types of S. epidermidis, each containing different genes, our goal is to determine how these different genes allow S. epidermidis to switch from healthy growth in the skin to being an infectious pathogen. Understanding this switch is critical to developing new strategies to prevent and treat S. epidermidis infections.},
}
@article {pmid36408539,
year = {2022},
author = {Prabhakara, AM and Nanjappa, DP and Kotian, A and Kalladka, K and Chakraborty, G and Vittal, R and Mohan Raj, JR and Deekshit, VK and Chakraborty, A},
title = {Wild-type and cancer-prone zebrafish exhibit distinct gut microbial diversity and differential anti-inflammatory response upon infection.},
journal = {Journal of biosciences},
volume = {47},
number = {},
pages = {},
pmid = {36408539},
issn = {0973-7138},
abstract = {The study investigated the gut microbial diversity and the role of gut-associated microorganisms in modulating the immune responses in normal (wild-type) and TP53[M214K] (cancer-prone) zebrafish. Biochemical tests, genus/species-specific PCR, and 16S rDNA sequencing were performed to characterize the bacteria isolated from the gut of wild-type (WT) and cancer-prone zebrafish. Gut microbiome analysis revealed greater diversity but reduced bacterial load in wild-type zebrafish compared with cancer-prone zebrafish, which had lesser diversity but higher bacterial load. Interestingly, the gut in cancer-prone fish showed selective colonization by opportunistic pathogens. The bacterial isolates showed resistance to antibiotics such as tetracycline, nalidixic acid, and ciprofloxacin. Gnotobiotic zebrafish embryos were established, and mono-colonization with the isolated bacteria was done to examine the expression of anti-inflammatory genes using real-time PCR. Variable expression of IL10 and IL4 was observed in germ-free (GF) wild-type embryos when mono-colonized with Staphylococcus sciuri and Vibrio cholerae. In contrast, germ-free TP53 mutant embryos showed a consistent downregulation of both the anti-inflammatory genes. Thus, a better immune response in WT embryos against S. sciuri or V. cholerae infection than in cancer-prone fish was observed, suggesting that genetic predisposition could contribute to disabling the immune system against infection.},
}
@article {pmid36407902,
year = {2022},
author = {Schweizer, M and Jauffrais, T and Choquel, C and Méléder, V and Quinchard, S and Geslin, E},
title = {Trophic strategies of intertidal foraminifera explored with single-cell microbiome metabarcoding and morphological methods: What is on the menu?.},
journal = {Ecology and evolution},
volume = {12},
number = {11},
pages = {e9437},
doi = {10.1002/ece3.9437},
pmid = {36407902},
issn = {2045-7758},
abstract = {In mudflats, interactions and transfers of nutrients and secondary metabolites may drive ecosystems and biodiversity. Foraminifera have complex trophic strategies as they often rely on bacteria and eukaryotes or on potential symbionts for carbon and nitrogen resources. The capacity of these protists to use a wide range of adaptive mechanisms requires clarifying the relationships between them and their microbial associates. Here, we investigate the interactions of three foraminiferal species with nearby organisms in situ, by coupling molecular (cloning/Sanger and high-throughput sequencing) and direct counting and morphological identification with microscopy. This coupling allows the identification of the organisms found in or around three foraminiferal species through molecular tools combined with a direct counting of foraminifera and diatoms present in situ through microscopy methods. Depending on foraminiferal species, and in addition to diatom biomass, diatom frustule shape, size and species are key factors driving the abundance and diversity of foraminifera in mudflat habitats. Three different trophic strategies were deduced for the foraminifera investigated in this study: Ammonia sp. T6 has an opportunistic strategy and is feeding on bacteria, nematoda, fungi, and diatoms when abundant; Elphidium oceanense is feeding mainly on diatoms, mixed with other preys when they are less abundant; and Haynesina germanica is feeding almost solely on medium-large pennate diatoms. Although there are limitations due to the lack of species coverage in DNA sequence databases and to the difficulty to compare morphological and molecular data, this study highlights the relevance of combining molecular with morphological tools to study trophic interactions and microbiome communities of protists at the single-cell scale.},
}
@article {pmid36407764,
year = {2022},
author = {Melamed, E and Palmer, JL and Fonken, C},
title = {Advantages and limitations of experimental autoimmune encephalomyelitis in breaking down the role of the gut microbiome in multiple sclerosis.},
journal = {Frontiers in molecular neuroscience},
volume = {15},
number = {},
pages = {1019877},
doi = {10.3389/fnmol.2022.1019877},
pmid = {36407764},
issn = {1662-5099},
abstract = {Since the first model of experimental autoimmune encephalomyelitis (EAE) was introduced almost a century ago, there has been an ongoing scientific debate about the risks and benefits of using EAE as a model of multiple sclerosis (MS). While there are notable limitations of translating EAE studies directly to human patients, EAE continues to be the most widely used model of MS, and EAE studies have contributed to multiple key breakthroughs in our understanding of MS pathogenesis and discovery of MS therapeutics. In addition, insights from EAE have led to a better understanding of modifiable environmental factors that can influence MS initiation and progression. In this review, we discuss how MS patient and EAE studies compare in our learning about the role of gut microbiome, diet, alcohol, probiotics, antibiotics, and fecal microbiome transplant in neuroinflammation. Ultimately, the combination of rigorous EAE animal studies, novel bioinformatic approaches, use of human cell lines, and implementation of well-powered, age- and sex-matched randomized controlled MS patient trials will be essential for improving MS patient outcomes and developing novel MS therapeutics to prevent and revert MS disease progression.},
}
@article {pmid36407542,
year = {2022},
author = {Khan, R and Shah, MD and Shah, L and Lee, PC and Khan, I},
title = {Bacterial polysaccharides-A big source for prebiotics and therapeutics.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {1031935},
doi = {10.3389/fnut.2022.1031935},
pmid = {36407542},
issn = {2296-861X},
abstract = {Bacterial polysaccharides are unique due to their higher purity, hydrophilic nature, and a finer three-dimensional fibrous structure. Primarily, these polymers provide protection, support, and energy to the microorganism, however, more recently several auxiliary properties of these biopolymers have been unmasked. Microbial polysaccharides have shown therapeutic abilities against various illnesses, augmented the healing abilities of the herbal and Western medicines, improved overall health of the host, and have exerted positive impact on the growth of gut dwelling beneficial bacteria. Specifically, the review is discussing the mechanism through which bacterial polysaccharides exert anti-inflammatory, antioxidant, anti-cancer, and anti-microbial properties. In addition, they are holding promising application in the 3D printing. The review is also discussing a perspective about the metagenome-based screening of polysaccharides, their integration with other cutting-edge tools, and synthetic microbiome base intervention of polysaccharides as a strategy for prebiotic intervention. This review has collected interesting information about the bacterial polysaccharides from Google Scholar, PubMed, Scopus, and Web of Science databases. Up to our knowledge, this is the first of its kind review article that is summarizing therapeutic, prebiotics, and commercial application of bacterial polysaccharides.},
}
@article {pmid36407539,
year = {2022},
author = {Zhang, G and Lee, Y and Liu, Y and Hao, Y},
title = {Editorial: The mechanism of plant-derived polysaccharides regulating the obesity and metabolic diseases in humans.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {988653},
doi = {10.3389/fnut.2022.988653},
pmid = {36407539},
issn = {2296-861X},
}
@article {pmid36407529,
year = {2022},
author = {Whittaker, DS and Tamai, TK and Bains, RS and Villanueva, SAM and Luk, SHC and Dell'Angelica, D and Block, GD and Ghiani, CA and Colwell, CS},
title = {Dietary ketosis improves circadian dysfunction as well as motor symptoms in the BACHD mouse model of Huntington's disease.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {1034743},
doi = {10.3389/fnut.2022.1034743},
pmid = {36407529},
issn = {2296-861X},
abstract = {Disturbances in sleep/wake cycles are common among patients with neurodegenerative diseases including Huntington's disease (HD) and represent an appealing target for chrono-nutrition-based interventions. In the present work, we sought to determine whether a low-carbohydrate, high-fat diet would ameliorate the symptoms and delay disease progression in the BACHD mouse model of HD. Adult WT and BACHD male mice were fed a normal or a ketogenic diet (KD) for 3 months. The KD evoked a robust rhythm in serum levels of β-hydroxybutyrate and dramatic changes in the microbiome of male WT and BACHD mice. NanoString analysis revealed transcriptional changes driven by the KD in the striatum of both WT and BACHD mice. Disturbances in sleep/wake cycles have been reported in mouse models of HD and are common among HD patients. Having established that the KD had effects on both the WT and mutant mice, we examined its impact on sleep/wake cycles. KD increased daytime sleep and improved the timing of sleep onset, while other sleep parameters were not altered. In addition, KD improved activity rhythms, including rhythmic power, and reduced inappropriate daytime activity and onset variability. Importantly, KD improved motor performance on the rotarod and challenging beam tests. It is worth emphasizing that HD is a genetically caused disease with no known cure. Life-style changes that not only improve the quality of life but also delay disease progression for HD patients are greatly needed. Our study demonstrates the therapeutic potential of diet-based treatment strategies in a pre-clinical model of HD.},
}
@article {pmid36407281,
year = {2023},
author = {Fan, Z and Tang, P and Li, C and Yang, Q and Xu, Y and Su, C and Li, L},
title = {Fusobacterium nucleatum and its associated systemic diseases: epidemiologic studies and possible mechanisms.},
journal = {Journal of oral microbiology},
volume = {15},
number = {1},
pages = {2145729},
doi = {10.1080/20002297.2022.2145729},
pmid = {36407281},
issn = {2000-2297},
abstract = {Background: Fusobacterium nucleatum (F. nucleatum) is an anaerobic oral commensal and the major coaggregation bridge organism linking early and late colonisers. In recent years, a large number of studies suggest that F. nucleatum is closely related to the development of various systemic diseases, such as cardiovascular diseases, adverse pregnancy outcomes, inflammatory bowel diseases, cancer, Alzheimer's disease, respiratory infection, rheumatoid arthritis, etc.<br><br>Objective: To review the effect of F. nucleatum on systemic diseases and its possible pathogenesis and to open new avenues for prevention and treatment of F. nucleatum-associated systemic diseases.<br><br>Design: The research included every article published up to July 2022 featuring the keywords 'Systemic diseases' OR 'Atherosclerotic cardiovascular diseases' OR 'Atherosclerosis' OR 'Adverse pregnancy outcomes' OR 'Inflammatory bowel disease' OR 'Ulcerative colitis' OR 'Crohn's disease' OR 'Cancers' OR 'Oral squamous cell carcinomas' OR 'Gastrointestinal cancers' OR 'Colorectal cancer' OR 'Breast cancer' OR 'Genitourinary cancers' OR 'Alzheimer's disease ' OR 'Rheumatoid arthritis' OR 'Respiratory diseases' AND 'Fusobacterium nucleatum' OR 'Periodontal pathogen' OR 'Oral microbiota' OR 'Porphyromonas gingivalis' and was conducted in the major medical databases.<br><br>Results: F. nucleatum can induce immune response and inflammation in the body through direct or indirect pathways, and thus affect the occurrence and development of systemic diseases. Only by continuing to investigate the pathogenic lifestyles of F. nucleatum will we discover the divergent pathways that may be leveraged for diagnostic, preventive and therapeutic purposes.},
}
@article {pmid36407280,
year = {2023},
author = {Mougeot, JC and Beckman, M and Paster, BJ and Lockhart, PB and Bahrani Mougeot, F},
title = {Oral microbiomes of patients with infective endocarditis (IE): a comparative pilot study of IE patients, patients at risk for IE and healthy controls.},
journal = {Journal of oral microbiology},
volume = {15},
number = {1},
pages = {2144614},
doi = {10.1080/20002297.2022.2144614},
pmid = {36407280},
issn = {2000-2297},
abstract = {Background: Infective endocarditis (IE) is an uncommon disease with high morbidity and mortality rates, which often develops from oral bacterial species entering circulation.<br><br>Objective: We compared oral microbiome profiles of three groups: IE patients (N 9 patients; n = 27 samples), disease controls at risk for IE (N = 28; n = 84), and healthy controls (N = 37; n = 111). Bacterial species in IE patients' blood cultures were identified for comparison with matched oral samples.<br><br>Design: Oral microbiome profiles were obtained from buccal mucosa, saliva, and tongue samples for all three groups and from sub- and supra-gingival plaque samples of the IE group (N = 9; n = 16) and disease controls (N = 28; n = 54). Alpha- and beta-diversities were determined based on relative abundance data. Discriminative species were identified by LEfSe, post hoc Mann-Whitney, and ROC analyses. Identity of the bacterial species in IE patients' blood cultures was confirmed by 16S-rRNA gene Sanger sequencing.<br><br>Results: Alpha- and beta-diversities differed between groups. Discriminative IE-associated species were identified, e.g. Haemophilus parainfluenzae and Streptococcus sanguinis. Two blood isolates were Staphylococcus aureus, also identified in one matched saliva sample. Streptococcus mutans was present in one patient's plaque samples and blood culture.<br><br>Conclusions: Oral microbiomes of IE, non-IE disease controls, and healthy controls differed significantly. A better understanding of IE-related bacterial-host interactions is warranted.},
}
@article {pmid36406988,
year = {2022},
author = {Jadhav, VV and Han, J and Fasina, Y and Harrison, SH},
title = {Connecting gut microbiomes and short chain fatty acids with the serotonergic system and behavior in Gallus gallus and other avian species.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {1035538},
doi = {10.3389/fphys.2022.1035538},
pmid = {36406988},
issn = {1664-042X},
abstract = {The chicken gastrointestinal tract has a diverse microbial community. There is increasing evidence for how this gut microbiome affects specific molecular pathways and the overall physiology, nervous system and behavior of the chicken host organism due to a growing number of studies investigating conditions such as host diet, antibiotics, probiotics, and germ-free and germ-reduced models. Systems-level investigations have revealed a network of microbiome-related interactions between the gut and state of health and behavior in chickens and other animals. While some microbial symbionts are crucial for maintaining stability and normal host physiology, there can also be dysbiosis, disruptions to nutrient flow, and other outcomes of dysregulation and disease. Likewise, alteration of the gut microbiome is found for chickens exhibiting differences in feather pecking (FP) behavior and this alteration is suspected to be responsible for behavioral change. In chickens and other organisms, serotonin is a chief neuromodulator that links gut microbes to the host brain as microbes modulate the serotonin secreted by the host's own intestinal enterochromaffin cells which can stimulate the central nervous system via the vagus nerve. A substantial part of the serotonergic network is conserved across birds and mammals. Broader investigations of multiple species and subsequent cross-comparisons may help to explore general functionality of this ancient system and its increasingly apparent central role in the gut-brain axis of vertebrates. Dysfunctional behavioral phenotypes from the serotonergic system moreover occur in both birds and mammals with, for example, FP in chickens and depression in humans. Recent studies of the intestine as a major site of serotonin synthesis have been identifying routes by which gut microbial metabolites regulate the chicken serotonergic system. This review in particular highlights the influence of gut microbial metabolite short chain fatty acids (SCFAs) on the serotonergic system. The role of SCFAs in physiological and brain disorders may be considerable because of their ability to cross intestinal as well as the blood-brain barriers, leading to influences on the serotonergic system via binding to receptors and epigenetic modulations. Examinations of these mechanisms may translate into a more general understanding of serotonergic system development within chickens and other avians.},
}
@article {pmid36406749,
year = {2022},
author = {Hashim, HM and Makpol, S},
title = {A review of the preclinical and clinical studies on the role of the gut microbiome in aging and neurodegenerative diseases and its modulation.},
journal = {Frontiers in cellular neuroscience},
volume = {16},
number = {},
pages = {1007166},
doi = {10.3389/fncel.2022.1007166},
pmid = {36406749},
issn = {1662-5102},
abstract = {As the world population ages, the burden of age-related health problems grows, creating a greater demand for new novel interventions for healthy aging. Advancing aging is related to a loss of beneficial mutualistic microbes in the gut microbiota caused by extrinsic and intrinsic factors such as diet, sedentary lifestyle, sleep deprivation, circadian rhythms, and oxidative stress, which emerge as essential elements in controlling and prolonging life expectancy of healthy aging. This condition is known as gut dysbiosis, and it affects normal brain function via the brain-gut microbiota (BGM) axis, which is a bidirectional link between the gastrointestinal tract (GIT) and the central nervous system (CNS) that leads to the emergence of brain disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). Here, we reviewed the role of the gut microbiome in aging and neurodegenerative diseases, as well as provided a comprehensive review of recent findings from preclinical and clinical studies to present an up-to-date overview of recent advances in developing strategies to modulate the intestinal microbiome by probiotic administration, dietary intervention, fecal microbiota transplantation (FMT), and physical activity to address the aging process and prevent neurodegenerative diseases. The findings of this review will provide researchers in the fields of aging and the gut microbiome design innovative studies that leverage results from preclinical and clinical studies to better understand the nuances of aging, gut microbiome, and neurodegenerative diseases.},
}
@article {pmid36406462,
year = {2022},
author = {Baraniya, D and Do, T and Chen, T and Albandar, JM and Chialastri, SM and Devine, DA and Marsh, PD and Al-Hebshi, NN},
title = {Optimization of conditions for in vitro modeling of subgingival normobiosis and dysbiosis.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1031029},
doi = {10.3389/fmicb.2022.1031029},
pmid = {36406462},
issn = {1664-302X},
abstract = {Modeling subgingival microbiome in health and disease is key to identifying the drivers of dysbiosis and to studying microbiome modulation. Here, we optimize growth conditions of our previously described in vitro subgingival microbiome model. Subgingival plaque samples from healthy and periodontitis subjects were used as inocula to grow normobiotic and dysbiotic microbiomes in MBEC assay plates. Saliva supplemented with 1%, 2%, 3.5%, or 5% (v/v) heat-inactivated human serum was used as a growth medium under shaking or non-shaking conditions. The microbiomes were harvested at 4, 7, 10 or 13 days of growth (384 microbiomes in total) and analyzed by 16S rRNA gene sequencing. Biomass significantly increased as a function of serum concentration and incubation period. Independent of growth conditions, the health- and periodontitis-derived microbiomes clustered separately with their respective inocula. Species richness/diversity slightly increased with time but was adversely affected by higher serum concentrations especially in the periodontitis-derived microbiomes. Microbial dysbiosis increased with time and serum concentration. Porphyromonas and Alloprevotella were substantially enriched in higher serum concentrations at the expense of Streptococcus, Fusobacterium and Prevotella. An increase in Porphyromonas, Bacteroides and Mogibacterium accompanied by a decrease in Prevotella, Catonella, and Gemella were the most prominent changes over time. Shaking had only minor effects. Overall, the health-derived microbiomes grown for 4 days in 1% serum, and periodontitis-derived microbiomes grown for 7 days in 3.5%-5% serum were the most similar to the respective inocula. In conclusion, normobiotic and dysbiostic subgingival microbiomes can be grown reproducibly in saliva supplemented with serum, but time and serum concentration need to be adjusted differently for the health and periodontitis-derived microbiomes to maximize similarity to in vivo inocula. The optimized model could be used to identify drivers of dysbiosis, and to evaluate interventions such as microbiome modulators.},
}
@article {pmid36406450,
year = {2022},
author = {Overgaard, CK and Tao, K and Zhang, S and Christensen, BT and Blahovska, Z and Radutoiu, S and Kelly, S and Dueholm, MKD},
title = {Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {942396},
doi = {10.3389/fmicb.2022.942396},
pmid = {36406450},
issn = {1664-302X},
abstract = {Intensive agriculture systems have paved the way for a growing human population. However, the abundant use of mineral fertilizers and pesticides may negatively impact nutrient cycles and biodiversity. One potential alternative is to harness beneficial relationships between plants and plant-associated rhizobacteria to increase nutrient-use efficiency and provide pathogen resistance. Plant-associated microbiota profiling can be achieved using high-throughput 16S rRNA gene amplicon sequencing. However, interrogation of these data is limited by confident taxonomic classifications at high taxonomic resolution (genus- or species level) with the commonly applied universal reference databases. High-throughput full-length 16S rRNA gene sequencing combined with automated taxonomy assignment (AutoTax) can be used to create amplicon sequence variant resolved ecosystems-specific reference databases that are superior to the traditional universal reference databases. This approach was used here to create a custom reference database for bacteria and archaea based on 987,353 full-length 16S rRNA genes from Askov and Cologne soils. We evaluated the performance of the database using short-read amplicon data and found that it resulted in the increased genus- and species-level classification compared to commonly use universal reference databases. The custom database was utilized to evaluate the ecosystem-specific primer bias and taxonomic resolution of amplicon primers targeting the V5-V7 region of the 16S rRNA gene commonly used within the plant microbiome field. Finally, we demonstrate the benefits of custom ecosystem-specific databases through the analysis of V5-V7 amplicon data to identify new plant-associated microbes for two legumes and two cereal species.},
}
@article {pmid36406449,
year = {2022},
author = {Li, S and Yang, M and Ji, L and Fan, H},
title = {A multi-omics machine learning framework in predicting the recurrence and metastasis of patients with pancreatic adenocarcinoma.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1032623},
doi = {10.3389/fmicb.2022.1032623},
pmid = {36406449},
issn = {1664-302X},
abstract = {Local recurrence and distant metastasis are the main causes of death in patients with pancreatic adenocarcinoma (PDAC). Microbial content in PDAC metastasis is still not well-characterized. Here, the tissue microbiome was comprehensively compared between metastatic and non-metastatic PDAC patients. We found that the pancreatic tissue microbiome of metastatic patients was significantly different from that of non-metastatic patients. Further, 10 potential bacterial biomarkers (Kurthia, Gulbenkiania, Acetobacterium and Planctomyces etc.) were identified by differential analysis. Meanwhile, significant differences in expression patterns across multiple omics (lncRNA, miRNA, and mRNA) of PDAC patients were found. The highest accuracy was achieved when these 10 bacterial biomarkers were used as features to predict recurrence or metastasis in PDAC patients, with an AUC of 0.815. Finally, the recurrence and metastasis in PDAC patients were associated with reduced survival and this association was potentially driven by the 10 biomarkers we identified. Our studies highlight the association between the tissue microbiome and recurrence or metastasis of pancreatic adenocarcioma patients, as well as the survival of patients.},
}
@article {pmid36406447,
year = {2022},
author = {Zhang, H and Wu, J and Ji, D and Liu, Y and Lu, S and Lin, Z and Chen, T and Ao, L},
title = {Microbiome analysis reveals universal diagnostic biomarkers for colorectal cancer across populations and technologies.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1005201},
doi = {10.3389/fmicb.2022.1005201},
pmid = {36406447},
issn = {1664-302X},
abstract = {The gut microbial dysbiosis is a risk of colorectal cancer (CRC) and some bacteria have been reported as potential markers for CRC diagnosis. However, heterogeneity among studies with different populations and technologies lead to inconsistent results. Here, we investigated six metagenomic profiles of stool samples from healthy controls (HC), colorectal adenoma (CA) and CRC, and six and four genera were consistently altered between CRC and HC or CA across populations, respectively. In FengQ cohort, which composed with 61 HC, 47 CA, and 46 CRC samples, a random forest (RF) model composed of the six genera, denoted as signature-HC, distinguished CRC from HC with an area under the curve (AUC) of 0.84. Similarly, another RF model composed of the four universal genera, denoted as signature-CA, discriminated CRC from CA with an AUC of 0.73. These signatures were further validated in five metagenomic sequencing cohorts and six independent 16S rRNA gene sequencing cohorts. Interestingly, three genera overlapped in the two models (Porphyromonas, Parvimonas and Peptostreptococcus) were with very low abundance in HC and CA, but sharply increased in CRC. A concise RF model on the three genera distinguished CRC from HC or CA with AUC of 0.87 and 0.67, respectively. Functional gene family analysis revealed that Kyoto Encyclopedia of Genes and Genomes Orthogroups categories which were significantly correlated with markers in signature-HC and signature-CA were mapped into pathways related to lipopolysaccharide and sulfur metabolism, which might be vital risk factors of CRC development. Conclusively, our study identified universal bacterial markers across populations and technologies as potential aids in non-invasive diagnosis of CRC.},
}
@article {pmid36406441,
year = {2022},
author = {Wei, Y and Li, H},
title = {Editorial: Exploring the insect microbiome: The potential future role in biotechnology industry.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1061360},
doi = {10.3389/fmicb.2022.1061360},
pmid = {36406441},
issn = {1664-302X},
}
@article {pmid36406426,
year = {2022},
author = {Lima, COC and De Castro, GM and Solar, R and Vaz, ABM and Lobo, F and Pereira, G and Rodrigues, C and Vandenberghe, L and Martins Pinto, LR and da Costa, AM and Koblitz, MGB and Benevides, RG and Azevedo, V and Uetanabaro, APT and Soccol, CR and Góes-Neto, A},
title = {Unraveling potential enzymes and their functional role in fine cocoa beans fermentation using temporal shotgun metagenomics.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {994524},
doi = {10.3389/fmicb.2022.994524},
pmid = {36406426},
issn = {1664-302X},
abstract = {Cocoa beans fermentation is a spontaneous process, essential for the generation of quality starting material for fine chocolate production. The understanding of this process has been studied by the application of high-throughput sequencing technologies, which grants a better assessment of the different microbial taxa and their genes involved in this microbial succession. The present study used shotgun metagenomics to determine the enzyme-coding genes of the microbiota found in two different groups of cocoa beans varieties during the fermentation process. The statistical evaluation of the most abundant genes in each group and time studied allowed us to identify the potential metabolic pathways involved in the success of the different microorganisms. The results showed that, albeit the distinction between the initial (0 h) microbiota of each varietal group was clear, throughout fermentation (24-144 h) this difference disappeared, indicating the existence of selection pressures. Changes in the microbiota enzyme-coding genes over time pointed to the distinct ordering of fermentation at 24-48 h (T1), 72-96 h (T2), and 120-144 h (T3). At T1, the significantly more abundant enzyme-coding genes were related to threonine metabolism and those genes related to the glycolytic pathway, explained by the abundance of sugars in the medium. At T2, the genes linked to the metabolism of ceramides and hopanoids lipids were clearly dominant, which are associated with the resistance of microbial species to extreme temperatures and pH values. In T3, genes linked to trehalose metabolism, related to the response to heat stress, dominated. The results obtained in this study provided insights into the potential functionality of microbial community succession correlated to gene function, which could improve cocoa processing practices to ensure the production of more stable quality end products.},
}
@article {pmid36406423,
year = {2022},
author = {Li, J and Lv, JL and Cao, XY and Zhang, HP and Tan, YJ and Chu, T and Zhao, LL and Liu, Z and Ren, YS},
title = {Gut microbiota dysbiosis as an inflammaging condition that regulates obesity-related retinopathy and nephropathy.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1040846},
doi = {10.3389/fmicb.2022.1040846},
pmid = {36406423},
issn = {1664-302X},
abstract = {Diabetes-specific microvascular disease is a leading cause of blindness, renal failure and nerve damage. Epidemiological data demonstrated that the high morbidity of T2DM occurs as a result of obesity and gradually develops into serious complications. To date, the mechanisms that underlie this observation are still ill-defined. In view of the effect of obesity on the gut microflora, Lepr[db/db] mice underwent antibiotic treatment and microbiota transplants to modify the gut microbiome to investigate whether microbes are involved in the development of diabetic nephropathy (DN) and/or diabetic retinopathy (DR). The mouse feces were collected for bacterial 16S ribosomal RNA gene sequencing. Cytokines including TNF-α, TGF-β1, IFN-γ, IL-1β, IL-6, IL-17A, IL-10, and VEGFA were detected by enzyme-linked immunosorbent assay (ELISA), flow cytometry, real-time PCR and immunofluorescent assay. Eyes and kidney were collected for histopathological assay. Intestinal permeability was also detected using Evans Blue. The results showed that obesity influenced metabolic variables (including fast/fed glucose, insulin, and triglyceride), retinopathy and nephropathy, and the gut microbiota. Obesity mainly reduced the ratio of Bacteroidetes/Firmicutes and influenced relative abundance of Proteobacteria, Actinobacteria, and Spirochetes. Obesity also increased intestinal permeability, metabolic endotoxemia, cytokines, and VEGFA. Microbiota transplants confirm that obesity aggravates retinopathy and nephropathy through the gut microbiota. These findings suggest that obesity exacerbates retinopathy and nephropathy by inducing gut microbiota dysbiosis, which further enhanced intestinal permeability and chronic low-grade inflammation.},
}
@article {pmid36406420,
year = {2022},
author = {Xu, M and Su, S and Zhang, Z and Jiang, S and Zhang, J and Xu, Y and Hu, X},
title = {Two sides of the same coin: Meta-analysis uncovered the potential benefits and risks of traditional fermented foods at a large geographical scale.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1045096},
doi = {10.3389/fmicb.2022.1045096},
pmid = {36406420},
issn = {1664-302X},
abstract = {Traditional fermented foods, which are well-known microbial resources, are also bright national cultural inheritances. Recently, traditional fermented foods have received great attention due to their potential probiotic properties. Based on shotgun metagenomic sequencing data, we analyzed the microbial diversity, taxonomic composition, metabolic pathways, and the potential benefits and risks of fermented foods through a meta-analysis including 179 selected samples, as well as our own sequencing data collected from Hainan Province, China. As expected, raw materials, regions (differentiated by climatic zones), and substrates were the main driving forces for the microbial diversity and taxonomic composition of traditional fermented foods. Interestingly, a higher content of beneficial bacteria but a low biomass of opportunistic pathogens and antibiotic resistance genes were observed in the fermented dairy products, indicating that fermented dairy products are the most beneficial and reliable fermented foods. In contrast, despite the high microbial diversity found in the fermented soy products, their consumption risk was still high due to the enrichment of opportunistic pathogens and transferable antibiotic resistance genes. Overall, we provided the most comprehensive assessment of the microbiome of fermented food to date and generated a new view of its potential benefits and risks related to human health.},
}
@article {pmid36406415,
year = {2022},
author = {Aoki, W and Kogawa, M and Matsuda, S and Matsubara, K and Hirata, S and Nishikawa, Y and Hosokawa, M and Takeyama, H and Matoh, T and Ueda, M},
title = {Massively parallel single-cell genomics of microbiomes in rice paddies.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1024640},
doi = {10.3389/fmicb.2022.1024640},
pmid = {36406415},
issn = {1664-302X},
abstract = {Plant growth-promoting microbes (PGPMs) have attracted increasing attention because they may be useful in increasing crop yield in a low-input and sustainable manner to ensure food security. Previous studies have attempted to understand the principles underlying the rhizosphere ecology and interactions between plants and PGPMs using ribosomal RNA sequencing, metagenomic sequencing, and genome-resolved metagenomics; however, these approaches do not provide comprehensive genomic information for individual species and do not facilitate detailed analyses of plant-microbe interactions. In the present study, we developed a pipeline to analyze the genomic diversity of the rice rhizosphere microbiome at single-cell resolution. We isolated microbial cells from paddy soil and determined their genomic sequences by using massively parallel whole-genome amplification in microfluidic-generated gel capsules. We successfully obtained 3,237 single-amplified genomes in a single experiment, and these genomic sequences provided insights into microbial functions in the paddy ecosystem. Our approach offers a promising platform for gaining novel insights into the roles of microbes in the rice rhizomicrobiome and to develop microbial technologies for improved and sustainable rice production.},
}
@article {pmid36406409,
year = {2022},
author = {Zhang, Y and Yang, H and Lin, L and Yang, W and Xiong, G and Gao, G},
title = {The relationship between pelvic floor functions and vaginal microbiota in 6-8 weeks postpartum women.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {975406},
doi = {10.3389/fmicb.2022.975406},
pmid = {36406409},
issn = {1664-302X},
abstract = {The impairment of pelvic floor muscle functions and Lactobacillus-deficient vaginal microbiota is common in postpartum women. However, few studies have explored the correlation between pelvic floor muscle functions and vaginal microbiota. Given this research gap, our study aims to investigate any potential association between these two conditions of postpartum women (6-8 weeks after childbirth). A total of 230 women who required postpartum pelvic floor function examination at Peking University International Hospital from December 2021 to April 2022 were enrolled in this study. The collected questionnaire information included progestational weight, body mass index (BMI), weight gain during pregnancy, neonatal weight, delivery type, multiparity, postpartum time, and urinary incontinence (UI). A total of 187 samples of vaginal secretions were collected, and the vaginal microbiota was detected by 16S rRNA sequence analysis. Finally, 183 samples were analyzed in the trial. All individuals were divided into two groups according to the results of pelvic floor muscle assessment to explore the difference between the incidence of postpartum urinary incontinence and vaginal microbiota. We found that the prevalence of UI was higher in the group with weakened pelvic floor muscles. Vaginal delivery, overweight, age, neonatal weight, and weight gain during pregnancy were all risk factors for postpartum urinary incontinence. The vaginal microbiome was no longer Lactobacillus dominant of most postpartum women (91.8%), while the diversity of microbiota increased. The Lactobacillus-deficient community, commonly labeled as community state type (CST) IV, was sub-divided into four communities. The abundance of vaginal Lactobacillus decreased in the group with compromised pelvic muscle functions, while the species richness and diversity increased significantly. In conclusion, the decreased pelvic floor muscle functions of postpartum women 6-8 weeks after delivery may disrupt the balance of vaginal microbiota, and the restoration of pelvic floor functions may contribute to a healthy and balanced vaginal microbiota.},
}
@article {pmid36406398,
year = {2022},
author = {da Silva, MSRA and de Carvalho, LAL and Braos, LB and de Sousa Antunes, LF and da Silva, CSRA and da Silva, CGN and Pinheiro, DG and Correia, MEF and Araújo, EDS and Colnago, LA and Desoignies, N and Zonta, E and Rigobelo, EC},
title = {Effect of the application of vermicompost and millicompost humic acids about the soybean microbiome under water restriction conditions.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1000222},
doi = {10.3389/fmicb.2022.1000222},
pmid = {36406398},
issn = {1664-302X},
abstract = {Humic substances (HSs) are constituent fractions of organic matter and are highly complex and biologically active. These substances include humic acids (HA), fulvic acids (FA), and humin. HS are known to stimulate the root system and plant growth and to mitigate stress damage, including hydric stress. Humic acids have already been reported to increase microbial growth, affecting their beneficial effect on plants. However, there is scarce information on whether HA from vermicompost and millicompost, along with Bradyrhizobium, improves the tolerance of soybean to water restriction. This study aimed to evaluate the responses of soybean plants to the application of vermicompost HA (HA-V) and millicompost (HA-M) along with Bradyrhizobium sp. under water restriction. The experiment was carried out in a greenhouse, and the treatments received Bradyrhizobium sp. inoculation with or without the application of HA from vermicompost and millicompost with or without water restriction. The results showed that HA provided greater soybean growth and nodulation than the control. The application of HA-M stimulated an increase in the richness of bacterial species in roots compared to the other treatments. After the application of water stress, the difference between the treatments disappeared. Microbial taxa were differentially abundant in plants, with the fungal fraction most affected by HA application in stressed roots. HA-V appears to be more prominent in inducing taxa under stress conditions. Although the results showed slight differences between HA from vermicompost and millicompost regarding plant growth, both humic acids promoted an increase in plant development compared to the control.},
}
@article {pmid36406325,
year = {2023},
author = {Philips, CA and Ahamed, R and Abduljaleel, JKP and Rajesh, S and Augustine, P},
title = {Identification and Analysis of Gut Microbiota and Functional Metabolism in Decompensated Cirrhosis with Infection.},
journal = {Journal of clinical and translational hepatology},
volume = {11},
number = {1},
pages = {15-25},
doi = {10.14218/JCTH.2021.00428},
pmid = {36406325},
issn = {2310-8819},
abstract = {Background and Aims: Intestinal dysbiosis play a role in the adverse outcomes of sepsis and septic shock. However, variations in bacterial diversity and microbiota-related functional metabolic alterations within the gut microbiome in decompensated cirrhosis (DC) patients with infection remain unknown.<br><br>Methods: We conducted 16-srRNA sequencing on stool samples (n=51: sepsis, 27/no sepsis, 24) collected from consecutive DC patients upon admission. Bacterial diversity, significant taxa, and respective metabolic profiling were performed based on subgroup comparisons. Conet/Cytoscape was utilized to identify significant non-random patterns of bacterial copresence and mutual exclusion for clinical events.<br><br>Results: Genera associated with pathogenicity in conditions of immune exhaustion (Corynebacterium, Lautropia) were predominant in patients with sepsis. Metabolic pathways associated with oxidative stress and endotoxemia [lipopolysaccharide (LPS) synthesis and sulfur relay] were significantly upregulated in sepsis. Specific taxa were associated with sites of infection in DC patients. Protective oxidant pathways that increase glutathione were upregulated in those without sepsis. Gammaproteobacteria family of sulfur-metabolizing bacteria, exaggeration of orally predominant pathogens (Prevotella), and pathways of severe LPS-related hyperinflammatory stress were notable in those with interleukin-6 levels >1,000 pg/dL. Pathogenic genera related to an immune deficient state was significant in DC with ≥2 infection episodes. Megamonas was associated with survival during the same admission.<br><br>Conclusions: Specific gut microbiota and their metabolites were associated with sepsis and related events in patients with DC. Identifying beneficial strains that reduce immune exhaustion and supplementation of favorable metabolites could improve therapeutics for DC and sepsis, for which larger prospective, well controlled population-based studies remain an unmet need.},
}
@article {pmid36406312,
year = {2023},
author = {Ji, J and Wu, L and Wei, J and Wu, J and Guo, C},
title = {The Gut Microbiome and Ferroptosis in MAFLD.},
journal = {Journal of clinical and translational hepatology},
volume = {11},
number = {1},
pages = {174-187},
doi = {10.14218/JCTH.2022.00136},
pmid = {36406312},
issn = {2310-8819},
abstract = {Metabolic-associated fatty liver disease (MAFLD) is a new disease definition, and is proposed to replace the previous name, nonalcoholic fatty liver disease (NAFLD). Globally, MAFLD/NAFLD is the most common liver disease, with an incidence rate ranging from 6% to 35% in adult populations. The pathogenesis of MAFLD/NAFLD is closely related to insulin resistance (IR), and the genetic susceptibility to acquired metabolic stress-associated liver injury. Similarly, the gut microbiota in MAFLD/NAFLD is being revaluated by scientists, as the gut and liver influence each other via the gut-liver axis. Ferroptosis is a novel form of programmed cell death caused by iron-dependent lipid peroxidation. Emerging evidence suggests that ferroptosis has a key role in the pathological progression of MAFLD/NAFLD, and inhibition of ferroptosis may become a novel therapeutic strategy for the treatment of NAFLD. This review focuses on the main mechanisms behind the promotion of MAFLD/NAFLD occurrence and development by the intestinal microbiota and ferroptosis. It outlines new strategies to target the intestinal microbiota and ferroptosis to facilitate future MAFLD/NAFLD therapies.},
}
@article {pmid36406267,
year = {2022},
author = {Regmi, R and Penton, CR and Anderson, J and Gupta, VVSR},
title = {Do small RNAs unlock the below ground microbiome-plant interaction mystery?.},
journal = {Frontiers in molecular biosciences},
volume = {9},
number = {},
pages = {1017392},
doi = {10.3389/fmolb.2022.1017392},
pmid = {36406267},
issn = {2296-889X},
abstract = {Over the past few decades, regulatory RNAs, such as small RNAs (sRNAs), have received increasing attention in the context of host-microbe interactions due to their diverse roles in controlling various biological processes in eukaryotes. In addition, studies have identified an increasing number of sRNAs with novel functions across a wide range of bacteria. What is not well understood is why cells regulate gene expression through post-transcriptional mechanisms rather than at the initiation of transcription. The finding of a multitude of sRNAs and their identified associated targets has allowed further investigation into the role of sRNAs in mediating gene regulation. These foundational data allow for further development of hypotheses concerning how a precise control of gene activity is accomplished through the combination of transcriptional and post-transcriptional regulation. Recently, sRNAs have been reported to participate in interkingdom communication and signalling where sRNAs originating from one kingdom are able to target or control gene expression in another kingdom. For example, small RNAs of fungal pathogens that silence plant genes and vice-versa plant sRNAs that mediate bacterial gene expression. However, there is currently a lack of evidence regarding sRNA-based inter-kingdom signalling across more than two interacting organisms. A habitat that provides an excellent opportunity to investigate interconnectivity is the plant rhizosphere, a multifaceted ecosystem where plants and associated soil microbes are known to interact. In this paper, we discuss how the interconnectivity of bacteria, fungi, and plants within the rhizosphere may be mediated by bacterial sRNAs with a particular focus on disease suppressive and non-suppressive soils. We discuss the potential roles sRNAs may play in the below-ground world and identify potential areas of future research, particularly in reference to the regulation of plant immunity genes by bacterial and fungal communities in disease-suppressive and non-disease-suppressive soils.},
}
@article {pmid36406074,
year = {2022},
author = {Li, G and Wang, X and Liu, Y and Wang, C and Yang, Y and Gong, S and Zhu, L and He, D and Wang, H},
title = {Supplementation with honeysuckle extract improves growth performance, immune performance, gut morphology, and cecal microbes in geese.},
journal = {Frontiers in veterinary science},
volume = {9},
number = {},
pages = {1006318},
doi = {10.3389/fvets.2022.1006318},
pmid = {36406074},
issn = {2297-1769},
abstract = {The study aimed to investigate the effects of honeysuckle extract (HE) on growth performance, serum biochemical indexes, immune organ indexes, gut morphology, and gut microbes in geese. A total of 180 28-day-old Holdobaki geese were randomly divided into three groups. Each group contained 6 replicates (10 geese, with 5 males and 5 females). The BD group was fed the basal diet, the HE1 group was fed the basal diet supplemented with 1 g/kg of HE, and the HE2 group was fed the basal diet supplemented with 2 g/kg of HE. The experiment lasted for 42 days. The results showed that, compared with the BD group, the average daily gain (ADG) of the HE1 and HE2 groups tended to increase (0.05 < P < 0.10), but the average daily feed intake (ADFI) and final body weight (BW) did not differ significantly, and the feed/gain ratio (F/G) was significantly lower (P < 0.01). The bursa index and the thymus index tended to increase (0.05 < P < 0.10), and serum immunoglobulin A (IgA) and immunoglobulin G (IgG) levels increased significantly (P < 0.05). In the HE1 and HE2 groups, the crypt depth (CD) in the jejunum tended to decrease (0.05 < P < 0.10), and the villus height/crypt depth ratio (V/C) increased significantly in the jejunum and the ileum (P < 0.05). According to 16sRNA microbial community diversity analysis, Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the dominant phyla. The abundance of Firmicutes was significantly decreased (P < 0.01), while that of Bacteroidetes was significantly increased (P < 0.01), in the HE1 and HE2 groups compared with the BD group. Bacteroides barnesiae, Subdoligranulum variabile, Bacteroides plebeius, and Faecalibacterium prausnitzii were the dominant species, and the abundance of B. plebeius and F. prausnitzii was significantly increased (P < 0.05). According to the LEfSe analysis, BD enriched g_Dorea and g_Dehalobacterium; HE1 enriched g_Faecalibacterium, g_Dialister, g_Prevotella, g_Megamonas, g_Phascolarctobacterium, g_Paraprevotella, g_Anaerostipes, g_Staphylococcus, g_Odoribacter, g_Succinivibrio, and g_Sutterella; and HE2 enriched g_Parabacteroides, g_Olsenella, g_human, and g_Rikenella. According to the Spearman correlation analysis, Bacteroides plebeius was positively correlated with final BW, ADG, IgA, IgG, VH (ileum), and V/C (ileum) and was negatively correlated with F/G and CD (ileum); Ruminococcus gnavus was negatively correlated with final BW, ADG, IgA, and IgG. HE supplementation at 1 g/kg improved growth performance, immune performance, gut morphology, and cecal microbes.},
}
@article {pmid36405964,
year = {2022},
author = {Couret, J and Schofield, S and Narasimhan, S},
title = {The environment, the tick, and the pathogen - It is an ensemble.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1049646},
doi = {10.3389/fcimb.2022.1049646},
pmid = {36405964},
issn = {2235-2988},
abstract = {Ixodes scapularis is one of the predominant vectors of Borrelia burgdorferi, the agent of Lyme disease in the USA. The geographic distribution of I. scapularis, endemic to the northeastern and northcentral USA, is expanding as far south as Georgia and Texas, and northwards into Canada and poses an impending public health problem. The prevalence and spread of tick-borne diseases are influenced by the interplay of multiple factors including microbiological, ecological, and environmental. Molecular studies have focused on interactions between the tick-host and pathogen/s that determine the success of pathogen acquisition by the tick and transmission to the mammalian host. In this review we draw attention to additional critical environmental factors that impact tick biology and tick-pathogen interactions. With a focus on B. burgdorferi we highlight the interplay of abiotic factors such as temperature and humidity as well as biotic factors such as environmental microbiota that ticks are exposed to during their on- and off-host phases on tick, and infection prevalence. A molecular understanding of this ensemble of interactions will be essential to gain new insights into the biology of tick-pathogen interactions and to develop new approaches to control ticks and tick transmission of B. burgdorferi, the agent of Lyme disease.},
}
@article {pmid36404958,
year = {2022},
author = {Yao, YF and Wang, MY and Dou, XY},
title = {Gastrointestinal microbiome and primary Sjögren's syndrome: a review of the literature and conclusions.},
journal = {International journal of ophthalmology},
volume = {15},
number = {11},
pages = {1864-1872},
doi = {10.18240/ijo.2022.11.19},
pmid = {36404958},
issn = {2222-3959},
abstract = {The recognition of the profound impact of the human gastrointestinal microbiome (GM) on human autoimmune diseases has gradually increased thanks to deeper research efforts. As a systemic autoimmune disease, primary Sjögren's syndrome (pSS) cannot be completely cured. Human studies have revealed that GM species and diversity are altered in patients with pSS compared with healthy individuals. Animal studies have provided possible mechanisms for the association between pSS and GM. The potential role of GM in pSS is exerted through several mechanisms. GM dysbiosis leads to increased intestinal permeability, which increases the risk of GM antigen exposure and activates specific autoreactive T lymphocytes via "molecular mimicry". In addition, GM antigen exposure and intestinal immune tolerance loss caused by GM dysbiosis together induce chronic local gut mucosal inflammation, which deteriorates to systemic chronic non-specific inflammation with the circulation of pro-inflammatory lymphocytes and cytokines. These factors eventually activate autoreactive B lymphocytes and lead to pSS. If GM plays a key role in the pathogenesis of pSS, clarifying the underlying mechanisms will be helpful for the development of new therapies targeting GM for dry eye associated with pSS. This review summarizes the latest knowledge about the relationship between GM and pSS, with the aim of contributing to future research and to the development of new clinical applications.},
}
@article {pmid36404932,
year = {2022},
author = {Noel, ZA and Longley, R and Benucci, GMN and Trail, F and Chilvers, MI and Bonito, G},
title = {Non-target impacts of fungicide disturbance on phyllosphere yeasts in conventional and no-till management.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {},
doi = {10.1038/s43705-022-00103-w},
pmid = {36404932},
issn = {2730-6151},
abstract = {Fungicides reduce fungal pathogen populations and are essential to food security. Understanding the impacts of fungicides on crop microbiomes is vital to minimizing unintended consequences while maintaining their use for plant protection. However, fungicide disturbance of plant microbiomes has received limited attention, and has not been examined in different agricultural management systems. We used amplicon sequencing of fungi and prokaryotes in maize and soybean microbiomes before and after foliar fungicide application in leaves and roots from plots under long-term no-till and conventional tillage management. We examined fungicide disturbance and resilience, which revealed consistent non-target effects and greater resiliency under no-till management. Fungicides lowered pathogen abundance in maize and soybean and decreased the abundance of Tremellomycetes yeasts, especially Bulleribasidiaceae, including core microbiome members. Fungicide application reduced network complexity in the soybean phyllosphere, which revealed altered co-occurrence patterns between yeast species of Bulleribasidiaceae, and Sphingomonas and Hymenobacter in fungicide treated plots. Results indicate that foliar fungicides lower pathogen and non-target fungal abundance and may impact prokaryotes indirectly. Treatment effects were confined to the phyllosphere and did not impact belowground microbial communities. Overall, these results demonstrate the resilience of no-till management to fungicide disturbance, a potential novel ecosystem service provided by no-till agriculture.},
}
@article {pmid36404915,
year = {2022},
author = {de Jesus, VC and Mittermuller, BA and Hu, P and Schroth, RJ and Chelikani, P},
title = {Genetic variants in taste genes play a role in oral microbial composition and severe early childhood caries.},
journal = {iScience},
volume = {25},
number = {12},
pages = {105489},
doi = {10.1016/j.isci.2022.105489},
pmid = {36404915},
issn = {2589-0042},
abstract = {Severe early childhood caries (S-ECC) is a multifactorial disease with strong evidence of genetic inheritance. Previous studies suggest that variants in taste genes are associated with dental caries due to the role of taste proteins in mediating taste preferences, oral innate immunity, and important host-microbial interactions. However, few taste genes have been investigated in caries studies. Therefore, the associations of genetic variants in sweet, bitter, umami, salt, sour, carbonation, and fat taste-related genes with S-ECC and plaque microbial composition (16S and ITS1 rRNA sequencing) were evaluated. The results showed that sixteen variants in seven taste genes (SCNN1D, CA6, TAS2R3, OTOP1, TAS2R5, TAS2R60, and TAS2R4) were associated with S-ECC. Twenty-one variants in twelve taste genes were correlated with relative abundances of bacteria or fungi. These results suggest that S-ECC risk and composition of the plaque microbiome can be partially influenced by genetic variants in genes related to taste sensation.},
}
@article {pmid36404833,
year = {2022},
author = {James, MM and Pal, N and Sharma, P and Kumawat, M and Shubham, S and Verma, V and Tiwari, RR and Singh, B and Nagpal, R and Sarma, DK and Kumar, M},
title = {Role of butyrogenic Firmicutes in type-2 diabetes.},
journal = {Journal of diabetes and metabolic disorders},
volume = {21},
number = {2},
pages = {1873-1882},
doi = {10.1007/s40200-022-01081-5},
pmid = {36404833},
issn = {2251-6581},
abstract = {Objective: The aim of this review is to speculate the pre-clinical and clinical evidences indicating the association between butyrate-synthesizing firmicutes and development and progression of type 2 diabetes mellitus.<br><br>Methodology: Literature was searched using 'Google Scholar' and 'PubMed' to find out most relevant articles for the scope of this review. Information was also gathered from authentic sources such as the World Health Organisation and the International Diabetes Federation.<br><br>Results: Evidences suggest that an abnormal perturbation in the gut microbiome characterized by subsided levels of butyrate-producing bacteria may gradually result in the progression of type-2 diabetes; however, the explicit mechanisms underlying and implicating the role of specific butyrate-producing microbes remain unclear.<br><br>Conclusions: This review explicitly summarizes the role of butyrate-synthesizing firmicutes known to be reduced in the subjects with type-2 diabetes mellitus in host metabolic health and contemplates the putative and reported mechanisms underlying its implication in the pathophysiology of type-2 diabetes mellitus.},
}
@article {pmid36404627,
year = {2022},
author = {Silva, LM and Kim, TS and Moutsopoulos, NM},
title = {Neutrophils are gatekeepers of mucosal immunity.},
journal = {Immunological reviews},
volume = {},
number = {},
pages = {},
doi = {10.1111/imr.13171},
pmid = {36404627},
issn = {1600-065X},
support = {1K99DE030124-01A1/DE/NIDCR NIH HHS/United States ; },
abstract = {Mucosal tissues are constantly exposed to the outside environment. They receive signals from the commensal microbiome and tissue-specific triggers including alimentary and airborne elements and are tasked to maintain balance in the absence of inflammation and infection. Here, we present neutrophils as sentinel cells in mucosal immunity. We discuss the roles of neutrophils in mucosal homeostasis and overview clinical susceptibilities in patients with neutrophil defects. Finally, we present concepts related to specification of neutrophil responses within specific mucosal tissue microenvironments.},
}
@article {pmid36404584,
year = {2022},
author = {de Cock, M and Fonville, M and de Vries, A and Bossers, A and van den Bogert, B and Hakze-van der Honing, R and Koets, A and Sprong, H and van der Poel, W and Maas, M},
title = {Screen the unforeseen: Microbiome-profiling for detection of zoonotic pathogens in wild rats.},
journal = {Transboundary and emerging diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/tbed.14759},
pmid = {36404584},
issn = {1865-1682},
abstract = {Wild rats can host various zoonotic pathogens. Detection of these pathogens is commonly performed using molecular techniques targeting one or a few specific pathogens. However, this specific way of surveillance could lead to (emerging) zoonotic pathogens staying unnoticed. This problem may be overcome by using broader microbiome-profiling techniques, which enable broad screening of a sample's bacterial or viral composition. In this study, we investigated if 16S rRNA gene amplicon sequencing would be a suitable tool for detection of zoonotic bacteria in wild rats. Also, we used virome-enriched (VirCapSeq) sequencing to detect zoonotic viruses. DNA from kidney samples of 147 wild brown rats (Rattus norvegicus) and 42 black rats (Rattus rattus) was used for 16S rRNA gene amplicon sequencing of the V3-V4 hypervariable region. Blocking primers were developed to reduce amplification of rat host DNA. The kidney bacterial composition was studied using alpha- and beta-diversity metrics and statistically assessed using PERMANOVA and SIMPER analyses. From the sequencing data, 14 potentially zoonotic bacterial genera were identified from which the presence of zoonotic Leptospira spp. and Bartonella tribocorum was confirmed by (q)PCR or Sanger sequencing. In addition, more than 65% of all samples were dominated (>50% reads) by one of three bacterial taxa: Streptococcus (n = 59), Mycoplasma (n = 39) and Leptospira (n = 25). These taxa also showed the highest contribution to the observed differences in beta-diversity. VirCapSeq sequencing in rat liver samples detected the potentially zoonotic rat hepatitis E virus in three rats. Although 16S rRNA gene amplicon sequencing was limited in its capacity for species level identifications and can be more difficult to interpret due to the influence of contaminating sequences in these low microbial biomass samples, we believe it has potential to be a suitable pre-screening method in the future to get a better overview of potentially zoonotic bacteria that are circulating in wildlife. This article is protected by copyright. All rights reserved.},
}
@article {pmid36404545,
year = {2022},
author = {Liu, S and Dashper, SG and Zhao, R},
title = {Association Between Oral Bacteria and Alzheimer's Disease: A Systematic Review and Meta-Analysis.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {},
doi = {10.3233/JAD-220627},
pmid = {36404545},
issn = {1875-8908},
abstract = {BACKGROUND: Pre-clinical evidence implicates oral bacteria in the pathogenesis of Alzheimer's disease (AD), while clinical studies show diverse results.<br><br>OBJECTIVE: To comprehensively assess the association between oral bacteria and AD with clinical evidence.<br><br>METHODS: Studies investigating the association between oral bacteria and AD were identified through a systematic search of six databases PubMed, Embase, Cochrane Central Library, Scopus, ScienceDirect, and Web of Science. Methodological quality ratings of the included studies were performed. A best evidence synthesis was employed to integrate the results. When applicable, a meta-analysis was conducted using a random-effect model.<br><br>RESULTS: Of the 16 studies included, ten investigated periodontal pathobionts and six were microbiome-wide association studies. Samples from the brain, serum, and oral cavity were tested. We found over a ten-fold and six-fold increased risk of AD when there were oral bacteria (OR = 10.68 95% CI: 4.48-25.43; p < 0.00001, I2 = 0%) and Porphyromonas gingivalis (OR = 6.84 95% CI: 2.70-17.31; p < 0.0001, I2 = 0%) respectively in the brain. While AD patients exhibited lower alpha diversity of oral microbiota than healthy controls, the findings of bacterial communities were inconsistent among studies. The best evidence synthesis suggested a moderate level of evidence for an overall association between oral bacteria and AD and for oral bacteria being a risk factor for AD.<br><br>CONCLUSION: Current evidence moderately supports the association between oral bacteria and AD, while the association was strong when oral bacteria were detectable in the brain. Further evidence is needed to clarify the interrelationship between both individual species and bacterial communities and the development of AD.},
}
@article {pmid36404489,
year = {2022},
author = {Loganathan, T and Priya Doss C, G},
title = {The influence of machine learning technologies in gut microbiome research and cancer studies - A review.},
journal = {Life sciences},
volume = {311},
number = {Pt A},
pages = {121118},
doi = {10.1016/j.lfs.2022.121118},
pmid = {36404489},
issn = {1879-0631},
abstract = {Gut microbial profiles induce cancer growth and impact treatment effectiveness, tolerance, and safety. There is still more to discover about the relationship between diseases and the microbiota and its clinical consequences. Even though much of the study is still in its early phases, the 'omics' technologies were widely used for microbiome analysis due to the increased size of datasets available in public databases. However, recognizing the potential of these new technologies is difficult at times, limiting our ability to analyze a vast amount of available data critically. In this context, two subsets of AI methods, Machine Learning (ML) and Deep Learning (DL), can aid clinicians in analyzing and comprehending these large datasets. Here, we reviewed the most up-to-date ML methodologies, databases, and tools used in human microbiome research. The proposed review forecast the use of ML in microbiome research involving associations and clinical applications for diagnostics, prognostics, and therapies.},
}
@article {pmid36404456,
year = {2022},
author = {Schill, EM and Floyd, AN and Newberry, RD},
title = {Neonatal development of intestinal neuroimmune interactions.},
journal = {Trends in neurosciences},
volume = {45},
number = {12},
pages = {928-941},
doi = {10.1016/j.tins.2022.10.002},
pmid = {36404456},
issn = {1878-108X},
abstract = {Interactions between the enteric nervous system (ENS), immune system, and gut microbiota regulate intestinal homeostasis in adults, but their development and role(s) in early life are relatively underexplored. In early life, these interactions are dynamic, because the mucosal immune system, microbiota, and the ENS are developing and influencing each other. Moreover, disrupting gut microbiota and gut immune system development, and potentially ENS development, by early-life antibiotic exposure increases the risk of diseases affecting the gut. Here, we review the development of the ENS and immune/epithelial cells, and identify potential critical periods for their interactions and development. We also highlight knowledge gaps that, when addressed, may help promote intestinal homeostasis, including in the settings of early-life antibiotic exposure.},
}
@article {pmid36403817,
year = {2022},
author = {Juthi, RT and Sazed, SA and Sarmin, M and Haque, R and Alam, MS},
title = {COVID-19 and Diarrhea: Putative Mechanisms and Management.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijid.2022.11.018},
pmid = {36403817},
issn = {1878-3511},
abstract = {BACKGROUND: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19), has recently posed a threat to global health by spreading at a high rate and taking millions of lives worldwide. Along with the respiratory symptoms, there are gastrointestinal manifestations and one of the most common gastrointestinal symptoms is diarrhea which is seen in a significant percentage of COVID-19 patients.<br><br>LITERATURE REVIEW: Several studies have shown the plausible correlation between overexpressed angiotensin converting enzyme 2 (ACE2) in enterocytes and SARS-CoV-2, as ACE2 is the only known receptor for the virus entry. Along with the dysregulated ACE2, there are other contributing factors such as gut microbiome dysbiosis, adverse effects of antiviral and antibiotics for treating infections and inflammatory response to SARS-CoV-2 which bring about increased permeability of gut cells and subsequent occurrence of diarrhea. Few studies found that the SARS-CoV-2 is capable of damaging liver cells too. No single effective treatment option is available.<br><br>LIMITATIONS: Confirmed pathophysiology is still unavailable. Studies regarding global population are also insufficient.<br><br>CONCLUSION: In this review, based on the previous works and literature, we summarized the putative molecular pathophysiology of COVID-19 associated diarrhea, concomitant complications and the standard practices of management of diarrhea and hepatic manifestations in international setups.},
}
@article {pmid36403657,
year = {2022},
author = {Soumana, IH and Ryu, MH and Studart, F and Yang, J and Orach, J and Nislow, C and Leung, JM and Rider, CF and Carlsten, C},
title = {Exposure to diesel exhaust alters the functional metagenomic composition of the airway microbiome in former smokers.},
journal = {Environmental research},
volume = {},
number = {},
pages = {114826},
doi = {10.1016/j.envres.2022.114826},
pmid = {36403657},
issn = {1096-0953},
abstract = {The lung microbiome plays a crucial role in airway homeostasis, yet we know little about the effects of exposures such as air pollution therein. We conducted a controlled human exposure study to assess the impact of diesel exhaust (DE) on the human airway microbiome. Twenty-four participants (former smokers with mild to moderate COPD (N = 9), healthy former smokers (N = 7), and control healthy never smokers (N = 8)) were exposed to DE (300 μg/m[3] PM2.5) and filtered air (FA) for 2 h in a randomized order, separated by a 4-week washout. Endobronchial brushing samples were collected 24 h post-exposure and sequenced for the 16S microbiome, which was analyzed using QIIME2 and PICRUSt2 to examine diversity and metabolic functions, respectively. DE exposure altered airway microbiome metabolic functions in spite of statistically stable microbiome diversity. Affected functions included increases in: superpathway of purine deoxyribonucleosides degradation (pathway differential abundance 743.9, CI 95% 201.2 to 1286.6), thiazole biosynthesis I (668.5, CI 95% 139.9 to 1197.06), and L-lysine biosynthesis II (666.5, CI 95% 73.3 to 1257.7). There was an exposure-by-age effect, such that menaquinone biosynthesis superpathways were the most enriched function in the microbiome of participants aged >60, irrespective of smoking or health status. Moreover, exposure-by-phenotype analysis showed metabolic alterations in former smokers after DE exposure. These observations suggest that DE exposure induced substantial changes in the metabolic functions of the airway microbiome despite the absence of diversity changes.},
}
@article {pmid36403411,
year = {2022},
author = {He, R and Peng, C and Jiang, L and Han, H and Chu, YX and Wang, J and Liu, CY and Zhao, N},
title = {Characteristic pollutants and microbial community in underlying soils for evaluating landfill leakage.},
journal = {Waste management (New York, N.Y.)},
volume = {155},
number = {},
pages = {269-280},
doi = {10.1016/j.wasman.2022.11.015},
pmid = {36403411},
issn = {1879-2456},
abstract = {Leachate leakage poses a serious environmental risk to the safety of surrounding soils and groundwater. A much faster approach to reflect landfill leakage is the premise to mitigate the ecological risk of landfills. In this study, two landfills (BJ and WZ) were selected to investigate the leaching characteristics of various pollutants along the vadose soil depths. The physiochemical properties of underlying soils including NO3[-]-N, NO2[-]-N, NH4[+]-N, OM, TN, EC and Cl[-] exhibited a typical leaching dynamic along the depths. Among them, TN, NH4[+]-N, OM, NO3[-]-N, and EC might be used as characteristic pollutants to evaluate the leachate leakage issues in landfilled sites. The genera Thiopseudomonas, Acinetobacter, Pseudomonas, and Hydrogenispora dominated in underlying soils. Compared to BJ samples, a more diverse and active microbiome capable of carbon and nitrogen cycles was observed in WZ samples, which was mainly ascribed to nutrients and elements contained in different types of soils. Among the environmental factors, nitrogenous compounds, SO4[2-], pH and EC had significant effects on the microbial community structures in the underlying soils. The relative abundances of Hydrogenispora and Caldicoprobacter might be used as characteristic microorganisms to evaluate the leachate leakage issues in landfilled sites. These results provided a deep insight into effects of leachate leakage in underlying soils, especially the pollutants vertical distribution and the corresponding microbial community structures.},
}
@article {pmid36403347,
year = {2022},
author = {Xia, F and Guo, L and Cui, P and Xu, Q and Huang, J and Zhou, H and Shen, W},
title = {A sensitive and accurate GC-MS method for analyzing microbial metabolites short chain fatty acids and their hydroxylated derivatives in newborn fecal samples.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {223},
number = {},
pages = {115148},
doi = {10.1016/j.jpba.2022.115148},
pmid = {36403347},
issn = {1873-264X},
abstract = {Short chain fatty acids (SCFAs), crucial intestinal bacterial metabolites, have been widely accepted as potential diagnostic markers in neonatal medicine. Nevertheless, it is still a great challenge to accurately quantify SCFAs in newborn fecal samples due to the huge variation of water content, limited commercial isotope-labeled internal standards and poor sensitivity. In this study, Na2CO3 solution (50 μg/mL) was applied to convert the free SCFAs to SCFA sodium salts, which could prevent the loss of violate SCFAs during lyophilization process. Furthermore, N-methylbenzylamine-d0/d3 was applied as the chemical derivatization regent to enhance the sensitivity and accuracy. Based on this method, the SCFA contents in meconium and neonatal fecal samples were analyzed to illustrate the change of SCFAs during the gut microbiome development. Chemical derivatization based on N-methylbenzylamine-d0/d3 could not only significantly promote the sensitivity (323-1280 folds compared to free SCFAs) by promoting the ionization efficiency, but also provide one-to-one isotope internal standards. Moreover, 7 SCFAs, including acetic acid (2), n-butyric acid (4), isobutyric acid (5), 2-hydroxybutyric acid (11), 2-hydroxy-3-methylbutyric acid (13), 3-hydroxybutyric acid (14), 2-hydroxy-2-methylbutyric acid (17) were found to be significantly increased in neonatal fecal samples compared to the meconium fecal samples. All these results proved that this method could be applied for SCFA analysis in newborn fecal samples with perfect accuracy and sensitivity.},
}
@article {pmid36403170,
year = {2022},
author = {Sindhu, SS and Sehrawat, A and Glick, BR},
title = {The involvement of organic acids in soil fertility, plant health and environment sustainability.},
journal = {Archives of microbiology},
volume = {204},
number = {12},
pages = {720},
pmid = {36403170},
issn = {1432-072X},
abstract = {Increasing demand for safe food by an ever-growing human population emphasizes the urgency for increasing crop yields and reducing the losses caused by abiotic and biotic stresses; a partial solution to this problem is to develop a better understanding of plant-microbe interactions. Plant roots continuously release a wide range of compounds including organic acids in root exudates. These root exudates stimulate growth of specific microbial communities in the rhizosphere, which affect complex biological and physico-chemical interactions occurring between plant roots and the surrounding soil environment. In addition, organic acids are also released by different microbes and during decomposition of organic matter and plant residues in the soil. Interestingly, the available organic acids in the rhizosphere play crucial roles in various physio-chemical processes including the chemoattraction of microbes (both beneficial and pathogenic), mineralization and solubilization of complex minerals (P, K and Zn), biocontrol of phytopathogens, induction of systemic resistance, biogas formation, mitigation of abiotic stresses and, detoxification of metals and residual pesticides. Thus, organic acids play a significant role in the sustainable management of the soil ecosystem and in environmental sustainability. This review discusses the role of organic acids in the stimulation or enrichment of specific root-associated microbial communities and their effect on plant-microbe interactions at the root surface. In addition, the potential for root microbiome modification to enhance nutrient cycling and nutrient acquisition, and in amelioration of environmental stresses for increasing food production is discussed.},
}
@article {pmid36403054,
year = {2022},
author = {Li, W and Wang, B and Tan, M and Song, X and Xie, S and Wang, C},
title = {Analysis of sputum microbial metagenome in COPD based on exacerbation frequency and lung function: a case control study.},
journal = {Respiratory research},
volume = {23},
number = {1},
pages = {321},
pmid = {36403054},
issn = {1465-993X},
support = {18410720900//Shanghai Science and Technology/ ; 18410720900//Shanghai Science and Technology/ ; 18410720900//Shanghai Science and Technology/ ; 18410720900//Shanghai Science and Technology/ ; 18410720900//Shanghai Science and Technology/ ; 18410720900//Shanghai Science and Technology/ ; },
abstract = {BACKGROUND: The role of the sputum microbiome in chronic obstructive pulmonary disease (COPD) progression remains elusive. As the advent of the new culture-independent microbial sequencing technique makes it possible to disclose the complex microbiome community of the respiratory tract. The aim of this study was to use metagenomic next-generation sequencing (mNGS) to confirm whether there are differences in sputum microbiome of COPD between different exacerbation frequencies and lung function.<br><br>METHODS: Thirty-nine COPD patients were divided into a frequent exacerbators (FE) group (n = 20) and a non-frequent exacerbators (NFE) (n = 19) group according to their exacerbation history, or a mild group (FEV1/pre ≥ 50%, n = 20) and a severe group (FEV1/pre < 50%, n = 19) according to the lung function. Sputum was collected during their stable phase, followed by DNA extraction, untargeted metagenomic next-generation sequencing (mNGS) and bioinformatic analysis.<br><br>RESULTS: mNGS identified 3355 bacteria, 71 viruses and 22 fungi at the specie level. It was found that Shannon index and Simpson index in FE group was lower than that in NFE group (p = 0.005, 0.008, respectively) but similar between mild and severe groups. Out of top 10 bacteria taxa, Veillonella, Fusobacterium and Prevotella jejuni had a higher abundance in NFE group, Rothia had a higher abundance in mild group. Linear discriminant analysis revealed that many bacterial taxa were more abundant in NFE group, and they mostly belonged to Actinobacteria, Bacteroidetes and Fusobacteria phyla. Frequency of exacerbations was also found to be negatively correlated with alpha diversity (with Shannon index, r = - 0.423, p = 0.009; with Simpson index, r = - 0.482, p = 0.002). No significant correlation was observed between alpha diversity and FEV1/pre.<br><br>CONCLUSIONS: Microbiome diversity in FE group was lower than that in NFE group. There was a significant difference in microbiome taxa abundance between FE and NFE groups, or mild and severe groups. These findings demonstrated that sputum microbiome community dysbiosis was associated with different exacerbation frequencies and lung function in stable COPD.},
}
@article {pmid36403022,
year = {2022},
author = {Wang, WW and Mao, B and Liu, Y and Gu, SY and Lu, HW and Bai, JW and Liang, S and Yang, JW and Li, JX and Su, X and Hu, HY and Wang, C and Xu, JF},
title = {Altered fecal microbiome and metabolome in adult patients with non-cystic fibrosis bronchiectasis.},
journal = {Respiratory research},
volume = {23},
number = {1},
pages = {317},
pmid = {36403022},
issn = {1465-993X},
support = {81925001//National Natural Science Fund for Distinguished Young Scholar/ ; 2016036//Shanghai Leading Talent Program/ ; },
abstract = {BACKGROUND: Emerging experimental and epidemiological evidence highlights a crucial cross-talk between the intestinal flora and the lungs, termed the "gut-lung axis". However, the function of the gut microbiota in bronchiectasis remains undefined. In this study, we aimed to perform a multi-omics-based approach to identify the gut microbiome and metabolic profiles in patients with bronchiectasis.<br><br>METHODS: Fecal samples collected from non-CF bronchiectasis patients (BE group, n = 61) and healthy volunteers (HC group, n = 37) were analyzed by 16 S ribosomal RNA (rRNA) sequencing. The BE group was divided into two groups based on their clinical status: acute exacerbation (AE group, n = 31) and stable phase (SP group, n = 30). Further, metabolome (lipid chromatography-mass spectrometry, LC-MS) analyses were conducted in randomly selected patients (n = 29) and healthy volunteers (n = 31).<br><br>RESULTS: Decreased fecal microbial diversity and differential microbial and metabolic compositions were observed in bronchiectasis patients. Correlation analyses indicated associations between the differential genera and clinical parameters such as bronchiectasis severity index (BSI). Disease-associated gut microbiota was screened out, with eight genera exhibited high accuracy in distinguishing SP patients from HCs in the discovery cohort and validation cohort using a random forest model. Further correlation networks were applied to illustrate the relations connecting disease-associated genera and metabolites.<br><br>CONCLUSION: The study uncovered the relationships among the decreased fecal microbial diversity, differential microbial and metabolic compositions in bronchiectasis patients by performing a multi-omics-based approach. It is the first study to characterize the gut microbiome and metabolome in bronchiectasis, and to uncover the gut microbiota's potentiality as biomarkers for bronchiectasis.<br><br>TRIAL REGISTRATION: This study is registered with ClinicalTrials.gov, number NCT04490447.},
}
@article {pmid36402713,
year = {2022},
author = {Hrbáček, J and Tláskal, V and Čermák, P and Hanáček, V and Zachoval, R},
title = {Bladder cancer is associated with decreased urinary microbiota diversity and alterations in microbial community composition.},
journal = {Urologic oncology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.urolonc.2022.09.018},
pmid = {36402713},
issn = {1873-2496},
abstract = {INTRODUCTION: Human urine microbiota (UM) research has uncovered associations between composition of microbial communities of the lower urinary tract and various disease states including several reports on the putative link between UM and bladder cancer (BC). The aim of this study was to investigate male UM in patients with BC and controls using catheterised urine specimens unlike in previous studies.<br><br>METHODS: Urine samples were obtained in theatre after surgical prepping and draping using aseptic catheterisation. DNA was extracted and hypervariable region V4 of the 16S rRNA gene was amplified using 515F and 806R primers. Sequencing was performed on Illumina MiSeq platform. Sequencing data were processed using appropriate software tools. Alpha diversity measures were calculated and compared between groups. Prevalence Interval for Microbiome Evaluation was used to test differences in beta diversity.<br><br>RESULTS: A total of 63 samples were included in the analysis. Mean age of study subjects was 65.1 years (SD 12.5). Thirty-four men had bladder cancer and 29 participants were undergoing interventions for benign conditions (benign prostate hyperplasia or upper urinary tract stone disease). BC patients had lower UM richness and diversity than controls (83 vs. 139 operational taxonomic units, P = 0.015; Shannon index: 2.46 vs. 2.94, P = 0.049). There were specific taxa enriched in cancer (Veillonella, Varibaculum, Methylobacterium-Methylorubrum) and control groups (Pasteurella, Corynebacterium, Acinetobacter), respectively.<br><br>CONCLUSION: BC patients had lower bladder microbiota richness and diversity than controls. Specific genera were enriched in cancer and control groups, respectively. These results corroborate some of previous reports while contradicting others. Future microbiota research would benefit from parallel transcriptomic/metabolomic analysis.},
}
@article {pmid36402501,
year = {2023},
author = {Spivak, NM and Haroon, J and Swenson, A and Turnbull, SA and Dang, N and Ganeles, M and Price, C and Distler, M and Nurmi, E and Lavretsky, H and Bystritsky, A},
title = {Microbiome in Anxiety and Other Psychiatric Disorders.},
journal = {The Medical clinics of North America},
volume = {107},
number = {1},
pages = {73-83},
doi = {10.1016/j.mcna.2022.08.010},
pmid = {36402501},
issn = {1557-9859},
abstract = {Initial studies suggested that the fluctuations in the quantity, variety, and composition of the gut microbiota can significantly affect disease processes. This change in the gut microbiota causing negative health benefits was coined dysbiosis. Initial research focused on gastrointestinal illnesses. However, the gut microbiome was found to affect more than just gastrointestinal diseases. Numerous studies have proven that the gut microbiome can influence neuropsychiatric diseases such as Parkinson's disease, Alzheimer's disease, and multiple sclerosis.},
}
@article {pmid36402387,
year = {2022},
author = {Zhang, H and Zhang, Y and Mu, T and Cao, J and Liu, X and Yang, X and Ren, D and Zhao, K},
title = {Response of gut microbiota and ileal transcriptome to inulin intervention in HFD induced obese mice.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijbiomac.2022.11.151},
pmid = {36402387},
issn = {1879-0003},
abstract = {Inulin, as a dietary fiber, exerted prominent anti-obesity effects by modulating gut microbiota. However, the possible relationship and interplay of gut microbiome and function of distal intestine is still unclear now. This study aimed to investigate the possible targets of microbes and the related intestinal genes mediated by inulin. C57 BL/6 male mice were randomly allocated to chow diet (Chow) group, high-fat diet (HFD) group, and HFD supplemented with 3 % inulin (Inulin) group. Compared with HFD treatment, inulin supplementation significantly decreased the body weight, fat deposition, and fasting blood glucose level. In addition, mice treated with inulin had a remarkable alteration in the structure of cecal microbiota and transcriptomic profiling of ileum. In particular, inulin supplementation significantly reversed the HFD induced expression of Bacteroides, Allobaculum and nonrank_f_Bacteroidates_S24-7_group, and reversed the expression of genes belonging to phospholipase A2 (PLA2) family and cytochrome P450 (CYP450) family. In summary, inulin might alleviate HFD-induced fat deposition and metabolic disorders via regulating lipid metabolism of ileum, while the interaction between the sPLA2s and gut microbes might play important roles in the process.},
}
@article {pmid36402341,
year = {2022},
author = {Yang, Y and Chai, Y and Xie, H and Zhang, L and Zhang, Z and Yang, X and Hao, S and Gai, J and Chen, Y},
title = {Responses of soil microbial diversity, network complexity and multifunctionality to three land-use changes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {160255},
doi = {10.1016/j.scitotenv.2022.160255},
pmid = {36402341},
issn = {1879-1026},
abstract = {Land-use change is one of the greatest challenges for natural ecosystem services. Soil microbiomes are essential for modulating multiple ecosystem functions. However, little is known about the impact of land-use changes on soil microbial communities and their associated soil functions. In this study, 150 alpine soil samples representing conversion of forests to shrublands or grasslands, and of shrublands to grasslands were investigated for bacterial, fungal and protistan community diversity, co-occurrence network, as well as their relationships with soil multifunctionality via a sampling strategy of space-for-time substitution. The conversion of forest to grassland increased the diversity of fungi and bacteria, and altered the microbial community structures of bacteria, fungi and protists, resulting a greater impact on soil microbiome than other land-use conversions. Cross-trophic interaction analyses demonstrated this conversion increased microbial network complexity and robustness, whereas forest to shrubland had the opposite trend. The land-use induced changes in soil multifunctionality were related with microbial network modules, but were not always associated with variations of microbial diversity. Random forest modeling further suggested the significant role of microbial modules in explaining soil multifunctionality, together with environmental factors. These findings indicate divergent responses of belowground multitrophic organisms to land-use changes, and the potential role of microbial module in forecasting soil multifunctionality.},
}
@article {pmid36402257,
year = {2022},
author = {Roy, H and Bescos, R and McColl, E and Rehman, U and Cray, E and Belfield, LA and Nweze, KD and Tsang, K and Singleton, W and Whitfield, P and Brookes, Z},
title = {Oral microbes and the formation of cerebral abscesses: a single-centre retrospective study.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {104366},
doi = {10.1016/j.jdent.2022.104366},
pmid = {36402257},
issn = {1879-176X},
abstract = {OBJECTIVE: Intracranial abscesses are relatively uncommon, but can result in significant mortality and morbidity. Whilst many potential causes of brain abscesses are recognised, in many cases the origin of infection remains clinically unidentified. Our objective was to investigate the role of bacteria found in the oral cavity in the development of brain abscesses.<br><br>METHODS: A retrospective analysis was performed using data from 87 patients admitted to a single UK neurosurgical unit with brain abscesses over a 16-year period. Using microbiological data obtained from abscess sampling and peripheral cultures, species of bacteria were categorised in patients where no primary source of infection was identified (NSI) for their brain abscess (n=52), or where an infective source (ISI) was identified. The microbiological data was then screened to identify common oral bacteria in each group.<br><br>RESULTS: Brain abscesses from the ISI group (n=35) demonstrated a significantly lower preponderance of oral bacteria (n=8), than the NSI group (n=29) (p<0.05). Brain abscesses from the NSI group also had significantly higher counts of Streptococcus Anginosus compared to ISI (p<0.05), with brain abscesses being most common in the frontal and parietal lobes for both ISI and NSI.<br><br>CONCLUSIONS: These findings suggest that the oral cavity could be considered as a source of occult infection in cases of brain abscess where no clear cause has been identified. Future studies should include oral screening and microbiome analysis to better understand the mechanisms involved and develop approaches for prevention.<br><br>Oral bacteria may be an under-recognised cause of brain abscesses. Careful review of oral health in brain abscess patients may help establish causation, particularly in patients with no cause for their abscess identified. Good levels of oral health may help prevent the development of brain abscesses in some individuals.},
}
@article {pmid36402032,
year = {2022},
author = {Li, Q and Xue, X and Qi, S and Zhao, L and Zhang, W and Fan, M and Wu, L and Wang, M},
title = {Disinfectant dodecyl dimethyl benzyl ammonium chloride (DDBAC) disrupts gut microbiota, phospholipids, and calcium signaling in honeybees (Apis mellifera) at an environmentally relevant level.},
journal = {Environment international},
volume = {170},
number = {},
pages = {107639},
doi = {10.1016/j.envint.2022.107639},
pmid = {36402032},
issn = {1873-6750},
abstract = {One of the impacts of the Coronavirus disease 2019 (COVID-19) pandemic has been a profound increase in the application amounts of disinfectants. Dodecyl dimethyl benzyl ammonium chloride (DDBAC) is a widely used disinfectant, yet its hazards to non-target species remain largely unknown. We are unaware of any studies assessing DDBAC's impacts on honeybee, a pollinator species that is a useful indicator of environmental pollution essential for many forms of agricultural production. Here, we assessed the potentially negative effects of DDBAC on honeybees. After conducting a formal toxicity evaluation of DDBAC on honeybee mortality, we detected an accumulation of DDBAC in the honeybee midgut. We subsequently studied the midgut tissues of honeybees exposed to sub-lethal concentrations of DDBAC: histopathological examination revealed damage to midgut tissue upon DDBAC exposure, microbiome analysis showed a decreased abundance of beneficial midgut microbiota, lipidomics analysis revealed a significant reduction in cell membrane phospholipids with known functions in signal transduction, and a transcriptome analysis detected altered expression of genes involved in calcium signaling pathways (that variously function in calcium absorption, muscle contraction, and neurotransmission). Thus, our study establishes that DDBAC impacts honeybee midgut functions at multiple levels. Our study represents an early warning about the hazards of DDBAC and appeals for the proper stewardship of DDBAC to ensure the protection of our ecological environment.},
}
@article {pmid36402008,
year = {2022},
author = {Li, X and Xue, Q and Ma, H and Champagne, CM and Bray, GA and Sacks, FM and Qi, L},
title = {Genetically determined gut microbial abundance and 2-year changes in central adiposity and body composition: The POUNDS lost trial.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {41},
number = {12},
pages = {2817-2824},
doi = {10.1016/j.clnu.2022.11.002},
pmid = {36402008},
issn = {1532-1983},
abstract = {BACKGROUND AND AIM: Growing evidence has linked gut microbiota with regulation of adiposity. We aimed to examine whether the genetically determined relative abundance of gut microbial taxa was associated with long-term changes in adiposity and body composition among individuals who were overweight or obese in weight-loss diet interventions.<br><br>METHODS: The study included 692 participants with overweight or obese from the POUNDS Lost trial. We created a genetic risk score (GRS) for the relevant abundance of gut microbial taxa using 20 single nucleotide polymorphisms identified from a recent genome-wide association study. Body composition was assessed using dual-energy X-ray absorptiometry.<br><br>RESULTS: Higher GRS for the relative abundance of gut microbial taxa was significantly associated with greater reductions in waist circumference, total fat mass (FM), whole-body total percentage of fat mass (FM%), and percentage of trunk fat (TF%) at 2 years (p = 0.022, 0.034, 0.023, 0.023, respectively). In addition, dietary protein significantly modified the association between GRS for gut microbial abundance and changes in total FM, FM%, and TF% (p-interactions = 0.04, 0.013, and 0.006, respectively) at 6-month, when the maximum weight loss was achieved, even though such interactions were attenuated at 2 years. In the average-protein diet group, a higher microbial abundance GRS was associated with greater reductions in total FM (p = 0.007), FM% (p = 0.002), and TF% (p < 0.001) at 6 months, while no associations were found in the high-protein diet group (p > 0.05).<br><br>CONCLUSION: Our results suggest that the higher genetically determined relative abundance of gut microbial taxa may be related to long-term improvement of whole-body and central fatness and body composition in response to low-calorie diet interventions.},
}
@article {pmid36401835,
year = {2022},
author = {Rampanelli, E and Nieuwdorp, M},
title = {Gut microbiome in type 1 diabetes: the immunological perspective.},
journal = {Expert review of clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1080/1744666X.2023.2150612},
pmid = {36401835},
issn = {1744-8409},
abstract = {INTRODUCTION: Type 1 diabetes (T1D) is a prevalent, and yet uncurable, autoimmune disease targeting insulin-producing pancreatic β-cells. Despite a known genetic component in T1D onset, genetics alone cannot explain the alarming worldwide rise in T1D incidence, which is attributed to a growing impact of environmental factors, including perturbations of the gut microbiome.<br><br>AREAS COVERED: Intestinal commensal bacteria plays a crucial role in host physiology in health and disease by regulating endocrine and immune functions. An aberrant gut microbiome structure and metabolic function have been documented prior and during T1D onset. In this review, we summarize and discuss the current studies depicting the taxonomic profile and role of the gut microbial communities in murine models of T1D, diabetic patients and human interventional trials.<br><br>EXPERT OPINION: Compelling evidence have shown that the intestinal microbiota is instrumental in driving differentiation and functions of immune cells. Therefore any alterations in the intestinal microbiome composition or microbial metabolite production, particularly early in life, may impact disease susceptibility and amplify inflammatory responses and hence accelerate the course of T1D pathogenesis.},
}
@article {pmid36401687,
year = {2022},
author = {Jacinto-Castillo, DF and Canto, A and Medina-Medina, LA and O'Connor-Sánchez, A},
title = {Living in honey: bacterial and fungal communities in honey of sympatric populations of Apis mellifera and the stingless bee Melipona beecheii, in Yucatan, Mexico.},
journal = {Archives of microbiology},
volume = {204},
number = {12},
pages = {718},
pmid = {36401687},
issn = {1432-072X},
support = {734531//Consejo Nacional de Ciencia y Tecnología/ ; INFR 2016 01 269833//Consejo Nacional de Ciencia y Tecnología/ ; },
abstract = {Bacterial and fungal communities in the honey of sympatric populations of the bee species Apis mellifera and Melipona beecheii were profiled by amplicon sequencing of the 16S gene and the ITS of the ribosomal DNA. Results showed that the structure of the honey microbiota of these two bee species was very different from each other. Both the bacterial and fungal species in A. mellifera honey were more similar to those of A. mellifera honey reported for other parts of the world than to those in M. beecheii honey. Nevertheless, in both, the most abundant bacterial species belonged to the family Lactobacillaeae.},
}
@article {pmid36401664,
year = {2022},
author = {Hasuda, H and Ikeda, T and Makizaki, Y and Yokota, H and Tanaka, Y and Ohno, H and Shimokawa, M and Matsuoka, H and Kimura, Y and Oki, E and Yoshizumi, T},
title = {Alterations in the gut microbiome in patients with esophageal carcinoma in response to esophagectomy and neoadjuvant treatment.},
journal = {Surgery today},
volume = {},
number = {},
pages = {},
pmid = {36401664},
issn = {1436-2813},
support = {KAKENHI / JP20K09035//Japan Society for the Promotion of Science/ ; },
abstract = {PURPOSE: Analyzing the gut microbiome is essential for planning treatment strategies to manage esophageal squamous cell carcinoma. This study aimed to characterize the gut microbiome of patients with esophageal squamous cell carcinoma and to identify alterations in its composition during treatment.<br><br>METHODS: We observed alterations in the gut microbiome in 21 consecutive patients with esophageal squamous cell carcinoma at five different time points, from neoadjuvant treatment to postoperative surgery. Ten healthy individuals were used as a non-cancer control group. Fecal samples were collected and analyzed using 16S ribosomal ribonucleic acid sequencing.<br><br>RESULTS: Before treatment, participants with esophageal squamous cell carcinoma had different alpha and beta diversity in comparison to healthy controls. The number of Streptococcus, a facultative anaerobic bacterium, was significantly higher, whereas that of Faecalibacterium, an obligate anaerobic bacterium, was significantly lower. Both alpha and beta diversity remained unchanged during neoadjuvant treatment, but the alterations were pronounced after surgery. The increase in the relative abundance of Streptococcus and the decrease in that of Faecalibacterium also tended to be more pronounced after surgery.<br><br>CONCLUSIONS: The gut microbiome in patients with esophageal squamous cell carcinoma is altered with surgical intervention.},
}
@article {pmid36401290,
year = {2022},
author = {Ramsay, TG and Arfken, AM and Summers, KL},
title = {Enteroendocrine peptides, growth, and the microbiome during the porcine weaning transition.},
journal = {Animal microbiome},
volume = {4},
number = {1},
pages = {56},
pmid = {36401290},
issn = {2524-4671},
abstract = {BACKGROUND: Growth rate in pigs can be affected by numerous factors that also affect feeding behavior and the microbiome. Recent studies report some communication between the microbiome and the enteroendocrine system. The present study examined if changes in the piglet microbiome between birth and during the weaning transition can be correlated either positively or negatively with growth rate and plasma concentrations of enteroendocrine peptides.<br><br>RESULTS: During the post-weaning transition, a 49% reduction in average daily gain was observed at day 24 (P < 0.05) relative to day 21. Pigs recovered by day 28 with body weight and average daily gain increases of 17% and 175%, respectively relative to day 24 and the highest rate of gain was measured at day 35 (462 g/day). The time interval between day 21-24 had the highest number of correlations (n = 25) between the relative abundance differences in taxa over time and corresponding percent weight gain. Amplicon sequence variants with the greatest correlation with percent weight gain between day 21-24 belonged to families Prevotellaceae NK3B31 (ρ = 0.65, P < 0.001), Veillonellaceae (ρ = 0.63, P < 0.001) and Rikenellaceae RC9 (ρ = 0.62, P < 0.001). Seven taxa were positively correlated with percent weight gain between day 24-28. Eight taxa were positively correlated with percent weight gain between day 28-35, of which four were Clostridia. Only Lactobacillus reuteri was positively correlated across both day 24-28 and day 28-35 analyses. Insulin-like growth factor 1 (IGF-1; R2 = 0.61, P < 0.001), glucose-dependent insulinotropic polypeptide (GIP; R2 = 0.20, P < 0.001), glucagon-like peptide 1 (GLP-1; R2 = 0.51, P < 0.001), and glucagon-like peptide 2 (GLP-2; R2 = 0.21, P < 0.001) were significantly associated with the piglet fecal community NMDS, while serotonin showed no significant association (R2 = 0.03, P = 0.15). Higher concentrations of GLP-1 and GLP-2 characterized day 1 fecal communities, while GIP levels had the strongest relationship primarily with samples ordinated with the day 21 cluster.<br><br>CONCLUSIONS: Demonstration of an association of certain taxa with individual gut peptides at specific ages suggests the potential for the microbiome to elicit changes in the gut enteroendocrine system during early postnatal development in the pig.},
}
@article {pmid36401288,
year = {2022},
author = {Smith, RH and Glendinning, L and Walker, AW and Watson, M},
title = {Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome.},
journal = {Animal microbiome},
volume = {4},
number = {1},
pages = {57},
pmid = {36401288},
issn = {2524-4671},
support = {BB/M010996/1//EASTBIO (East of Scotland Bioscience Doctoral Training Partnership DTP, funded by BBSRC)/ ; BB/S006680/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S006680/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/30002276//UK Research and Innovation/ ; BBS/E/D/30002276//UK Research and Innovation/ ; },
abstract = {Microbiome analysis is quickly moving towards high-throughput methods such as metagenomic sequencing. Accurate taxonomic classification of metagenomic data relies on reference sequence databases, and their associated taxonomy. However, for understudied environments such as the rumen microbiome many sequences will be derived from novel or uncultured microbes that are not present in reference databases. As a result, taxonomic classification of metagenomic data from understudied environments may be inaccurate. To assess the accuracy of taxonomic read classification, this study classified metagenomic data that had been simulated from cultured rumen microbial genomes from the Hungate collection. To assess the impact of reference databases on the accuracy of taxonomic classification, the data was classified with Kraken 2 using several reference databases. We found that the choice and composition of reference database significantly impacted on taxonomic classification results, and accuracy. In particular, NCBI RefSeq proved to be a poor choice of database. Our results indicate that inaccurate read classification is likely to be a significant problem, affecting all studies that use insufficient reference databases. We observed that adding cultured reference genomes from the rumen to the reference database greatly improved classification rate and accuracy. We also demonstrated that metagenome-assembled genomes (MAGs) have the potential to further enhance classification accuracy by representing uncultivated microbes, sequences of which would otherwise be unclassified or incorrectly classified. However, classification accuracy was strongly dependent on the taxonomic labels assigned to these MAGs. We therefore highlight the importance of accurate reference taxonomic information and suggest that, with formal taxonomic lineages, MAGs have the potential to improve classification rate and accuracy, particularly in environments such as the rumen that are understudied or contain many novel genomes.},
}
@article {pmid36401254,
year = {2022},
author = {Yue, S and Zhang, J and Li, J and Hao, Y and Wang, S and Liu, T and Zhong, W and Chen, C and Wang, F and Li, B},
title = {A study protocol for a randomized controlled trial to assess the efficacy of Baduanjin exercise on older adults with sarcopenia in China.},
journal = {BMC complementary medicine and therapies},
volume = {22},
number = {1},
pages = {298},
pmid = {36401254},
issn = {2662-7671},
support = {2021MS058//Sichuan Provincial Administration of Traditional Chinese Medicine/ ; CGY2022-504//Health Commission of Sichuan Province/ ; YB-20-13//National Traditional Chinese Medicine Education Development Center (CN)/ ; },
abstract = {BACKGROUND: Accompanied by the decline of physiological functions, the decrease of physical activity, and comorbidities, older adults are susceptible to sarcopenia because of accelerated loss of muscle mass. Resistance training is recommended by different clinical practice guidelines. However, most older adults have difficulty in taking recommended high-load resistance training programs, and there are limited exercise options form them. Baduanjin, a traditional Chinese mind-body exercise with relatively low intensity and simple movements, has the potential benefits of improving physical functions and may be feasible in treating sarcopenia and preventing its adverse health outcomes in older patients. With the emergence of the concept of gut-muscle axis, this study aims to determine the efficacy of Baduanjin exercise on Chinese older adults with sarcopenia and explore its underlying mechanism.<br><br>METHODS: This is a 24-week, assessor-blinded, randomized controlled trial. Individuals aged 60 to 84 years old will be screened for sarcopenia. 90 participants with sarcopenia will be enrolled and randomly assigned (1:1) into the Baduanjin exercise or resistance training group, and 20 participants without sarcopenia will be set as the non-sarcopenia control group. The primary outcome is the scores of Short Physical Performance Battery. The secondary outcomes are body composition, handgrip strength, walking speed, global cognitive function, and incidence of falls. These outcomes will be assessed at baseline, the 12th week and the 24th week. While stool samples from participants will be collected at baseline and the 24th week for analyzing the abundance of gut microbiome. Data will be analyzed in an intention-to-treat protocol.<br><br>DISCUSSION: The results of this study will determine whether Baduanjin exercise can be an alternative non-pharmacological approach for older adults with sarcopenia. If they can show positive significance, it will promote Baduanjin exercise in clinical practice among these patients and inform further research involving exercise interventions on the optimal types, timing, and intensity to ameliorate sarcopenia for elderly people.<br><br>TRIAL REGISTRATION: Chinese Clinical Trial Registry; Registration number: ChiCTR2100051871; Prospectively registered on October 8th, 2021.},
}
@article {pmid36401221,
year = {2022},
author = {Liu, J and Tao, Y and Haikun, W and Lanfang, Y and Jingyi, L and Ping, Y},
title = {Triclosan exposure induced disturbance of gut microbiota and exaggerated experimental colitis in mice.},
journal = {BMC gastroenterology},
volume = {22},
number = {1},
pages = {469},
pmid = {36401221},
issn = {1471-230X},
support = {81760100//National Science Funding of China/ ; 81760100//National Science Funding of China/ ; 81760100//National Science Funding of China/ ; 81760100//National Science Funding of China/ ; 81760100//National Science Funding of China/ ; 81760100//National Science Funding of China/ ; },
abstract = {BACKGROUND: Triclosan, an antimicrobial agent in personal care products, could be absorbed into the human body through the digestive tract. This animal experiment aimed to clarify the effects of triclosan exposure on the microbiome and intestinal immune functions in healthy and ulcerative colitis models.<br><br>METHODS: Balb/c mice were maintained on an AIN-93G diet containing 80ppm triclosan dissolved in polyethylene as vehicle or vehicle alone for 1 week or 4 weeks. In the end, the mice were sacrificed, blood samples and colon tissues were collected for analysis of inflammation, and fecal samples were collected for 16 S rRNA sequencing of gut microbiota. To establish ulcerative colitis mice model, at the beginning of the 4th week, mice maintained on the diet with or without triclosan were treated with 2% Dextran sulfate sodium(DSS) in drinking water for 1 week. Then mice were sacrificed for analysis of colitis and gut microbiota.<br><br>RESULTS: Triclosan exposure to common mice enhanced the levels of p-NF-κb and Toll-like receptor 4 (TLR4), and decreased the Occludin in the colon. Triclosan exposure to DSS-induced mice increased the level of inflammatory cytokines, reduced the levels of Occludin, and exacerbated the degree of damage to intestinal mucosa and crypt, infiltration of inflammatory cells and atypia of glandular cells. Low-grade intraepithelial neoplasia appeared. Both in common and DSS-induced mice, triclosan exposure changed the diversity and composition of gut microbiota. Fecal samples showed higher enrichment of sulfate-reducing bacteria and Bacteroides, and less butyrate-producing bacteria.<br><br>CONCLUSION: Triclosan exposure induced disturbance of gut microbiota and exaggerated experimental colitis in mice. And changes in the composition of gut microbiota were characterized by the increase of harmful bacteria, including sulfate-reducing bacteria and Bacteroides, and the reduction of protective probiotics, butyrate-producing bacteria.},
}
@article {pmid36401143,
year = {2022},
author = {Koç, N and Nalbantoğlu, S},
title = {Microbiome comparison of Dermanyssus gallinae populations from different farm rearing systems and the presence of common endosymbiotic bacteria at developmental stages.},
journal = {Parasitology research},
volume = {},
number = {},
pages = {},
pmid = {36401143},
issn = {1432-1955},
abstract = {The hematophagous arthropod, Dermanyssus gallinae (Poultry red mite, PRM) can cause remarkable economic losses in the poultry industry across the globe. Although overall composition of endosymbiotic bacteria has been shown in previous studies, how farm habitats influence the microbiome remains unclear. In the present study, we compared the bacterial communities of D. gallinae populations collected from the cage and free-range farms using next-generation sequences targeting the V3-V4 hypervariable region of the 16S rRNA gene. The QIIME2 pipeline was followed in bioinformatic analyses. Proteobacteria represented a great majority of the total bacterial community of D. gallinae from both farming systems. More specifically, Bartonella-like bacteria (40.8%) and Candidatus Cardinium (21.5%) were found to be predominant genera in free-range and cage rearing systems, respectively. However, the microbiome variation based on farming systems was not statistically significant. In addition, the presence of the five common endosymbiotic bacteria (Wolbachia, Cardinium, Rickettsiella, Spiroplasma, and Schineria) was screened in different developmental stages of D. gallinae. Cardinium was detected in all developmental stages of D. gallinae. On the other hand, Wolbachia and Rickettsiella were only found in adults/nymphs, but neither in the eggs nor larvae. To our knowledge, this study provides the first microbiome comparison at genus-level in D. gallinae populations collected from different farm habitats and will contribute to the knowledge of the biology of D. gallinae.},
}
@article {pmid36401142,
year = {2022},
author = {de Angeli Dutra, D and Salloum, PM and Poulin, R},
title = {Vector microbiome: will global climate change affect vector competence and pathogen transmission?.},
journal = {Parasitology research},
volume = {},
number = {},
pages = {},
pmid = {36401142},
issn = {1432-1955},
abstract = {Vector-borne diseases are among the greatest causes of human suffering globally. Several studies have linked climate change and increasing temperature with rises in vector abundance, and in the incidence and geographical distribution of diseases. The microbiome of vectors can have profound effects on how efficiently a vector sustains pathogen development and transmission. Growing evidence indicates that the composition of vectors' gut microbiome might change with shifts in temperature. Nonetheless, due to a lack of studies on vector microbiome turnover under a changing climate, the consequences for vector-borne disease incidence are still unknown. Here, we argue that climate change effects on vector competence are still poorly understood and the expected increase in vector-borne disease transmission might not follow a relationship as simple and straightforward as past research has suggested. Furthermore, we pose questions that are yet to be answered to enhance our current understanding of the effect of climate change on vector microbiomes, competence, and, ultimately, vector-borne diseases transmission.},
}
@article {pmid36400919,
year = {2022},
author = {Scorrano, G and Nielsen, SH and Vetro, DL and Sawafuji, R and Mackie, M and Margaryan, A and Fotakis, AK and Martínez-Labarga, C and Fabbri, PF and Allentoft, ME and Carra, M and Martini, F and Rickards, O and Olsen, JV and Pedersen, MW and Cappellini, E and Sikora, M},
title = {Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1262},
pmid = {36400919},
issn = {2399-3642},
support = {751349//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; },
abstract = {Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.},
}
@article {pmid36400818,
year = {2022},
author = {Wang, J and Li, R and Zhang, M and Gu, C and Wang, H and Feng, J and Bao, L and Wu, Y and Chen, S and Zhang, X},
title = {Author Correction: Influence of Huangqin Decoction on the immune function and fecal microbiome of chicks after experimental infection with Escherichia coli O78.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {19901},
doi = {10.1038/s41598-022-24320-4},
pmid = {36400818},
issn = {2045-2322},
}
@article {pmid36400799,
year = {2022},
author = {Tong, Z and Zhou, X and Chu, Y and Zhang, T and Zhang, J and Zhao, X and Wang, Z and Ding, R and Meng, Q and Yu, J and Wang, J and Kang, Y},
title = {Implications of oral streptococcal bacteriophages in autism spectrum disorder.},
journal = {NPJ biofilms and microbiomes},
volume = {8},
number = {1},
pages = {91},
pmid = {36400799},
issn = {2055-5008},
support = {31970568//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31671350//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Growing evidence suggests altered oral and gut microbiota in autism spectrum disorder (ASD), but little is known about the alterations and roles of phages, especially within the oral microbiota in ASD subjects. We enrolled ASD (n = 26) and neurotypical subjects (n = 26) with their oral hygiene controlled, and the metagenomes of both oral and fecal samples (n = 104) are shotgun-sequenced and compared. We observe extensive and diverse oral phageome comparable to that of the gut, and clear signals of mouth-to-gut phage strain transfer within individuals. However, the overall phageomes of the two sites are widely different and show even less similarity in the oral communities between ASD and control subjects. The ASD oral phageome exhibits significantly reduced abundance and alpha diversity, but the Streptococcal phages there are atypically enriched, often dominating the community. The over-representation of Streptococcal phages is accompanied by enriched oral Streptococcal virulence factors and Streptococcus bacteria, all exhibiting a positive correlation with the severity of ASD clinical manifestations. These changes are not observed in the parallel sampling of the gut flora, suggesting a previously unknown oral-specific association between the excessive Streptococcal phage enrichment and ASD pathogenesis. The findings provide new evidence for the independent microbiome-mouth-brain connection, deepen our understanding of how the growth dynamics of bacteriophages and oral microbiota contribute to ASD, and point to novel effective therapeutics.},
}
@article {pmid36400333,
year = {2022},
author = {D'Acquisto, F},
title = {The microbiome, IgGs and schizophrenia. A R20+ adult-only story.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2022.11.009},
pmid = {36400333},
issn = {1090-2139},
}
@article {pmid36400238,
year = {2022},
author = {Hurley, MJ and Bates, R and Macnaughtan, J and Schapira, AHV},
title = {Bile acids and neurological disease.},
journal = {Pharmacology &amp; therapeutics},
volume = {},
number = {},
pages = {108311},
doi = {10.1016/j.pharmthera.2022.108311},
pmid = {36400238},
issn = {1879-016X},
abstract = {This review will focus on how bile acids are being used in clinical trials to treat neurological diseases due to their central involvement with the gut-liver-brain axis and their physiological and pathophysiological roles in both normal brain function and multiple neurological diseases. The synthesis of primary and secondary bile acids species and how the regulation of the bile acid pool may differ between the gut and brain is discussed. The expression of several bile acid receptors in brain and their currently known functions along with the tools available to manipulate them pharmacologically are examined, together with discussion of the interaction of bile acids with the gut microbiome and their lesser-known effects upon brain glucose and lipid metabolism. How dysregulation of the gut microbiome, aging and sex differences may lead to disruption of bile acid signalling and possible causal roles in a number of neurological disorders are also considered. Finally, we discuss how pharmacological treatments targeting bile acid receptors are currently being tested in an array of clinical trials for several different neurodegenerative diseases.},
}
@article {pmid36400114,
year = {2022},
author = {Tóth, Z and Bezzegh, A and Tordé, Á and Vásárhelyi, B and Gyarmati, B},
title = {Short term ciprofloxacin and clindamycin combination antibiotic therapy before and after transrectal ultrasound scan and prostate biopsy: Its impact on major components of gut microbiome.},
journal = {Molecular and cellular probes},
volume = {},
number = {},
pages = {101874},
doi = {10.1016/j.mcp.2022.101874},
pmid = {36400114},
issn = {1096-1194},
abstract = {The perturbation of gut microbiome is a risk factor for a number of adverse conditions. Among other factors antibiotic therapy is a common culprit. We characterized the short-term alteration of gut microbiome after antibiotic therapy. Nine patients (age (median [range]): 67 [57-75 years]) were subjected to prostate biopsy. Ciprofloxacin and clindamycin, 500 mg and 150 mg, respectively, were administered twice a day; this combination therapy was started the day before and continued until 5th and 8th day, respectively, following biopsy. 16s RNA sequencing data from fecal swabs taken before antibiotic therapy and 14 days after biopsy were analysed. At phylum level, the abundance of Actinobacteria and Firmicutes decreased, while that of Bacteroides and Proteobacteria increased after antibiotic therapy. The ratio of Firmicutes:Bacteroides inversed (from 2.81 to 0.74, p = 0.035). At order level, the abundance of Bacteroidales and Veillonellales increased, while that of Clostridiales and Coriobacteriales decreased. At genus level the abundance of Bacteroides increased, while those of Roseburia, Faecalibacterium and Collinsella decreased. These findings indicate that short-term antibiotic exposure skews gut microbiome composition. The current level of knowledge does not allow to decide whether this skewness is detrimental and has any long-term effect on disease including prostate pathology.},
}
@article {pmid36399893,
year = {2022},
author = {Sharma, S and Hegde, P and Panda, S and Orimoloye, MO and Aldrich, CC},
title = {Drugging the microbiome: targeting small microbiome molecules.},
journal = {Current opinion in microbiology},
volume = {71},
number = {},
pages = {102234},
doi = {10.1016/j.mib.2022.102234},
pmid = {36399893},
issn = {1879-0364},
abstract = {The human microbiome represents a large and diverse collection of microbes that plays an integral role in human physiology and pathophysiology through interactions with the host and within the microbial community. While early work exploring links between microbiome signatures and diseases states has been associative, emerging evidence demonstrates the metabolic products of the human microbiome have more proximal causal effects on disease phenotypes. The therapeutic implications of this shift are profound as manipulation of the microbiome by the administration of live biotherapeutics, ongoing, can now be pursued alongside research efforts toward describing inhibitors of key microbiome enzymes involved in the biosynthesis of metabolites implicated in various disease states and processing of host-derived metabolites. With growing interest in 'drugging the microbiome', we review few notable microbial metabolites for which traditional drug-development campaigns have yielded compounds with therapeutic promise.},
}
@article {pmid36399881,
year = {2022},
author = {Cheng, YH and Chang, SC and Lai, YL and Hu, CC},
title = {Microbiome reengineering by four environmental factors for the rapid biodegradation of trichloroethylene.},
journal = {Journal of environmental management},
volume = {326},
number = {Pt A},
pages = {116658},
doi = {10.1016/j.jenvman.2022.116658},
pmid = {36399881},
issn = {1095-8630},
abstract = {Trichloroethylene (TCE) was once a widely applied industrial solvent, but is now an infamous contaminant in groundwater. Although anaerobic reductive dechlorination is considered a greener remediation approach, the accumulation of toxic intermediates, such as vinyl chloride (VC), and a longer remediation period are highly concerning. Biostimulation and bioaugmentation have been developed to solve these problems. The former method may not be effective, and the latter may introduce foreign genes. Here, we propose a new approach by applying environmental stresses to reshape the indigenous microbiome. In this study, by using the Taguchi method, the effects of heating, pH, salinity, and desiccation were systematically examined. The optimum conditions were defined as 50 °C, pH 9, 3.50% salinity (w/v), and 21% volumetric water content (θW). The top performing group, G7, can complete the conversion of 11.81 mg/L TCE into ethene in 3.0 days with a 1.23% abundance of Dehalococcoides mccartyi 195 (Dhc 195). Redundancy analysis confirmed that temperature and salinity were the predominant factors in reorganizing the microbiomes. The microbiome structure and its effectiveness can last for at least 90 d. The repetitive selection conditions and sustainable degradation capability strongly supported that microbiome reengineering is feasible for the rapid bioremediation of TCE-contaminated environmental matrices.},
}
@article {pmid36399821,
year = {2022},
author = {Huang, YH and Yang, YJ and Wu, X and Zhu, CL and Lü, H and Zhao, HM and Xiang, L and Li, H and Mo, CH and Li, YW and Cai, QY and Li, QX},
title = {Adaptation of bacterial community in maize rhizosphere for enhancing dissipation of phthalic acid esters in agricultural soil.},
journal = {Journal of hazardous materials},
volume = {444},
number = {Pt A},
pages = {130292},
doi = {10.1016/j.jhazmat.2022.130292},
pmid = {36399821},
issn = {1873-3336},
abstract = {Rhizospheric degradation is a green and in situ strategy to accelerate dissipation of organic pollutants in soils. However, the mechanism on microbial degradation of phthalic acid esters (PAEs) in rhizosphere is still unclear. Here, the bacterial community and function genes in bulk and rhizospheric soils of maize (Zea mays L.) exposed to gradient concentrations of di-(2-ethylhexyl) phthalate (DEHP) were analyzed with 16 S rRNA, metagenomic sequencing and quantitative PCR (qPCR). Maize rhizosphere significantly increased the dissipation of DEHP by 4.02-11.5% in comparison with bulk soils. Bacterial community in rhizosphere exhibited more intensive response and shaped its beneficial structure and functions to DEHP stress than that in bulk soils. Both rhizospheric and pollution effects enriched more PAE-degrading bacteria (e.g., Bacillus and Rhizobium) and function genes in rhizosphere than in bulk soil, which played important roles in degradation of PAEs in rhizosphere. The PAE-degrading bacteria (including genera Sphingomonas, Sphingopyxis and Lysobacter) identified as keystone species participated in DEHP biodegradation. Identification of PAE intermediates and metagenomic reconstruction of PAE degradation pathways demonstrated that PAE-degrading bacteria degraded PAEs through cooperation with PAE-degrading and non-PAE-degrading bacteria. This study provides a comprehensive knowledge for the microbial mechanism on the superior dissipation of PAEs in rhizosphere.},
}
@article {pmid36399658,
year = {2022},
author = {Simmer, RA and Schnoor, JL},
title = {Phytoremediation, Bioaugmentation, and the Plant Microbiome.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.2c05970},
pmid = {36399658},
issn = {1520-5851},
abstract = {Understanding plant biology and related microbial ecology as a means to phytoremediate soil and groundwater contamination has broadened and advanced the field of environmental engineering and science over the past 30 years. Using plants to transform and degrade xenobiotic organic pollutants delivers new methods for environmental restoration. Manipulations of the plant microbiome through bioaugmentation, endophytes, adding various growth factors, genetic modification, and/or selecting the microbial community via insertion of probiotics or phages for gene transfer are future areas of research to further expand this green, cost-effective, aesthetically pleasing technology─phytoremediation.},
}
@article {pmid36399503,
year = {2022},
author = {Zheng, J and Hu, B and Zhang, X and Ge, Q and Yan, Y and Akresi, J and Piyush, V and Huang, L and Yin, Y},
title = {dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkac1068},
pmid = {36399503},
issn = {1362-4962},
support = {R01GM140370/NH/NIH HHS/United States ; DBI-1933521//National Science Foundation/ ; 58-8042-9-089//United States Department of Agriculture/ ; },
abstract = {Carbohydrate Active EnZymes (CAZymes) are significantly important for microbial communities to thrive in carbohydrate rich environments such as animal guts, agricultural soils, forest floors, and ocean sediments. Since 2017, microbiome sequencing and assembly have produced numerous metagenome assembled genomes (MAGs). We have updated our dbCAN-seq database (https://bcb.unl.edu/dbCAN_seq) to include the following new data and features: (i) ∼498 000 CAZymes and ∼169 000 CAZyme gene clusters (CGCs) from 9421 MAGs of four ecological (human gut, human oral, cow rumen, and marine) environments; (ii) Glycan substrates for 41 447 (24.54%) CGCs inferred by two novel approaches (dbCAN-PUL homology search and eCAMI subfamily majority voting) (the two approaches agreed on 4183 CGCs for substrate assignments); (iii) A redesigned CGC page to include the graphical display of CGC gene compositions, the alignment of query CGC and subject PUL (polysaccharide utilization loci) of dbCAN-PUL, and the eCAMI subfamily table to support the predicted substrates; (iv) A statistics page to organize all the data for easy CGC access according to substrates and taxonomic phyla; and (v) A batch download page. In summary, this updated dbCAN-seq database highlights glycan substrates predicted for CGCs from microbiomes. Future work will implement the substrate prediction function in our dbCAN2 web server.},
}
@article {pmid36399457,
year = {2022},
author = {Phillips, S and Watt, R and Atkinson, T and Rajan, S and Hayhoe, A and Savva, GM and Hornberger, M and Burton, BJL and Saada, J and Cambell-Kelly, M and Rushbrook, S and Carding, SR},
title = {A protocol paper for the MOTION Study-A longitudinal study in a cohort aged 60 years and older to obtain mechanistic knowledge of the role of the gut microbiome during normal healthy ageing in order to develop strategies that will improve lifelong health and wellbeing.},
journal = {PloS one},
volume = {17},
number = {11},
pages = {e0276118},
doi = {10.1371/journal.pone.0276118},
pmid = {36399457},
issn = {1932-6203},
abstract = {BACKGROUND: Advances in medicine and public health mean that people are living longer; however, a significant proportion of that increased lifespan is spent in a prolonged state of declining health and wellbeing which places increasing pressure on medical, health and social services. There is a social and economic need to develop strategies to prevent or delay age-related disease and maintain lifelong health. Several studies have suggested links between the gut microbiome and age-related disease, which if confirmed would present a modifiable target for intervention development. The MOTION study aims to determine whether and how changes in the gut microbiome are associated with physical and mental capacity. A comprehensive longitudinal multiparameter study such as this has not been previously undertaken.<br><br>METHODS: MOTION is a longitudinal prospective cohort study with a focus on gut health and cognitive function. 360 healthy individuals aged 60 years and older, living in East Anglia, UK will be recruited to the study, stratified into one of three risk groups (cohorts) for developing dementia based on their cognitive function. Participants will attend study appointments every six months over four years, providing stool and blood samples and a health questionnaire. Participants will also undergo physical measurements and cognitive tests at alternating appointments, and undergo Optical Coherence Tomography scans at 3 timepoints. Two subgroups of participants in the study will provide colonic tissue biopsies (n = ≥30 from each cohort), and brain imaging (n = 30) at two timepoints.<br><br>DISCUSSION: This study will provide new insights into the gut-(microbiota)-brain axis and the relationship between age-associated changes in gut microbe populations and cognitive health. Such insights could help develop new microbe-based strategies to improve lifelong health and wellbeing.<br><br>TRIAL REGISTRATION: This study is registered in the ClinicalTrials.gov Database with ID: NCT04199195 Registered: May 14, 2019.},
}
@article {pmid36399245,
year = {2022},
author = {Swer, NM and Venkidesh, BS and Murali, TS and Mumbrekar, KD},
title = {Gut microbiota-derived metabolites and their importance in neurological disorders.},
journal = {Molecular biology reports},
volume = {},
number = {},
pages = {},
pmid = {36399245},
issn = {1573-4978},
support = {2019//MAHE Intramural/ ; },
abstract = {Microbial-derived metabolites are the intermediate or end products of bacterial digestion. They are one of the most important molecules for the gut to connect with the brain. Depending on the levels of specific metabolites produced in the host, it can exert beneficial or detrimental effects on the brain and have been linked to several neurodegenerative and neuropsychiatric disorders. However, the underlying mechanisms remain largely unexplored. Insight into these mechanisms could reveal new pathways or targets, resulting in novel treatment approaches targeting neurodegenerative diseases. We have reviewed selected metabolites, including short-chain fatty acids, aromatic amino acids, trimethylamine-N-oxide, urolithin A, anthocyanins, equols, imidazole, and propionate to highlight their mechanism of action, underlying role in maintaining intestinal homeostasis and regulating neuro-immunoendocrine function. Further discussed on how altered metabolite levels can influence the gut-brain axis could lead to new prevention strategies or novel treatment approaches to neural disorders.},
}
@article {pmid36399198,
year = {2022},
author = {Iwama, N and Matsuda, M and Tsuruta, M and Okabayashi, K and Shigeta, K and Kanai, T and Kitagawa, Y},
title = {Relationship between obesity-related colorectal tumors and the intestinal microbiome: an animal-based trial.},
journal = {Journal of cancer research and clinical oncology},
volume = {},
number = {},
pages = {},
pmid = {36399198},
issn = {1432-1335},
abstract = {PURPOSE: Obesity is a risk factor for colorectal cancer (CRC), and the intestinal microbiome is considered to contribute to CRC and obesity. Nonetheless, the role of the intestinal microbiome in obesity-related CRC is unclear. This study aimed to clarify the relationship between obesity-related CRC and the intestinal microbiome using a mouse model.<br><br>METHODS: We compared an obese and insulin-resistant type 2 diabetes mouse model [KKAy] to wild-type mice (WT) [C57BL/6 J]. Azoxymethane was intraperitoneally injected to develop a mouse model CRC. At 26 weeks, we compared the number of tumors and the intestinal microbiome. We also compared them across two models, namely, antibiotic cocktail and co-housing.<br><br>RESULTS: In all models, KKAy mice had a significantly greater number of tumors than WT mice. Analysis showed that the distribution of the intestinal microbiome changed in both models; however, no difference in tumor development was observed. Tumor expression was suppressed only in the antibiotic cocktail model of WT, whereas KKAy mice bore tumors (C57Bl/6 J: KKAy, 0/9:8/8; p < 0.001). KKAy mice remained predominantly tumor-bearing in all treatments.<br><br>CONCLUSION: Based on the results, the intestinal microbiome may not be associated with tumorigenesis in obesity-related CRC. It may be necessary to think of other facts linked to obesity-related CRC.},
}
@article {pmid36399171,
year = {2022},
author = {Iyer, LR and Chandel, N and Verma, AK and Thakur, V and Paul, J and Mandal, AK and Bhattacharya, A},
title = {Effect of Entamoeba histolytica infection on gut microbial diversity and composition in diarrheal patients from New Delhi.},
journal = {Parasitology research},
volume = {},
number = {},
pages = {},
pmid = {36399171},
issn = {1432-1955},
support = {Research Associateship//Department of Biotechnology, Ministry of Science and Technology, India/ ; Research Associateship//Department of Biotechnology, Ministry of Science and Technology, India/ ; Research Associateship//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {During amoebiasis, colonization of the gut by Entamoeba histolytica can lead to alterations of the host microbiota. In this study, we have compared the gut microbiota of patients of amoebiasis with healthy controls using 16S rRNA gene variable regions, (V1-V3) and (V3-V5), of the bacterial genome. From this 16S rRNA gene amplicon data, one paired-end and two single-end datasets were selected and compared by the number of OTUs obtained, sequence count, and diversity analysis. Our results showed that the V1-V3-paired-end dataset gave the maximum number of OTUs in comparison to the two single-end datasets studied. The amoebiasis samples showed a significant drop in richness in the alpha diversity measurements and lower intra group similarity compared to the healthy controls. Bacteria of genus Prevotella, Sutterella, and Collinsella were more abundant in healthy controls whereas Escherichia, Klebsiella, and Ruminococcus were more abundant in the E. histolytica-positive patients. All the healthy controls harbored bacteria belonging to Faecalibacterium, Prevotella, Ruminococcus, Subdoligranulum, and Escherichia genera while all the E. histolytica-positive patient samples contained genus Enterobacter. The compositional changes in the gut microbiome observed in our study indicated a higher prevalence of pathogenic bacteria along with a depletion of beneficial bacteria in E. histolytica-infected individuals when compared with healthy controls. These results underline the interplay between E. histolytica and the human gut microbiome, giving important inputs for future studies and treatments.},
}
@article {pmid36399059,
year = {2022},
author = {Zhang, Y and Jiang, F and Yang, B and Wang, S and Wang, H and Wang, A and Xu, D and Fan, W},
title = {Improved microbial genomes and gene catalog of the chicken gut from metagenomic sequencing of high-fidelity long reads.},
journal = {GigaScience},
volume = {11},
number = {},
pages = {},
doi = {10.1093/gigascience/giac116},
pmid = {36399059},
issn = {2047-217X},
support = {32000408//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Due to the importance of chicken production and the remarkable influence of the gut microbiota on host health and growth, tens of thousands of metagenome-assembled genomes (MAGs) have been constructed for the chicken gut microbiome. However, due to the limitations of short-read sequencing and assembly technologies, most of these MAGs are far from complete, are of lower quality, and include contaminant reads.<br><br>RESULTS: We generated 332 Gb of high-fidelity (HiFi) long reads from the 5 chicken intestinal compartments and assembled 461 and 337 microbial genomes, of which 53% and 55% are circular, at the species and strain levels, respectively. For the assembled microbial genomes, approximately 95% were regarded as complete according to the "RNA complete" criteria, which requires at least 1 full-length ribosomal RNA (rRNA) operon encoding all 3 types of rRNA (16S, 23S, and 5S) and at least 18 copies of full-length transfer RNA genes. In comparison with the short-read-derived chicken MAGs, 384 (83% of 461) and 89 (26% of 337) strain-level and species-level genomes in this study are novel, with no matches to previously reported sequences. At the gene level, one-third of the 2.5 million genes in the HiFi-derived gene catalog are novel and cannot be matched to the short-read-derived gene catalog. Moreover, the HiFi-derived genomes have much higher continuity and completeness, as well as lower contamination; the HiFi-derived gene catalog has a much higher ratio of complete gene structures. The dominant phylum in our HiFi-assembled genomes was Firmicutes (82.5%), and the foregut was highly enriched in 5 genera: Ligilactobacillus, Limosilactobacillus, Lactobacillus, Weissella, and Enterococcus, all of which belong to the order Lactobacillales. Using GTDB-Tk, all 337 species-level genomes were successfully classified at the order level; however, 2, 35, and 189 genomes could not be classified into any known family, genus, and species, respectively. Among these incompletely classified genomes, 9 and 49 may belong to novel genera and species, respectively, because their 16S rRNA genes have identities lower than 95% and 97% to any known 16S rRNA genes.<br><br>CONCLUSIONS: HiFi sequencing not only produced metagenome assemblies and gene structures with markedly improved quality but also recovered a substantial portion of novel genomes and genes that were missed in previous short-read-based metagenome studies. The novel genomes and species obtained in this study will facilitate gut microbiome and host-microbiota interaction studies, thereby contributing to the sustainable development of poultry resources.},
}
@article {pmid36398902,
year = {2022},
author = {Diebold, M and Meola, M and Purushothaman, S and Siewert, LK and Pössnecker, E and Roloff, T and Lindberg, RL and Kuhle, J and Kappos, L and Derfuss, T and Egli, A and Pröbstel, AK},
title = {Gut microbiota composition as a candidate risk factor for dimethyl fumarate-induced lymphopenia in multiple sclerosis.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2147055},
doi = {10.1080/19490976.2022.2147055},
pmid = {36398902},
issn = {1949-0984},
abstract = {Mounting evidence points towards a pivotal role of gut microbiota in multiple sclerosis (MS) pathophysiology. Yet, whether disease-modifying treatments alter microbiota composition and whether microbiota shape treatment response and side-effects remain unclear. In this prospective observational pilot study, we assessed the effect of dimethyl fumarate (DMF) on gut microbiota and on host/microbial metabolomics in a cohort of 20 MS patients. Combining state-of-the-art microbial sequencing, metabolome mass spectrometry, and computational analysis, we identified longitudinal changes in gut microbiota composition under DMF-treatment and an increase in citric acid cycle metabolites. Notably, DMF-induced lymphopenia, a clinically relevant safety concern, was correlated with distinct baseline microbiome signatures in MS patients. We identified gastrointestinal microbiota as a key therapeutic target for metabolic properties of DMF. By characterizing gut microbial composition as a candidate risk factor for DMF-induced lymphopenia, we provide novel insights into the role of microbiota in mediating clinical side-effects.},
}
@article {pmid36398739,
year = {2022},
author = {Kaibori, Y and Yamashita, K and Nagakubo, D},
title = {The altered production and property of saliva induced by ingesting fermented food ingredients affect the oral microbiome composition in mice.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbac186},
pmid = {36398739},
issn = {1347-6947},
abstract = {Oral functions are diverse and critical to human health. Therefore, insufficient secretion or poor quality of saliva, which is secreted into the oral cavity and plays various roles, could have a crucial influence on the oral microenvironment and be associated with systemic disease development. Here, we investigated the effects of food ingredients on saliva quantity and quality, including fermented ones. Through the in vitro submandibular glands organ culture analyses, we found that "Yomo gyutto," fermented Japanese mugwort (Artemisia princeps), altered the expression of aquaporin-5, a water channel protein. We also found that Yomo gyutto increased saliva volume, along with the amount of α-amylase in mice, and caused changes in the oral microbiome composition of mice. These results suggested that by ingesting Yomo gyutto, we could directly and effectively manipulate the quantity and quality of saliva secreted from the salivary glands, potentially altering the oral microbiome composition for individual health.},
}
@article {pmid36398663,
year = {2022},
author = {Miyake, M and Oda, Y and Owari, T and Iida, K and Ohnishi, S and Fujii, T and Nishimura, N and Tatsuki, M and Shimizu, T and Ohnishi, K and Hori, S and Morizawa, Y and Gotoh, D and Nakai, Y and Torimoto, K and Tanaka, N and Fujimoto, K},
title = {Probiotics enhances anti-tumor immune response induced by gemcitabine plus cisplatin chemotherapy for urothelial cancer.},
journal = {Cancer science},
volume = {},
number = {},
pages = {},
doi = {10.1111/cas.15666},
pmid = {36398663},
issn = {1349-7006},
abstract = {Chemotherapy drugs, such as gemcitabine and cisplatin (GC), are frequently administered to patients with advanced urothelial carcinoma, however, the influence of the gut microbiota on their action is unclear. Thus, we investigated the effects of GC on the gut microbiome and determined whether oral supplementation with a probiotic mixture of Lactobacillus casei Shirota and Bifidobacterium breve enhanced the anti-tumor immune response. After subcutaneous inoculation with MBT2 murine bladder cancer cells, syngenic C3H mice were randomly allocated into eight groups. Gut microbiome cluster pattern was altered in both the GC and oral probiotic groups (P = 0.025). Both tumor-bearing conditions (no treatment) and GC chemotherapy influenced Pseudoclostridium, Robinsoniella, Merdimonas, and Phocea in the gut. Furthermore, comparison of the GC-treated and GC+probiotics groups revealed an association of four methyltransferase family enzymes and two short-change fatty acid-related enzymes with oral probiotics use. A significant difference in tumor volume was observed between the GC and GC+probiotic groups at week 2 of treatment. Additionally, decreased recruitment of cancer-associated fibroblasts and regulatory T cells, and activation of CD8+ T cells and dendritic cells were observed in the tumor microenvironment. Our findings reveal the positive effects of a probiotic mixture of Lactobacillus and Bifidobacterium in enhancing anti-tumor effects through the gut-tumor immune response axis. Future clinical trials are needed to evaluate the full benefits of this novel supplement with oral probiotics in patients with advanced urothelial carcinoma.},
}
@article {pmid36398501,
year = {2022},
author = {Cömert, TK and Akpinar, F and Erkaya, S and Durmaz, B and Durmaz, R},
title = {The effect of pre-pregnancy obesity on gut and meconium microbiome and relationship with fetal growth.},
journal = {The journal of maternal-fetal &amp; neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/14767058.2022.2148098},
pmid = {36398501},
issn = {1476-4954},
abstract = {OBJECTIVE: To investigate the effect of pre-pregnancy obesity on maternal and newborn microbiomes and fetal growth.<br><br>METHODS: Individuals who gained body weight in accordance with the recommendations during pregnancy and normal gestastional age are included in the study and were separated into two groups, normal (n = 20) and obese (n = 20), based on their body mass index (BMI) value of pre-pregnancy. Maternal stool samples collected during the first trimester of pregnancy and meconium samples collected at birth were evaluated using 16S rRNA gene-based microbiome analysis.<br><br>RESULTS: The stool samples of mothers who were obese before pregnancy harbored a higher (59.9 versus 52.3%) relative abundance of Firmicutes and a lower (7.1 versus 4.1%) relative abundance of Proteobacteria than the stool samples of mothers with normal body weight pre-pregnancy. In contrast, in the meconium samples of mothers who were obese pre-pregnancy, compared to those of mothers who had a normal body weight pre-pregnancy, the phylum Firmicutes was less (56.0 versus 69.0%) abundant and Proteobacteria (9.0 versus 8.5%) was more abundant. There was a negative correlation between pre-pregnancy BMI, birth weight, weight/height ratio and alpha diversity indices (Shannon and Chao1).<br><br>CONCLUSIONS: Pre-pregnancy obesity can affect pregnant and newborn gut microbiota, which might related to fetal growth of the newborn.},
}
@article {pmid36398438,
year = {2022},
author = {Song, EJ and Shin, JH},
title = {Personalized Diets based on the Gut Microbiome as a Target for Health Maintenance: from Current Evidence to Future Possibilities.},
journal = {Journal of microbiology and biotechnology},
volume = {32},
number = {12},
pages = {1-9},
doi = {10.4014/jmb.2209.09050},
pmid = {36398438},
issn = {1738-8872},
abstract = {Recently, the concept of personalized nutrition has been developed, which states that food components do not always lead to the same metabolic responses, but vary from person to person. Although this concept has been studied based on individual genetic backgrounds, researchers have recently explored its potential role in the gut microbiome. The gut microbiota physiologically communicates with humans by forming a bidirectional relationship with the micronutrients, macronutrients, and phytochemicals consumed by the host. Furthermore, the gut microbiota can vary from person to person and can be easily shifted by diet. Therefore, several recent studies have reported the application of personalized nutrition to intestinal microflora. This review provides an overview of the interaction of diet with the gut microbiome and the latest evidence in understanding the inter-individual differences in dietary responsiveness according to individual baseline gut microbiota and microbiome-associated dietary intervention in diseases. The diversity of the gut microbiota and the presence of specific microorganisms can be attributed to physiological differences following dietary intervention. The difference in individual responsiveness based on the gut microbiota has the potential to become an important research approach for personalized nutrition and health management, although further well-designed large-scale studies are warranted.},
}
@article {pmid36398428,
year = {2022},
author = {Makkar, H and Zhou, Y and Tan, KS and Lim, CT and Sriram, G},
title = {Modelling crevicular fluid flow and host-Oral microbiome interactions in a gingival crevice-on-Chip.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2202376},
doi = {10.1002/adhm.202202376},
pmid = {36398428},
issn = {2192-2659},
abstract = {Gingival crevice and gingival crevicular fluid (GCF) flow play a crucial role at the gingiva-oral microbiome interface which contributes towards maintaining the balance between gingival health and periodontal disease. Interstitial flow of GCF strongly impacts the host-microbiome interactions and tissue responses. However, currently available in vitro preclinical models largely disregard the dynamic nature of gingival crevicular microenvironment, thus limiting the progress in the development of periodontal therapeutics. Here, a proof-of-principle "gingival crevice-on-chip" microfluidic platform to culture gingival connective tissue equivalent (CTE) under dynamic interstitial fluid flow mimicking the GCF is described. On-chip co-culture using oral symbiont (S. oralis) showed the potential to recapitulate microbial colonization, formation of biofilm-like structures at the tissue-microbiome interface, long-term co-culture and bacterial clearance secondary to simulated GCF (s-GCF) flow. Further, on-chip exposure of the gingival CTEs to TLR-2 agonist or periodontal pathogen F. nucleatum demonstrated the potential to mimic early gingival inflammation. In contrast to direct exposure, the induction of s-GCF flow towards the bacterial front, attenuated the secretion of inflammatory mediators demonstrating the protective effect of GCF flow. This proposed in vitro platform offers the potential to study complex host-microbe interactions in periodontal disease and the development of periodontal therapeutics under near-microphysiological conditions. This article is protected by copyright. All rights reserved.},
}
@article {pmid36398283,
year = {2021},
author = {Jeganathan, P and Holmes, SP},
title = {A Statistical Perspective on the Challenges in Molecular Microbial Biology.},
journal = {Journal of agricultural, biological, and environmental statistics},
volume = {26},
number = {2},
pages = {131-160},
doi = {10.1007/s13253-021-00447-1},
pmid = {36398283},
issn = {1085-7117},
abstract = {High throughput sequencing (HTS)-based technology enables identifying and quantifying non-culturable microbial organisms in all environments. Microbial sequences have enhanced our understanding of the human microbiome, the soil and plant environment, and the marine environment. All molecular microbial data pose statistical challenges due to contamination sequences from reagents, batch effects, unequal sampling, and undetected taxa. Technical biases and heteroscedasticity have the strongest effects, but different strains across subjects and environments also make direct differential abundance testing unwieldy. We provide an introduction to a few statistical tools that can overcome some of these difficulties and demonstrate those tools on an example. We show how standard statistical methods, such as simple hierarchical mixture and topic models, can facilitate inferences on latent microbial communities. We also review some nonparametric Bayesian approaches that combine visualization and uncertainty quantification. The intersection of molecular microbial biology and statistics is an exciting new venue. Finally, we list some of the important open problems that would benefit from more careful statistical method development.},
}
@article {pmid36398033,
year = {2022},
author = {Larson, PJ and Zhou, W and Santiago, A and Driscoll, S and Fleming, E and Voigt, AY and Chun, OK and Grady, JJ and Kuchel, GA and Robison, JT and Oh, J},
title = {Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults.},
journal = {Nature aging},
volume = {2},
number = {10},
pages = {941-955},
doi = {10.1038/s43587-022-00287-9},
pmid = {36398033},
issn = {2662-8465},
abstract = {Older adults represent a vulnerable population with elevated risk for numerous morbidities. To explore the association of the microbiome with aging and age-related susceptibilities including frailty and infectious disease risk, we conducted a longitudinal study of the skin, oral, and gut microbiota in 47 community- or skilled nursing facility-dwelling older adults vs. younger adults. We found that microbiome changes were not associated with chronological age so much as frailty: we identified prominent changes in microbiome features associated with susceptibility to pathogen colonization and disease risk, including diversity, stability, heterogeneity, and biogeographic determinism, which were moreover associated with a loss of Cutibacterium (C.) acnes in the skin microbiome. Strikingly, the skin microbiota were also the primary reservoir for antimicrobial resistance, clinically important pathobionts, and nosocomial strains, suggesting a potential role particularly for the skin microbiome in disease risk and dissemination of multidrug resistant pathogens.},
}
@article {pmid36397449,
year = {2022},
author = {Luo, J and Wu, X and Gang, X and Zhang, N and Wang, F and Rong, C},
title = {Mycoplasma hominis and Ureaplasma urealyticum infections after knee arthroplasty: A case report.},
journal = {Medicine},
volume = {101},
number = {45},
pages = {e31202},
doi = {10.1097/MD.0000000000031202},
pmid = {36397449},
issn = {1536-5964},
abstract = {RATIONALE: Artificial joint infection caused by Mycoplasma hominis and Ureaplasma urealyticum is rare and has not been reported.<br><br>PATIENTS CONCERNS: A 59-year-old man underwent left total knee arthroplasty for 1 year of pain in the left knee joint. The indwelling urinary catheter was removed after 48 hour of the surgery. On day 8 after the surgery, the patient had fever, increased skin temperature, swelling and redness around the surgical site, and floating patella test (+). According to experience, Vancomycin, Ciprofloxacin and Linezolid were administrated. Evident decrease in C-reactive protein was observed after Linezolid administration, while there was no significant improvement in clinical symptoms. Microbiome sequencing was performed, resulting in diagnosis of positive M hominis and U urealyticum. The patient was then treated with Doxycycline in the following 3 months. During the 11-month outpatient follow-up, there was no evidence of recurrence of infection.<br><br>DIAGNOSIS: Microbiome sequencing was performed, resulting in diagnosis of positive M hominis and Ureaplasma urealyticum.<br><br>INTERVENTIONS: The patient recovered following with Doxycycline in the following 3 months.<br><br>OUTCOMES: During the 11-month outpatient follow-up, there was no evidence of recurrence of infection.<br><br>LESSONS: M hominis and U urealyticum are common pathogens of the urinary system infections but they are rare in osteoarticular infections. In cases of fever, swelling and heat pain around the surgical site, joint fluid, negative blood culture and being irresponsive to anti-bacterial agents against the cell wall, special bacteria-related infection should be highly suspected.},
}
@article {pmid36397429,
year = {2022},
author = {Nikolic, DM and Dimitrijevic-Sreckovic, V and Ranin, LT and Stojanovic, MM and Ilic, ID and Gostiljac, DM and Soldatovic, IA},
title = {Homeostatic microbiome disruption as a cause of insulin secretion disorders. Candida albicans, a new factor in pathogenesis of diabetes: A STROBE compliant cross-sectional study.},
journal = {Medicine},
volume = {101},
number = {45},
pages = {e31291},
doi = {10.1097/MD.0000000000031291},
pmid = {36397429},
issn = {1536-5964},
abstract = {The study aimed to test the hypothesis that homeostatic microbiome (HM) disorders lead to the increased indirect influence of certain microorganisms (MO) in the gastrointestinal tract, causing a disorder of insulin secretion, insulin resistance, and diabetes. We highlighted Candida and certain types of bacteria since previous in vitro research showed they significantly affect insulin secretion and can cause insulin resistance in obese patients with metabolic syndrome. After determining the type of MO present in the throat swab and the stool, the oral glucose tolerance test (OGTT) test, and analysis of glucose and insulin secretion were performed in patients (n = 38) who were positive for certain types of MO compared to negative patients. Finally, all patients were divided into two groups: overweight patients (body mass index [BMI] < 30) and obese patients (BMI > 30). These two groups were compared for the percentage of certain types of MO to determine which MO can affect an increase in obesity and BMI. The presence of Diphtheroids in the throat (60.5%) reduces insulin secretion in patients compared with the negative group (194.5: 332.4) and the difference was statistically significant (P = .030). The presence of Candida in the throat (10%) increases insulin secretion, but the difference was statistically insignificant. The presence of Candida in the stool (28.9%) also increases insulin secretion and the difference was statistically significant (P = .038). Cumulative results (throat + stool) were similar (180: 332, P = .022). Analysis of BMI showed that the percentage of Diphtheroids in the throat decreases with increased body weight (53.8: 75%) while the percentage of Candida (38.5: 8.3%) and Enterobacter (61.5: 25%) increases, but these differences were statistically insignificant (P > .05). Diphtheroids in the throat can reduce insulin secretion by synthesizing their metabolites. Candida albicans is a conditional pathogen and as a significant indirect factor induces increased insulin secretion and insulin resistance. There are indications that elevated levels of Candida in the intestinal system can cause increased body weight of patients. C albicans should be considered a new factor in the pathogenesis of diabetes.},
}
@article {pmid36397174,
year = {2022},
author = {Wesołowska, A},
title = {Sex-the most underappreciated variable in research: insights from helminth-infected hosts.},
journal = {Veterinary research},
volume = {53},
number = {1},
pages = {94},
pmid = {36397174},
issn = {1297-9716},
support = {2019/35/B/NZ6/04002//Narodowe Centrum Nauki/ ; },
abstract = {The sex of a host affects the intensity, prevalence, and severity of helminth infection. In many cases, one sex has been found to be more susceptible than the other, with the prevalence and intensity of helminth infections being generally higher among male than female hosts; however, many exceptions exist. This observed sex bias in parasitism results primarily from ecological, behavioural, and physiological differences between males and females. Complex interactions between these influences modulate the risk of infection. Indeed, an interplay among sex hormones, sex chromosomes, the microbiome and the immune system significantly contributes to the generation of sex bias among helminth-infected hosts. However, sex hormones not only can modulate the course of infection but also can be exploited by the parasites, and helminths appear to have developed molecules and pathways for this purpose. Furthermore, host sex may influence the efficacy of anti-helminth vaccines; however, although little data exist regarding this sex-dependent efficacy, host sex is known to influence the response to vaccines. Despite its importance, host sex is frequently overlooked in parasitological studies. This review focuses on the key contributors to sex bias in the case of helminth infection. The precise nature of the mechanisms/factors determining these sex-specific differences generally remains largely unknown, and this represents an obstacle in the development of control methods. There is an urgent need to identify any protective elements that could be targeted in future therapies to provide optimal disease management with regard to host sex. Hence, more research is needed into the impact of host sex on immunity and protection.},
}
@article {pmid36397169,
year = {2022},
author = {Springer, A and Wagner, L and Koehler, S and Klinger, S and Breves, G and Brüggemann, DA and Strube, C},
title = {Modulation of the porcine intestinal microbiota in the course of Ascaris suum infection.},
journal = {Parasites &amp; vectors},
volume = {15},
number = {1},
pages = {433},
pmid = {36397169},
issn = {1756-3305},
support = {STR 1171/16-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: The porcine roundworm Ascaris suum impairs feed conversion and weight gain, but its effects on intestinal microbiota remain largely unexplored.<br><br>METHODS: Modulation of the intestinal microbiota was assessed in pigs that were infected once with 10,000 A. suum eggs and pigs that received a trickle infection (1000 eggs/day over 10 days), compared with a non-infected control group. Six pigs each were sacrificed per group at days 21, 35 and 49 post-infection (p.i.). Faecal samples taken weekly until slaughter and ingesta samples from different intestinal compartments were subjected to next-generation sequencing of the bacterial 16S rRNA gene.<br><br>RESULTS: The results revealed marked differences between the single- and the trickle-infected group. Single infection caused a remarkable but transient decrease in microbial diversity in the caecum, which was not observed in the trickle-infected group. However, an increase in short-chain fatty acid-producing genera in the caecum on day 21 p.i., which shifted to a decrease on day 35 p.i., was common to both groups, possibly related to changes in excretory-secretory products following the parasite's final moult. Faecal microbial interaction networks were more similar between the single-infected and control group than the trickle-infected group. In addition, a lower degree of similarity over time indicated that A. suum trickle infection prevented microbiota stabilization.<br><br>CONCLUSIONS: These different patterns may have important implications regarding the comparability of experimental infections with natural scenarios characterized by continuous exposure, and should be confirmed by further studies.},
}
@article {pmid36397044,
year = {2022},
author = {Dudek-Wicher, R and Junka, AF and Migdał, P and Korzeniowska-Kowal, A and Wzorek, A and Bartoszewicz, M},
title = {The antibiofilm activity of selected substances used in oral health prophylaxis.},
journal = {BMC oral health},
volume = {22},
number = {1},
pages = {509},
pmid = {36397044},
issn = {1472-6831},
support = {SUBZ.D230.22.026//Uniwersytet Medyczny im. Piastów Slaskich we Wroclawiu/ ; SUBZ.D230.22.026//Uniwersytet Medyczny im. Piastów Slaskich we Wroclawiu/ ; SUBZ.D230.22.026//Uniwersytet Medyczny im. Piastów Slaskich we Wroclawiu/ ; 12/492227/SPUB/SP/2021//Hirszfeld Institute of Immunology and Experimental Therapy Polish Academy of Sciences/ ; 12/492227/SPUB/SP/2021//Hirszfeld Institute of Immunology and Experimental Therapy Polish Academy of Sciences/ ; },
abstract = {Oral health is a window to a patient's general well-being. Balance in oral microbiome functions is crucial for health maintenance. A state of oral dysbiosis may lead to a variety of local and systemic pathological conditions. The presence of dental plaque is related to the majority of oral infections. Proper oral hygiene is crucial and the most economic practice contributing to oral health prophylaxis. Aside from prophylactic treatments provided by dental practitioners, mouth rinses, containing antimicrobial agents, are one of the possible tools used for oral care. Our study was to determine whether available mouth rinses and selected products dedicated for professional use are efficient to eradicate biofilm formed by reference and clinical strains of Streptococcus mutans, Streptococcus sanguinis, Streptococcus oralis, Streptococcus mitis, Staphylococcus aureus, Enterococcus faecalis, Lactobacillus rhamnosus and Candida albicans on the surface of hydroxyapatite - major mineral component of a tooth. Therefore, such antimicrobials as chlorhexidine, cetylpyridine chloride, polyhexanide, silver nanoparticles, sulphonated phenolics, and natural antiplaque essential oils and coconut oil were analyzed. Applied experimental settings in in vitro models were designed to reflect accurately the recommended use of the tested substances, therefore four types of eradication procedure were conducted. Sialorrhea simulation was also performed to evaluate antibiofilm potential of diluted mouth rinses. Biofilm was investigated with quantitative method where absorbance values were measured. Statistical differences were assessed using the Kruskal-Wallis test with a post-hoc Dunnett's analysis. Results have shown that biofilms displayed a diversified sensitivity to the tested antimicrobials. The highest antibiofilm activity was detected for cetylpyridine chloride while the lowest for chlorhexidine. However the differences in E. faecalis biofilm reduction observed after the use of these two compounds were not statistically significant (p > 0.05), whereas all observed differences in S. aureus survival after exposure to the examined antimicrobial agents were statistically significant (p < 0.5). The PHMB, both in standard and in sialorrhea simulated conditions had the highest potential against streptococci. The coconut oil reduced C. albicans fungus biofilm by 65.48% but low eradication level was observed in case of bacterial biofilms. The dehydrating mechanism of action of sulfonated phenolics turned out to be ineffective against streptococcal biofilm which in turn was effectively eradicated by silver nanoparticles. The implementation of Antibiofilm Dressing's Activity Measurement method allowed to observe strain-related differences in terms of antimicrobial sensitivity. The obtained results may be introduced in everyday out-patient dental plaque prophylaxis as well as clinical environment.},
}
@article {pmid36396898,
year = {2022},
author = {O'Brien, MT and O'Sullivan, O and Claesson, MJ and Cotter, PD},
title = {The Athlete Gut Microbiome and its Relevance to Health and Performance: A Review.},
journal = {Sports medicine (Auckland, N.Z.)},
volume = {},
number = {},
pages = {},
pmid = {36396898},
issn = {1179-2035},
abstract = {The human gut microbiome is a complex ecosystem of microorganisms that play an important role in human health, influencing functions such as vitamin uptake, digestion and immunomodulation. While research of the gut microbiome has expanded considerably over the past decade, some areas such as the relationship between exercise and the microbiome remain relatively under investigated. Despite this, multiple studies have shown a potential bidirectional relationship between exercise and the gut microbiome, with some studies demonstrating the possibility of influencing this relationship. This, in turn, could provide a useful route to influence athletic performance via microbiome manipulation, a valuable prospect for many elite athletes and their teams. The evidence supporting the potential benefits of pursuing this route and associated future perspectives are discussed in this review.},
}
@article {pmid36396738,
year = {2022},
author = {Ninkov, M and Schmerk, CL and Moradizadeh, M and Parvathy, SN and Figueredo, R and Burton, JP and Silverman, MS and Fernandes, R and Maleki Vareki, S and Haeryfar, SMM},
title = {Improved MAIT cell functions following fecal microbiota transplantation for metastatic renal cell carcinoma.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {},
number = {},
pages = {},
pmid = {36396738},
issn = {1432-0851},
support = {Keith Samitt Translational Research Catalyst Grant//London Regional Cancer Program/ ; Innovation Grant 706396//Canadian Cancer Society/ ; },
abstract = {Strategies to modify the gut microbiome in cancer patients using fecal microbiota transplantation (FMT) have gained momentum as a therapeutic intervention. However, how FMT impacts innate-like, antimicrobial T lymphocytes is unclear. In this study, we assessed peripheral blood (PB) mucosa-associated invariant T (MAIT) cell frequencies and functions in patients with metastatic renal cell carcinoma (mRCC) before and seven days after they received FMT as part of a clinical trial. We found comparable MAIT cell frequencies in healthy controls and mRCC patients. In contrast, γδ T cells exhibited a numerical decline in mRCC, which was partially reversed by FMT. We also found a significant increase in the PB CD4[+] MAIT cell compartment of mRCC patients with or without FMT. Paired sample analyses revealed CD69 upregulation on MAIT cells accompanied by decreased PD-1 levels post-FMT. These changes were unique to MAIT cells as non-MAIT T lymphocytes showed either no trend or a trend in the opposite direction. Importantly, FMT did not render MAIT cells exhausted as also judged by their stable expression of TIM-3, LAG-3, BTLA, CTLA-4, TIGIT and VISTA. These findings were corroborated in functional assays in which MAIT cells were stimulated with MR1 ligands or with a combination of IL-12 and IL-18 to produce inflammatory cytokines and granzyme B. Indeed, when stimulated ex vivo with IL-12 and IL-18, MAIT cells mounted a more rigorous TNF-α response post-FMT. In conclusion, FMT improves MAIT cell functions, which should serve patients well in subsequent microbial challenges in the face of cancer-elicited immunosuppression. Trial Registration: https://clinicaltrials.gov/ Identifier: NCT04163289 (registration date: November 14, 2019).},
}
@article {pmid36396730,
year = {2022},
author = {Baede, VO and Barray, A and Tavakol, M and Lina, G and Vos, MC and Rasigade, JP},
title = {Nasal microbiome disruption and recovery after mupirocin treatment in Staphylococcus aureus carriers and noncarriers.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {19738},
pmid = {36396730},
issn = {2045-2322},
support = {547001006/ZONMW_/ZonMw/Netherlands ; 16-JPEC-0006//Agence Nationale de la Recherche/ ; },
abstract = {Nasal decolonization procedures against the opportunistic pathogen Staphylococcus aureus rely on topical antimicrobial drug usage, whose impact on the nasal microbiota is poorly understood. We examined this impact in healthy S. aureus carriers and noncarriers. This is a prospective interventional cohort study of 8 S. aureus carriers and 8 noncarriers treated with nasal mupirocin and chlorhexidine baths. Sequential nasal swabs were taken over 6 months. S. aureus was detected by quantitative culture and genotyped using spa typing. RNA-based 16S species-level metabarcoding was used to assess the living microbial diversity. The species Dolosigranulum pigrum, Moraxella nonliquefaciens and Corynebacterium propinquum correlated negatively with S. aureus carriage. Mupirocin treatment effectively eliminated S. aureus, D. pigrum and M. nonliquefaciens, but not corynebacteria. S. aureus recolonization in carriers occurred more rapidly than recolonization by the dominant species in noncarriers (median 3 vs. 6 months, respectively). Most recolonizing S. aureus isolates had the same spa type as the initial isolate. The impact of mupirocin-chlorhexidine treatment on the nasal microbiota was still detectable after 6 months. S. aureus recolonization predated microbiota recovery, emphasizing the strong adaptation of this pathogen to the nasal niche and the transient efficacy of the decolonization procedure.},
}
@article {pmid36396724,
year = {2022},
author = {Prieto, JM and Wang, AW and Halbach, J and Cauvi, DM and Day, JMD and Gembicky, M and Ghassemian, M and Quehenberger, O and Kling, K and Ignacio, R and DeMaio, A and Bickler, SW},
title = {Elemental, fatty acid, and protein composition of appendicoliths.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {19764},
pmid = {36396724},
issn = {2045-2322},
abstract = {Appendicoliths are commonly found obstructing the lumen of the appendix at the time of appendectomy. To identify factors that might contribute to their formation we investigated the composition of appendicoliths using laser ablation inductively coupled plasma mass spectroscopy, gas chromatography, polarized light microscopy, X-ray crystallography and protein mass spectroscopy. Forty-eight elements, 32 fatty acids and 109 human proteins were identified within the appendicoliths. The most common elements found in appendicoliths are calcium and phosphorus, 11.0 ± 6.0 and 8.2 ± 4.2% weight, respectively. Palmitic acid (29.7%) and stearate (21.3%) are the most common fatty acids. Some stearate is found in crystalline form-identifiable by polarized light microscopy and confirmable by X-ray crystallography. Appendicoliths have an increased ratio of omega-6 to omega-3 fatty acids (ratio 22:1). Analysis of 16 proteins common to the appendicoliths analyzed showed antioxidant activity and neutrophil functions (e.g. activation and degranulation) to be the most highly enriched pathways. Considered together, these preliminary findings suggest oxidative stress may have a role in appendicolith formation. Further research is needed to determine how dietary factors such as omega-6 fatty acids and food additives, redox-active metals and the intestinal microbiome interact with genetic factors to predispose to appendicolith formation.},
}
@article {pmid36396669,
year = {2022},
author = {Gundersen, MS and Vadstein, O and De Schryver, P and Attramadal, KJK},
title = {Aquaculture rearing systems induce no legacy effects in Atlantic cod larvae or their rearing water bacterial communities.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {19812},
pmid = {36396669},
issn = {2045-2322},
abstract = {The microbial rearing quality influences the survival of marine larvae. Microbially matured water treatment systems (MMS) provide a more favourable rearing water microbiome than flow-through systems (FTS). It has previously been hypothesised, but not investigated, that initial rearing in MMS leaves a protective legacy effect in Atlantic cod larvae (Gadus morhua). We tested this hypothesis through a crossover 2 × 2 factorial experiment varying the rearing water treatment system (MMS vs FTS) and the microbial carrying capacity (+ /- added organic matter). At 9 days post-hatching, we switched the rearing water treatment system. By comparing switched and unswitched rearing tanks, we evaluated if legacy effects had been established in the larvae or their surrounding rearing water bacterial community. We analysed the bacterial communities with flow cytometry and 16S rRNA gene sequencing. We found no evidence that the initial rearing condition left a legacy effect in the communities by evaluating the bacterial community diversity and structure. Instead, the present rearing condition was the most important driver for differences in the rearing water microbiota. Furthermore, we found that MMS with high microbial carrying capacity appeared to seed a stable bacterial community to the rearing tanks. This finding highlights the importance of keeping a similar carrying capacity between the inlet and rearing water. Moreover, we reject the hypothesis that the initial rearing condition leaves a protective legacy effect in larvae, as the larval survival and robustness were linked to the present rearing condition. In conclusion, our results highlight the importance of maintaining a beneficial microbial rearing environment from hatching and throughout the larval rearing period.},
}
@article {pmid36396563,
year = {2022},
author = {Suarez Arbelaez, MC and Israeli, JM and Tipton, CD and Loloi, J and Deebel, N and Leong, JY and Ramasamy, R},
title = {Pilot Study: Next-generation Sequencing of the Semen Microbiome in Vasectomized Versus Nonvasectomized Men.},
journal = {European urology focus},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.euf.2022.11.010},
pmid = {36396563},
issn = {2405-4569},
abstract = {BACKGROUND: Approximately half a million vasectomies are performed every year in the USA. There is a paucity of literature on the impact of male sterilization on the semen microbiome and whether it prompts microbiota dysbiosis.<br><br>OBJECTIVE: To investigate if vasectomy induces changes in the seminal microbiome via comparison of semen samples from men before and after vasectomy, and if the seminal microbiome profiles for vasectomized men follow a particular pattern with respect to diversity and abundance.<br><br>From July 2021 to February 2022, we prospectively collected and analyzed semen samples from 58 men at one outpatient clinic. Eighteen men provided a semen sample before and 3 mo after vasectomy. We also collected semen samples from 22 fertile nonvasectomized men and from a further 18 vasectomized men at 3 mo after vasectomy.<br><br>Semen microbiome α-diversity, beta-diversity, and relative abundance were compared initially between paired and then between unpaired vasectomized and nonvasectomized samples. Analysis of variance (ANOVA), permutational multivariate ANOVA, and analysis of the composition of microbiomes with bias correction were used to assess differences.<br><br>RESULTS AND LIMITATIONS: In both paired and unpaired sets of samples, a decreasing trend for α-diversity in semen after vasectomy was observed. Shannon diversity, the relative abundance of species with an abundance >2%, and composition were not significantly changed. Sphingomonas, Brevundimonas, and Paracoccus abundance decreased after vasectomy, while Corynebacterium abundance increased. The results may be limited by the sample size and lack of demographic heterogeneity.<br><br>CONCLUSIONS: Vasectomy is followed by a decrease in α-diversity and changes in the relative abundance of bacterial species in the semen microbiome. Further investigation is necessary to understand the clinical significance of these changes after vasectomy.<br><br>PATIENT SUMMARY: We evaluated changes in the bacteria species in semen after vasectomy. We found that vasectomy decreased the richness and evenness of bacteria species in semen, but the overall bacterial community remained similar. Further studies are needed to assess the implications of changes in semen bacteria after vasectomy.},
}
@article {pmid36396443,
year = {2022},
author = {Young, G and Berrington, JE and Cummings, S and Dorling, J and Ewer, AK and Frau, A and Lett, L and Probert, C and Juszczak, E and Kirby, J and Beck, LC and Renwick, VL and Lamb, C and Lanyon, CV and McGuire, W and Stewart, C and Embleton, N},
title = {Mechanisms affecting the gut of preterm infants in enteral feeding trials: a nested cohort within a randomised controlled trial of lactoferrin.},
journal = {Archives of disease in childhood. Fetal and neonatal edition},
volume = {},
number = {},
pages = {},
doi = {10.1136/archdischild-2022-324477},
pmid = {36396443},
issn = {1468-2052},
abstract = {OBJECTIVE: To determine the impact of supplemental bovine lactoferrin on the gut microbiome and metabolome of preterm infants.<br><br>DESIGN: Cohort study nested within a randomised controlled trial (RCT). Infants across different trial arms were matched on several clinical variables. Bacteria and metabolite compositions of longitudinal stool and urine samples were analysed to investigate the impact of lactoferrin supplementation.<br><br>SETTING: Thirteen UK hospitals participating in a RCT of lactoferrin.<br><br>PATIENTS: 479 infants born <32 weeks' gestation between June 2016 and September 2017.<br><br>RESULTS: 10 990 stool and 22 341 urine samples were collected. Analyses of gut microbiome (1304 stools, 201 infants), metabolites (171 stools, 83 infants; 225 urines, 90 infants) and volatile organic compounds (314 stools, 117 infants) were performed. Gut microbiome Shannon diversity at 34 weeks corrected age was not significantly different between infants in the lactoferrin (mean=1.24) or placebo (mean=1.06) groups (p=0.11). Lactoferrin receipt explained less than 1% variance in microbiome compositions between groups. Metabolomic analysis identified six discriminative features between trial groups. Hospital site (16%) and postnatal age (6%) explained the greatest variation in microbiome composition.<br><br>CONCLUSIONS: This multiomic study identified minimal impacts of lactoferrin but much larger impacts of hospital site and postnatal age. This may be due to the specific lactoferrin product used, but more likely supports the findings of the RCT in which this study was nested, which showed no impact of lactoferrin on reducing rates of sepsis. Multisite mechanistic studies nested within RCTs are feasible and help inform trial interpretation and future trial design.},
}
@article {pmid36396342,
year = {2022},
author = {Ronchetti, F and Polidori, C and Schmitt, T and Steffan-Dewenter, I and Keller, A},
title = {Bacterial gut microbiomes of aculeate brood parasites overlap with their aculeate hosts', but have higher diversity and specialization.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiac137},
pmid = {36396342},
issn = {1574-6941},
abstract = {Despite growing interest in gut microbiomes of aculeate Hymenoptera, research so far focused on social bees, wasps and ants, whereas non-social taxa and their brood parasites have not received much attention. Brood parasitism however allows to distinguish between microbiome components horizontally transmitted by spill-over from the host with such inherited through vertical transmission by mothers. Here, we studied the bacterial gut microbiome of adults in seven aculeate species in four brood parasite-host systems: two bee-mutillid (host-parasitoid) systems, one halictid bee-cuckoo bee system and one wasp-chrysidid cuckoo wasp system. We addressed the following questions: 1) Do closely related species possess a more similar gut microbiome? 2) Do brood parasites share components of the microbiome with their host? 3) Do brood parasites have different diversity and specialization of microbiome communities compared with the hosts? Our results indicate that the bacterial gut microbiome of the studied taxa was species-specific, yet with a limited effect of host phylogenetic relatedness and a major contribution of shared microbes between hosts and parasites. However, contrasting patterns emerged between bee-parasite systems and the wasp-parasite system. We conclude that the gut microbiome in adult brood parasites is largely affected by their host-parasite relationships and the similarity of trophic food sources between hosts and parasites.},
}
@article {pmid36396066,
year = {2022},
author = {Kenfield, SA and Philip, EJ and Phillips, SM and Meyerhardt, JA and Chan, JM and Atreya, CE and Kim, MO and Harris, Q and Steiding, P and Macaire, G and McCullough, ML and Piawah, S and Johnson, WY and Kurttila, FA and Lewis, WL and Pesman, C and Watson, Y and Van Blarigan, EL},
title = {Optimizing intervention tools to improve nutrition and physical activity for colorectal cancer survivors (tools to be fit): Study protocol of a randomized factorial experiment.},
journal = {Contemporary clinical trials},
volume = {},
number = {},
pages = {107009},
doi = {10.1016/j.cct.2022.107009},
pmid = {36396066},
issn = {1559-2030},
abstract = {BACKGROUND: Colorectal cancer (CRC) is the 2nd leading cause of cancer death in the United States. The American Cancer Society (ACS) Nutrition and Physical Activity Guidelines are associated with longer survival among CRC survivors, but few report behaviors consistent with the guidelines.<br><br>METHODS: The Tools To Be Fit study, based on the Multiphase Optimization Strategy (MOST) framework, is a full factorial experimental to optimize a remotely delivered 48-week diet and physical activity intervention for non-metastatic CRC survivors. The intervention includes a core component (booklet and personal report). CRC survivors (N = 400) are additionally randomly assigned to one of 16 combinations of four candidate components, each with 2 options: 1) text messaging (on/off); 2) self-monitoring modality (digital/paper); 3) health coaching (on/off); and 4) support person coaching (on/off).<br><br>OUTCOMES: Our primary outcome is adherence to the ACS guidelines after 48 weeks using a score that includes physical activity from accelerometers, dietary intake from a food frequency questionnaire, and body mass index (BMI) measured by a technician. Secondary outcomes include the ACS score after 24 weeks and score components at 24 and 48 weeks. Exploratory outcomes include adherence and change in Social Cognitive Theory constructs. We will explore moderation by sociodemographic, clinical, and psychological/behavioral factors; and change in the ACS score in relation to change in levels of insulin, insulin sensitivity, inflammation, gut microbiome structure, fatigue, depression, and sleep disturbance.<br><br>DISCUSSION: The proposed study aims to inform a randomized controlled trial to determine whether an optimized intervention reduces risk of recurrence among CRC survivors.},
}
@article {pmid36395969,
year = {2022},
author = {Zhang, Z and Liu, C and Fang, W and Tang, Q and Zhan, L and Shi, Y and Tang, M and Liu, Z and Zhang, S and Liu, A},
title = {Research Progress on the Lipid-Lowering and Weight Loss Effects of Tea and the Mechanism of its Functional Components.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {109210},
doi = {10.1016/j.jnutbio.2022.109210},
pmid = {36395969},
issn = {1873-4847},
abstract = {Obesity caused by poor eating habits has become a great challenge faced by public health organizations worldwide. Optimizing dietary intake and ingesting special foods containing biologically active substances (such as polyphenols, alkaloids, and terpenes) is a safe and effective dietary intervention to prevent the occurrence and development of obesity. Tea contains several active dietary factors, and daily tea consumption has been shown to have various health benefits, especially in regulating human metabolic diseases. Here, we reviewed recent advances in research on tea and its functional components in improving obesity-related metabolic dysfunction, and gut microbiota homeostasis and related clinical research. Furthermore, the potential mechanisms by which the functional components of tea could promote lipid-lowering and weight-loss effects by regulating fat synthesis/metabolism, glucose metabolism, gut microbial homeostasis, and liver function were summarized. The research results showing a "positive effect" or "no effect" objectively evaluate the lipid-lowering and weight-loss effects of the functional components of tea. This review provides a new scientific basis for further research on the functional ingredients of tea for lipid lowering and weight loss and the development of lipid-lowering and weight-loss functional foods and beverages derived from tea.},
}
@article {pmid36395873,
year = {2022},
author = {Sun, J and DeBosch, B},
title = {Guardian, Intermediary, or Perpetrator? New insights into environmental exposure, the gut microbiome, and NAFLD.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2022.11.017},
pmid = {36395873},
issn = {1528-0012},
}
@article {pmid36395738,
year = {2022},
author = {Zhang, W and Huang, J and Gao, F and You, Q and Ding, L and Gong, J and Zhang, M and Ma, R and Zheng, S and Sun, X and Zhang, Y},
title = {Lactobacillus reuteri normalizes altered fear memory in male Cntnap4 knockout mice.},
journal = {EBioMedicine},
volume = {86},
number = {},
pages = {104323},
doi = {10.1016/j.ebiom.2022.104323},
pmid = {36395738},
issn = {2352-3964},
abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a common neurodevelopmental disease, characterized by deficits in social communication, restricted and repetitive behaviours, and impaired fear memory processing. Severe gastrointestinal dysfunction and altered gut microbiome have been reported in ASD patients and animal models. Contactin associated protein-like 4 (CNTNAP4) has been suggested to be a novel risk gene, though its role in ASD remains unelucidated.<br><br>METHODS: Cntnap4[-/-] mice were generated to explore its role in ASD-related behavioural abnormalities. Electrophysiological recording was employed to examine GABAergic transmission in the basolateral amygdala (BLA) and prefrontal cortex. RNA-sequencing was performed to assess underlying mechanisms. 16S rDNA analysis was performed to explore changes in faecal microbial composition. Male Cntnap4[-/-] mice were fed with Lactobacillus reuteri (L. reuteri) or faecal microbiota to evaluate the effects of microbiota supplementation on the impaired fear conditioning mediated by Cntnap4 deficiency.<br><br>FINDINGS: Male Cntnap4[-/-] mice manifested deficiency in social behaviours and tone-cue fear conditioning. Notably, reduced GABAergic transmission and GABA receptor expression were found in the BLA but not the prefrontal cortex. In addition, gut Lactobacillus were less abundant in male Cntnap4[-/-] mice, and L. reuteri treatment or faecal microbiota transplantation rescued abnormal tone-cued fear memory and improved local GABAergic transmission in the BLA of male Cntnap4[-/-] mice.<br><br>INTERPRETATION: Cntnap4 shapes GABAergic transmission of amygdala and fear conditioning, and microbial intervention represents a promising therapy in ASD intervention.<br><br>FUNDING: National Natural Science Foundation of China, Science and Technology Planning Project of Guangzhou, Guangzhou Medical University, and China Postdoctoral Science Foundation.},
}
@article {pmid36395362,
year = {2022},
author = {Moreira, FC and Sarquis, DP and Souza, JES and Avelar, DS and Araújo, TMT and Khayat, AS and Santos, SEBD and de Assumpção, PP},
title = {Treasures from trash in cancer research.},
journal = {Oncotarget},
volume = {13},
number = {},
pages = {1246-1257},
doi = {10.18632/oncotarget.28308},
pmid = {36395362},
issn = {1949-2553},
abstract = {INTRODUCTION: Cancer research has significantly improved in recent years, primarily due to next-generation sequencing (NGS) technology. Consequently, an enormous amount of genomic and transcriptomic data has been generated. In most cases, the data needed for research goals are used, and unwanted reads are discarded. However, these eliminated data contain relevant information. Aiming to test this hypothesis, genomic and transcriptomic data were acquired from public datasets.<br><br>MATERIALS AND METHODS: Metagenomic tools were used to explore genomic cancer data; additional annotations were used to explore differentially expressed ncRNAs from miRNA experiments, and variants in adjacent to tumor samples from RNA-seq experiments were also investigated.<br><br>RESULTS: In all analyses, new data were obtained: from DNA-seq data, microbiome taxonomies were characterized with a similar performance of dedicated metagenomic research; from miRNA-seq data, additional differentially expressed sncRNAs were found; and in tumor and adjacent to tumor tissue data, somatic variants were found.<br><br>CONCLUSIONS: These findings indicate that unexplored data from NGS experiments could help elucidate carcinogenesis and discover putative biomarkers with clinical applications. Further investigations should be considered for experimental design, providing opportunities to optimize data, saving time and resources while granting access to multiple genomic perspectives from the same sample and experimental run.},
}
@article {pmid36394926,
year = {2022},
author = {Fedotova, MM and Prokopyeva, VD and Dochkin, VA and Boguta, VD and Fedorova, OS},
title = {[Methods of gut microbiota correction for treatment and prevention of food allergy: a review of current research].},
journal = {Voprosy pitaniia},
volume = {91},
number = {5},
pages = {16-28},
doi = {10.33029/0042-8833-2022-91-5-16-28},
pmid = {36394926},
issn = {0042-8833},
abstract = {Food allergy (FA) is an actual problem in pediatric practice. The gut microbiota plays a crucial role in food sensitization development, since the maturation of immune system occurs under the influence of intestinal microorganisms. Immunoregulatory activity of gut microbiota is associated with the increase of IgA production and promotion of the barrier function of intestinal epithelium. Gut microbiota influence the activity of T-regulatory cells, as well. Violation of gut biocenosis, which occurs under the influence of various factors (artificial feeding, past diseases, the use of antibiotics, etc.), can lead to a shift in the balance of the immune system towards the increase of Th2-profile cytokines and the subsequent formation of hypersensitivity to food allergens. In this regard, the correction of the gut microbiome is a promising method of FA control, due to the ability of intestinal bacteria influence the production of T-regulatory cells and thus suppress allergy immune response. The aim of the review is to analyze experimental and clinical studies exploring effectiveness of methods modifying intestinal microbiota in order to treat and prevent FA. Material and methods. The analysis of the literature in eLIBRARY, MedLine and PubMed databases was carried out. Results. The analysis revealed the lack of rigorous evidence that pre-, pro- and synbiotics significantly increase the effectiveness of standard therapy of FA. However, the use of bifidobacteria, lactobacilli, lactic acid bacteria, in combination with the basic therapy of FA has general positive effect on the clinical outcome, especially in case of gastrointestinal symptoms. Also, the results of some studies indicate the effectiveness of synbiotics (Bifidobacterium breve M-16V, Lactobacillus rhamnosus GG in combination with oligosaccharides) for the prevention of FA in patients at risk of developing allergic diseases in the long-term period. Conclusion. At present, fecal microbiota transplantation is promising method for FA treatment. Polysaccharides fermented by the microflora, are also actively studied. Experimental studies and clinical trials are required to obtain substantiated conclusions about feasibility of these methods for treatment and prevention of FA.},
}
@article {pmid36394607,
year = {2022},
author = {Ralli, T and Saifi, Z and Tyagi, N and Vidyadhari, A and Aeri, V and Kohli, K},
title = {Deciphering the role of gut metabolites in non-alcoholic fatty liver disease.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/1040841X.2022.2142091},
pmid = {36394607},
issn = {1549-7828},
abstract = {Perturbations in microbial abundance or diversity in the intestinal lumen leads to intestinal inflammation and disruption of intestinal membrane which eventually facilitates the translocation of microbial metabolites or whole microbes to the liver and other organs through portal vein. This process of translocation finally leads to multitude of health disorders. In this review, we are going to focus on the mechanisms by which gut metabolites like SCFAs, tryptophan (Trp) metabolites, bile acids (BAs), ethanol, and choline can either cause the development/progression of non-alcoholic fatty liver disease (NAFLD) or serves as a therapeutic treatment for the disease. Alterations in some metabolites like SCFAs, Trp metabolites, etc., can serve as biomarker molecules whereas presence of specific metabolites like ethanol definitely leads to disease progression. Thus, proper understanding of these mechanisms will subsequently help in designing of microbiome-based therapeutic approaches. Furthermore, we have also focussed on the role of dysbiosis on the mucosal immune system. In addition, we would also compile up the microbiome-based clinical trials which are currently undergoing for the treatment of NAFLD and non-alcoholic steatohepatitis (NASH). It has been observed that the use of microbiome-based approaches like prebiotics, probiotics, symbiotics, etc., can act as a beneficial treatment option but more research needs to be done to know how to manipulate the composition of gut microbes.},
}
@article {pmid36394486,
year = {2022},
author = {Ferreira Vivolo, SR and da Rocha Fernandes, G},
title = {Are studies of human gut microbiome the new fad following the SNP mainstream?.},
journal = {Archives of endocrinology and metabolism},
volume = {66},
number = {6},
pages = {929-930},
doi = {10.20945/2359-3997000000568},
pmid = {36394486},
issn = {2359-4292},
}
@article {pmid36394327,
year = {2022},
author = {Mann, E and Shekarriz, S and Surette, MG},
title = {Human Gut Metagenomes Encode Diverse GH156 Sialidases.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0175522},
doi = {10.1128/aem.01755-22},
pmid = {36394327},
issn = {1098-5336},
abstract = {The intestinal lining is protected by a mucous barrier composed predominantly of complex carbohydrates. Gut microbes employ diverse glycoside hydrolases (GHs) to liberate mucosal sugars as a nutrient source to facilitate host colonization. Intensive catabolism of mucosal glycans, however, may contribute to barrier erosion, pathogen encroachment, and inflammation. Sialic acid is an acidic sugar featured at terminal positions of host glycans. Characterized sialidases from the microbiome belong to the GH33 family, according to CAZy (Carbohydrate-Active enZYmes Database). In 2018 a functional metagenomics screen using thermal spring DNA uncovered the founding member of the GH156 sialidase family, the presence of which has yet to be reported in the context of the human microbiome. A subset of GH156 sequences from the CAZy database containing key sialidase residues was used to build a hidden Markov model. HMMsearch against public databases revealed ~10× more putative GH156 sialidases than currently cataloged by CAZy. Represented phyla include Bacteroidota, Verrucomicrobiota, and Firmicutes_A from human microbiomes, all of which play notable roles in carbohydrate fermentation. Analyses of metagenomic data sets revealed that GH156s are frequently encoded in metagenomes, with a greater variety and abundance of GH156 genes observed in traditional hunter-gatherer or agriculturalist societies than in industrialized societies, particularly relative to individuals with inflammatory bowel disease (IBD). Nineteen GH156s were recombinantly expressed and assayed for sialidase activity. The five GH156 sialidases identified here share limited sequence identity to each other or the founding GH156 family member and are representative of a large subset of the family. IMPORTANCE Sialic acids occupy terminal positions of human glycans where they act as receptors for microbes, toxins, and immune signaling molecules. Microbial enzymes that remove sialic acids, sialidases, are abundant in the human microbiome where they may contribute to shaping the microbiota community structure or contribute to pathology. Furthermore, sialidases have proven to hold therapeutic potential for cancer therapy. Here, we examined the sequence space of a sialidase family of enzymes, GH156, previously unknown in the human gut environment. Our analyses suggest that human populations with disparate dietary practices harbor distinct varieties and abundances of GH156-encoding genes. Furthermore, we demonstrate the sialidase activity of 5 gut-derived GH156s. These results expand the diversity of sialidases that may contribute to host glycan degradation, and these sequences may have biotechnological or clinical utility.},
}
@article {pmid36394322,
year = {2022},
author = {Cole, TJ and Parker, JK and Feller, AL and Wilke, CO and Davies, BW},
title = {Evidence for Widespread Class II Microcins in Enterobacterales Genomes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0148622},
doi = {10.1128/aem.01486-22},
pmid = {36394322},
issn = {1098-5336},
abstract = {Microcins are a class of antimicrobial peptides produced by certain Gram-negative bacterial species to kill or inhibit the growth of competing bacteria. Only 10 unique, experimentally validated class II microcins have been identified, and the majority of these come from Escherichia coli. Although the current representation of microcins is sparse, they exhibit a diverse array of molecular functionalities, uptake mechanisms, and target specificities. This broad diversity from such a small representation suggests that microcins may have untapped potential for bioprospecting peptide antibiotics from genomic data sets. We used a systematic bioinformatics approach to search for verified and novel class II microcins in E. coli and other species within its family, Enterobacteriaceae. Nearly one-quarter of the E. coli genome assemblies contained one or more microcins, where the prevalence of hits to specific microcins varied by isolate phylogroup. E. coli isolates from human extraintestinal and poultry meat sources were enriched for microcins, while those from freshwater were depleted. Putative microcins were found in various abundances across all five distinct phylogenetic lineages of Enterobacteriaceae, with a particularly high prevalence in the "Klebsiella" clade. Representative genome assemblies from species across the Enterobacterales order, as well as a few outgroup species, also contained putative microcin sequences. This study suggests that microcins have a complicated evolutionary history, spanning far beyond our limited knowledge of the currently validated microcins. Efforts to functionally characterize these newly identified microcins have great potential to open a new field of peptide antibiotics and microbiome modulators and elucidate the ways in which bacteria compete with each other. IMPORTANCE Class II microcins are small bacteriocins produced by strains of Gram-negative bacteria in the Enterobacteriaceae. They are generally understood to play a role in interbacterial competition, although direct evidence of this is limited, and they could prove informative in developing new peptide antibiotics. However, few examples of verified class II microcins exist, and novel microcins are difficult to identify due to their sequence diversity, making it complicated to study them as a group. Here, we overcome this limitation by developing a bioinformatics pipeline to detect microcins in silico. Using this pipeline, we demonstrate that both verified and novel class II microcins are widespread within and outside the Enterobacteriaceae, which has not been systematically shown previously. The observed prevalence of class II microcins suggests that they are ecologically important, and the elucidation of novel microcins provides a resource that can be used to expand our knowledge of the structure and function of microcins as antibacterials.},
}
@article {pmid36394321,
year = {2022},
author = {Shetty, SA and Stege, PB and Hordijk, J and Gijsbers, E and Dierikx, CM and van Duijkeren, E and Franz, E and Willems, RJL and Paganelli, FL and Fuentes, S},
title = {Species-Specific Patterns of Gut Metabolic Modules in Dutch Individuals with Different Dietary Habits.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0051222},
doi = {10.1128/msphere.00512-22},
pmid = {36394321},
issn = {2379-5042},
abstract = {Diet is an important determinant of the human gut microbiome. Here, we analyzed fecal metagenomes of Dutch adults following omnivorous, pescatarian, vegan, and vegetarian diets. We compared the taxonomic composition of individuals from our study with publicly available gut metagenomes from westernized and non-westernized societies. We observed that, despite long-term transition to diets rich in plant fibers (vegan or vegetarian), the microbiomes of these were typical of westernized populations, and similar in composition to omnivores. Although there were no major differences in metabolic modules, we identified differences in the species that contributed to particular functions, such as carbohydrate degradation and short-chain fatty acid metabolism. Overall, this study shows functional redundancy of the microbiomes among westernized populations, which is independent of long-term individual dietary habits. IMPORTANCE Diet is an important modulator of the human gut microbiome, which is susceptible to increased consumption of plant fibers in vegan or vegetarian lifestyles. To investigate this, we compared the gut microbiome of Dutch adults following omnivorous, pescatarian, vegan and vegetarian diets. We did not observe major differences in the gut microbiome composition and function between individuals with different dietary habits. However, we observed differences in the species that contribute to the core functions of the gut microbiome. Our study thus emphasizes the need to better understand the species-specific functional changes associated with dietary habits in the human gut microbiome.},
}
@article {pmid36394280,
year = {2022},
author = {Thompson, KN and Oulhote, Y and Weihe, P and Wilkinson, JE and Ma, S and Zhong, H and Li, J and Kristiansen, K and Huttenhower, C and Grandjean, P},
title = {Effects of Lifetime Exposures to Environmental Contaminants on the Adult Gut Microbiome.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.2c03185},
pmid = {36394280},
issn = {1520-5851},
abstract = {Emerging experimental evidence indicates that toxicant-induced alterations in gut microbiota composition and activity may affect host homeostasis. However, data from human studies are scarce; to our knowledge, no previous studies have quantified the association of lifetime exposure to environmental chemicals, across multiple time points, with the composition of the adult gut microbiome. Here we studied 124 individuals born in the Faroe Islands in 1986-1987 who were followed approximately every seven years from birth through age 28 years. Organochlorine compounds, including polychlorinated biphenyls (PCBs) and pesticides, perfluoroalkyl substances (PFAS), and mercury (Hg), were measured in cord blood and longitudinally in participants' blood. At age 28, the gut microbiome was assessed using shotgun metagenomic sequencing. Historical contaminant exposures had little direct effect on the adult gut microbiome, while a small number of fastidious anaerobes were weakly linked to recent PFAS/PFOS exposures at age 28. In this cohort, our findings suggest no lasting effects of early life exposures on adult gut microbial composition, but proximal exposures may contribute to gut microbiome alterations. The methods developed and used for this investigation may help in future identification of small but lasting impacts of environmental toxicant exposure on the gut microbiome.},
}
@article {pmid36394178,
year = {2022},
author = {Malone, M},
title = {APMIS 2022 Focus Issue on Human microbiome in disease and pathology.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {},
number = {},
pages = {},
doi = {10.1111/apm.13283},
pmid = {36394178},
issn = {1600-0463},
}
@article {pmid36393885,
year = {2022},
author = {Saleh, S and Sullivan, SE and Bellile, E and Roxbury, C and Das, P and Hachem, RA and Ackall, F and Jang, D and Celtikci, E and Sahin, MM and D'souza, G and Evans, JJ and Nyquist, G and Khalafallah, A and Mukherjee, D and Rowan, NR and Camp, S and Choby, G and Gompel, JJV and Ghiam, MK and Levine, CG and Field, M and Adappa, N and Locke, TB and Rassekh, C and Sweis, AM and Goyal, N and Zacharia, B and Wilson, MN and Patel, S and Gardner, PA and Snyderman, CH and Wang, EW and Glancz, LJ and Bagchi, A and Dow, G and Robertson, I and Rangarajan, SV and Michael, LM and McKean, EL},
title = {Retrospective Review of Surgical Site Infections after Endoscopic Endonasal Sellar and Parasellar Surgery: Multicenter Quality Data from the North American Skull Base Society.},
journal = {Journal of neurological surgery. Part B, Skull base},
volume = {83},
number = {6},
pages = {579-588},
doi = {10.1055/a-1865-3202},
pmid = {36393885},
issn = {2193-6331},
abstract = {Introduction Transnasal access to the anterior skull base provides a minimally invasive approach for sellar and parasellar masses compared with its open counterparts. The unique microbiome of the sinonasal mucosa provides distinct challenges not encountered with other cranial approaches. The use of antibiotics in these cases has not been standardized, and data remain scarce regarding infectious outcomes. Methods We conducted a multicenter retrospective analysis of shared quality data points for the endoscopic endonasal approach (EEA) for pituitary adenomas, along with other sellar and parasellar region masses that were included by participating institutions. Patient and operative characteristics, perioperative and postoperative antibiotic regimens and their durations, intraoperative and postoperative cerebrospinal fluid leak, and onset of postoperative meningitis and sinusitis were compared. Results Fifteen institutions participated and provided 6 consecutive months' worth of case data. Five hundred ninety-three cases were included in the study, of which 564 were pituitary adenomectomies. The incidences of postoperative meningitis and sinusitis were low (0.67 and 2.87% for all pathologies, respectively; 0.35% meningitis for pituitary adenomas) and did not correlate with any specific antibiotic regimen. Immunocompromised status posed an increased odds of meningitis in pituitary adenomectomies (28.6, 95% confidence interval [1.72-474.4]). Conclusions The results show no clear benefit to postoperative antimicrobial use in EEA, with further larger studies needed.},
}
@article {pmid36389800,
year = {2022},
author = {Lv, H and Wang, Y and Gao, Z and Liu, P and Qin, D and Hua, Q and Xu, Y},
title = {Knowledge mapping of the links between the microbiota and allergic diseases: A bibliometric analysis (2002-2021).},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {1045795},
doi = {10.3389/fimmu.2022.1045795},
pmid = {36389800},
issn = {1664-3224},
abstract = {Background: In recent decades, dramatic changes in modern environmental exposures and lifestyles have resulted in a steep rise in the prevalence of allergic diseases such as asthma, allergic rhinitis, atopic dermatitis and food allergies. Evidence is mounting that the microbiota plays a crucial role in allergic disorder development and evolution. Therefore, a better understanding of allergic diseases within the context of the microbiota is urgently needed. This work aimed to comprehensively outline general characteristics, research hotspots, evolution routes, and emerging trends in this area.<br><br>Methods: Relevant publications from January 2002 to December 2021 were obtained from the Web of Science Core Collection on 5 August 2022. Bibliometric and visual analyses were performed using CiteSpace; VOSviewer; an online bibliometric platform; and Microsoft Excel 2019.<br><br>Results: In total, 2535 documents met the requirements. The annual number of publications has shown rapid growth in the last two decades. The USA, University of California System, and Isolauri E of the University of Turku were the most productive and influential country, institution, and author, respectively. The Journal of Allergy and Clinical Immunology was the most prolific and most cocited journal. High-frequency keywords included "gut microbiota", "asthma", "atopic dermatitis", "children", and "probiotics". Recent studies have focused on "atopic dermatitis", "skin", "asthma", and "probiotics", according to the cocitation analysis of references. Burst detection analysis of keywords showed that "community", "skin microbiome", "microbiome", "Staphylococcus aureus", and "chain fatty acid" were emerging research frontiers, which currently have ongoing bursts.<br><br>Conclusion: In the last 20 years, studies of the microbiota in allergic diseases have been flourishing, and the themes have been increasing in depth. These findings provide valuable references on the current research hotspots and gaps and development trends in the link between the microbiota and allergic diseases.},
}
@article {pmid36389795,
year = {2022},
author = {Johnson, SD and Knight, LA and Kumar, N and Olwenyi, OA and Thurman, M and Mehra, S and Mohan, M and Byrareddy, SN},
title = {Early treatment with anti-α4β7 antibody facilitates increased gut macrophage maturity in SIV-infected rhesus macaques.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {1001727},
doi = {10.3389/fimmu.2022.1001727},
pmid = {36389795},
issn = {1664-3224},
abstract = {Despite advances in combination antiretroviral therapy (cART), people living with HIV (PLWH) continue to experience gastrointestinal dysfunction. Infusions of anti-α4β7 monoclonal antibodies (mAbs) have been proposed to increase virologic control during simian immunodeficiency virus (SIV) infection in macaques with mixed results. Recent evidences suggested that therapeutic efficacy of vedolizumab (a humanized anti-α4β7 mAb), during inflammatory bowel diseases depends on microbiome composition, myeloid cell differentiation, and macrophage phenotype. We tested this hypothesis in SIV-infected, anti-α4β7 mAb-treated macaques and provide flow cytometric and microscopic evidence that anti-α4β7 administered to SIV-infected macaques increases the maturity of macrophage phenotypes typically lost in the small intestines during SIV disease progression. Further, this increase in mature macrophage phenotype was associated with tissue viral loads. These phenotypes were also associated with dysbiosis markers in the gut previously identified as predictors of HIV replication and immune activation in PLWH. These findings provide a novel model of anti-α4β7 efficacy offering new avenues for targeting pathogenic mucosal immune response during HIV/SIV infection.},
}
@article {pmid36389768,
year = {2022},
author = {Zhou, G and Zhang, N and Meng, K and Pan, F},
title = {Interaction between gut microbiota and immune checkpoint inhibitor-related colitis.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {1001623},
doi = {10.3389/fimmu.2022.1001623},
pmid = {36389768},
issn = {1664-3224},
abstract = {Immune checkpoint inhibitors (ICIs) have become a promising therapeutic strategy for malignant tumors, improving patient prognosis, along with a spectrum of immune-related adverse events (irAEs), including gastrointestinal toxicity, ICI-related colitis (IRC), and diarrhea. The gut microbiota has been suggested as an important regulator in the pathogenesis of IRC, and microbiota modulations like probiotics and fecal microbiota transplantation have been explored to treat the disease. This review discusses the interaction between the gut microbiota and IRC, focusing on the potential pathogenic mechanisms and promising interventions.},
}
@article {pmid36389730,
year = {2022},
author = {Liu, S and Yin, R and Yang, Z and Wei, F and Hu, J},
title = {The effects of rhein on D-GalN/LPS-induced acute liver injury in mice: Results from gut microbiome-metabolomics and host transcriptome analysis.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {971409},
doi = {10.3389/fimmu.2022.971409},
pmid = {36389730},
issn = {1664-3224},
abstract = {Background: Rhubarb is an important traditional Chinese medicine, and rhein is one of its most important active ingredients. Studies have found that rhein can improve ulcerative colitis by regulating gut microbes, but there are few reports on its effects on liver diseases. Therefore, this study aims to investigate these effects and underlying mechanisms.<br><br>Methods: Mice were given rhein (100 mg/kg), with both a normal control group and a model group receiving the same amount of normal saline for one week. Acute liver injury was induced in mice by intraperitoneal injection of D-GalN (800 mg/kg)/LPS (10 ug/kg). Samples (blood, liver, and stool) were then collected and assessed for histological lesions and used for 16S rRNA gene sequencing, high-performance liquid chromatography-mass spectrometry (LC-MS) and RNA-seq analysis.<br><br>Results: The levels of ALT and AST in the Model group were abnormal higher compared to the normal control group, and the levels of ALT and AST were significantly relieved in the rhein group. Hepatic HE staining showed that the degree of liver injury in the rhein group was lighter than that in the model group, and microbiological results showed that norank_o:Clostridia_UCG-014, Lachnoclostridium, and Roseburia were more abundant in the model group compared to the normal control group. Notably, the rhein treatment group showed reshaped disturbance of intestinal microbial community by D-GalN/LPS and these mice also had higher levels of Verrucomicrobia, Akkermansiaceae and Bacteroidetes. Additionally, There were multiple metabolites that were significantly different between the normal control group and the model group, such as L-α-amino acid, ofloxacin-N-oxide, 1-hydroxy-1,3-diphenylpropan-2-one,and L-4-hydroxyglutamate semialdehyde, but that returned to normal levels after rhein treatment. The gene expression level in the model group also changed significantly, various genes such as Cxcl2, S100a9, Tnf, Ereg, and IL-10 were up-regulated, while Mfsd2a and Bhlhe41 were down-regulated, which were recovered after rhein treatment.<br><br>Conclusion: Overall, our results show that rhein alleviated D-GalN/LPS-induced acute liver injury in mice. It may help modulate gut microbiota in mice, thereby changing metabolism in the intestine. Meanwhile, rhein also may help regulate genes expression level to alleviate D-GalN/LPS-induced acute liver injury.},
}
@article {pmid36389729,
year = {2022},
author = {Zhao, L and Hou, C and Yan, N},
title = {Neuroinflammation in retinitis pigmentosa: Therapies targeting the innate immune system.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {1059947},
doi = {10.3389/fimmu.2022.1059947},
pmid = {36389729},
issn = {1664-3224},
abstract = {Retinitis pigmentosa (RP) is an important cause of irreversible blindness worldwide and lacks effective treatment strategies. Although mutations are the primary cause of RP, research over the past decades has shown that neuroinflammation is an important cause of RP progression. Due to the abnormal activation of immunity, continuous sterile inflammation results in neuron loss and structural destruction. Therapies targeting inflammation have shown their potential to attenuate photoreceptor degeneration in preclinical models. Regardless of variations in genetic background, inflammatory modulation is emerging as an important role in the treatment of RP. We summarize the evidence for the role of inflammation in RP and mention therapeutic strategies where available, focusing on the modulation of innate immune signals, including TNFα signaling, TLR signaling, NLRP3 inflammasome activation, chemokine signaling and JAK/STAT signaling. In addition, we describe epigenetic regulation, the gut microbiome and herbal agents as prospective treatment strategies for RP in recent advances.},
}
@article {pmid36389714,
year = {2022},
author = {Zou, X and Wang, L and Xiao, L and Wang, S and Zhang, L},
title = {Gut microbes in cerebrovascular diseases: Gut flora imbalance, potential impact mechanisms and promising treatment strategies.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {975921},
doi = {10.3389/fimmu.2022.975921},
pmid = {36389714},
issn = {1664-3224},
abstract = {The high morbidity, mortality, and disability rates associated with cerebrovascular disease (CeVD) pose a severe danger to human health. Gut bacteria significantly affect the onset, progression, and prognosis of CeVD. Gut microbes play a critical role in gut-brain interactions, and the gut-brain axis is essential for communication in CeVD. The reflection of changes in the gut and brain caused by gut bacteria makes it possible to investigate early warning biomarkers and potential treatment targets. We primarily discussed the following three levels of brain-gut interactions in a systematic review of the connections between gut microbiota and several cerebrovascular conditions, including ischemic stroke, intracerebral hemorrhage, intracranial aneurysm, cerebral small vessel disease, and cerebral cavernous hemangioma. First, we studied the gut microbes in conjunction with CeVD and examined alterations in the core microbiota. This enabled us to identify the focus of gut microbes and determine the focus for CeVD prevention and treatment. Second, we discussed the pathological mechanisms underlying the involvement of gut microbes in CeVD occurrence and development, including immune-mediated inflammatory responses, variations in intestinal barrier function, and reciprocal effects of microbial metabolites. Finally, based on the aforementioned proven mechanisms, we assessed the effectiveness and potential applications of the current therapies, such as dietary intervention, fecal bacterial transplantation, traditional Chinese medicine, and antibiotic therapy.},
}
@article {pmid36389228,
year = {2022},
author = {Bashir, Y and Khan, AU},
title = {The interplay between the gut-brain axis and the microbiome: A perspective on psychiatric and neurodegenerative disorders.},
journal = {Frontiers in neuroscience},
volume = {16},
number = {},
pages = {1030694},
doi = {10.3389/fnins.2022.1030694},
pmid = {36389228},
issn = {1662-4548},
abstract = {What is the effect of our gut microbial flora on brain? Does the gut microbiome have any role in the causation of psychiatric and neurodegenerative diseases? Does the effect of gut microbiota traverse the gut-brain axis? Questions like these have captured the interest and imagination of the scientific community for quite some time now. Research in the quest for answers to these questions, to unravel the potential role of the microbiota inhabiting the gut in controlling brain functions, has progressed manifold over the last two decades. Although the possibility of microbiome as a key susceptibility factor for neurological disorders viz. Parkinson's disease, Alzheimer's disease, multiple sclerosis, and autism spectrum disorder has bolstered by an increase in the clinical and preclinical evidence, the field is still in its infancy. Given the fact that the diversity of the gut microbiota is affected by various factors including the diet and exercise, the interpretation of such data becomes all the more difficult. Also, such studies have been mostly conducted on animal models, so there is a need for randomized controlled trials in human subjects, corroborated by longitudinal studies, to establish if modulating the gut microbiota can unravel novel therapeutic interventions. Exploring the genomic, metagenomic and metabolomic data from clinical subjects with psychiatric and neurological diseases can prove to be a helpful guide in individual treatment selection.},
}
@article {pmid36389176,
year = {2022},
author = {Chen, H and Tang, N and Ye, Q and Yu, X and Yang, R and Cheng, H and Zhang, G and Zhou, X},
title = {Alternation of the gut microbiota in metabolically healthy obesity: An integrated multiomics analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1012028},
doi = {10.3389/fcimb.2022.1012028},
pmid = {36389176},
issn = {2235-2988},
abstract = {Background: Although the gut microbiota may be involved in obesity onset and progression, the exact association of the gut microbiota in metabolically healthy obesity (MHO) remains largely unknown.<br><br>Methods: An integrated paired-sample metagenomic analysis was conducted to investigate the gut microbial network and biomarkers of microbial species from the MHO and healthy non-obese subjects in the GMrepo database. Further explorations were performed in the MHO mice model using a multiomics analysis to detect changes in the composition and function of the intestinal microbiome and associated metabolites.<br><br>Results: In the human study, 314 matched metagenomic data were qualified for the final analysis. We identified seven significantly changed species possibly involved in MHO pathogenesis (MHO-enriched: Bacteroides vulgatus, Megamonas sp; MHO-depleted: Butyrivibrio crossotus, Faecalibacterium prausnitzii, Bacteroides cellulosilyticus; Eubacterium siraeum; Bacteroides massiliensis). In the murine study, we found 79 significantly-changed species which may have possible associations with the MHO phenotype. The depletion of Bacteroides cellulosilyticus was commonly recognized in the human and murine MHO phenotype. Consistent with the metagenomic data, liquid chromatography-mass spectrometry (LC/MS) revealed significantly changed gut metabolites, which may promote MHO pathogenesis by altering the amino acids and lipid metabolic pathways. In the microbe-metabolites interaction analysis, we identified certain fatty acids (Dodecanedioic acid, Arachidic Acid, Mevalonic acid, etc.) that were significantly correlated with the MHO-enriched or depleted species.<br><br>Conclusion: This study provides insights into identifying specific microbes and metabolites that may involve in the development of obesity without metabolic disorders. Future modalities for MHO intervention may be further validated by targeting these bacteria and metabolites.},
}
@article {pmid36389165,
year = {2022},
author = {Li, Z and Yu, X and Guo, H and Lee, T and Hu, J},
title = {A maximum-type microbial differential abundance test with application to high-dimensional microbiome data analyses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {988717},
doi = {10.3389/fcimb.2022.988717},
pmid = {36389165},
issn = {2235-2988},
abstract = {Background: High-throughput metagenomic sequencing technologies have shown prominent advantages over traditional pathogen detection methods, bringing great potential in clinical pathogen diagnosis and treatment of infectious diseases. Nevertheless, how to accurately detect the difference in microbiome profiles between treatment or disease conditions remains computationally challenging.<br><br>Results: In this study, we propose a novel test for identifying the difference between two high-dimensional microbiome abundance data matrices based on the centered log-ratio transformation of the microbiome compositions. The test p-value can be calculated directly with a closed-form solution from the derived asymptotic null distribution. We also investigate the asymptotic statistical power against sparse alternatives that are typically encountered in microbiome studies. The proposed test is maximum-type equal-covariance-assumption-free (MECAF), making it widely applicable to studies that compare microbiome compositions between conditions. Our simulation studies demonstrated that the proposed MECAF test achieves more desirable power than competing methods while having the type I error rate well controlled under various scenarios. The usefulness of the proposed test is further illustrated with two real microbiome data analyses. The source code of the proposed method is freely available at https://github.com/Jiyuan-NYU-Langone/MECAF.<br><br>Conclusions: MECAF is a flexible differential abundance test and achieves statistical efficiency in analyzing high-throughput microbiome data. The proposed new method will allow us to efficiently discover shifts in microbiome abundances between disease and treatment conditions, broadening our understanding of the disease and ultimately improving clinical diagnosis and treatment.},
}
@article {pmid36389146,
year = {2022},
author = {Leonardi, SS and Koh, EY and Deng, L and Huang, C and Tong, L and Wang, JW and Tan, KS},
title = {The synthesis of extracellular vesicles by the protistan parasite Blastocystis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1019789},
doi = {10.3389/fcimb.2022.1019789},
pmid = {36389146},
issn = {2235-2988},
abstract = {Blastocystis is a genus of single-celled protist belonging to the stramenopile group. Prior studies have shown that isolates of Blastocystis subtype 7 (ST7) induced higher levels of intestinal epithelial cell damage and gut microbiota dysbiosis in comparison to other subtypes in in vivo and in vitro settings. Prior research has shown a link between gut dysbiosis and exposure to extracellular vesicles (EVs) produced by pathogenic microorganisms. This study demonstrates a protocol for the isolation of EVs from Blastocystis ST7 via ultracentrifugation. Nanoparticle tracking analysis and transmission electron microscopy were used to assess EV size and morphology. The protein content of isolated EVs was assessed by mass spectrophotometry and the presence of EV markers were evaluated by Western blotting. Finally, the EVs were cocultured with prominent human gut microbiome species to observe their effect on prokaryote growth. Our data shows that Blastocystis ST7 secretes EVs that are similar in morphology to previously characterized EVs from other organisms and that these EVs contain a limited yet unique protein cargo with functions in host-parasite intercellular communication and cell viability. This cargo may be involved in mediating the effects of Blastocystis on its surrounding environment.},
}
@article {pmid36389140,
year = {2022},
author = {Kaźmierczak-Siedlecka, K and Marano, L and Merola, E and Roviello, F and Połom, K},
title = {Sodium butyrate in both prevention and supportive treatment of colorectal cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1023806},
doi = {10.3389/fcimb.2022.1023806},
pmid = {36389140},
issn = {2235-2988},
abstract = {Accumulating evidence suggests that selected microbiota-derived metabolites play a significant role in both tumor prevention and supportive treatment of cancer. Short-chain fatty acids (SCFAs), i.e., mainly acetate, proprionate, and butyrate, are one of them. Nowadays, it is known that butyrate is a key microbial metabolite. Therefore, in the current review, we focused on butyrate and sodium butyrate (NaB) in the context of colorectal cancer. Notably, butyrate is characterized by a wide range of beneficial properties/activities. Among others, it influences the function of the immune system, maintains intestinal barrier integrity, positively affects the efficiency of anti-cancer treatment, and may reduce the risk of mucositis induced by chemotherapy. Taking into consideration these facts, we analyzed NaB (which is a salt of butyric acid) and its impact on gut microbiota as well as anti-tumor activity by describing molecular mechanisms. Overall, NaB is available as, for instance, food with special medical purposes (depending on the country's regulation), and its administration seems to be a promising option for colorectal cancer patients.},
}
@article {pmid36389138,
year = {2022},
author = {Hu, Q and Liu, B and Fan, Y and Zheng, Y and Wen, F and Yu, U and Wang, W},
title = {Multi-omics association analysis reveals interactions between the oropharyngeal microbiome and the metabolome in pediatric patients with influenza A virus pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1011254},
doi = {10.3389/fcimb.2022.1011254},
pmid = {36389138},
issn = {2235-2988},
abstract = {Children are at high risk for influenza A virus (IAV) infections, which can develop into severe illnesses. However, little is known about interactions between the microbiome and respiratory tract metabolites and their impact on the development of IAV pneumonia in children. Using a combination of liquid chromatography tandem mass spectrometry (LC-MS/MS) and 16S rRNA gene sequencing, we analyzed the composition and metabolic profile of the oropharyngeal microbiota in 49 pediatric patients with IAV pneumonia and 42 age-matched healthy children. The results indicate that compared to healthy children, children with IAV pneumonia exhibited significant changes in the oropharyngeal macrobiotic structure (p = 0.001), and significantly lower microbial abundance and diversity (p < 0.05). These changes came with significant disturbances in the levels of oropharyngeal metabolites. Intergroup differences were observed in 204 metabolites mapped to 36 metabolic pathways. Significantly higher levels of sphingolipid (sphinganine and phytosphingosine) and propanoate (propionic acid and succinic acid) metabolism were observed in patients with IAV pneumonia than in healthy controls. Using Spearman's rank-correlation analysis, correlations between IAV pneumonia-associated discriminatory microbial genera and metabolites were evaluated. The results indicate significant correlations and consistency in variation trends between Streptococcus and three sphingolipid metabolites (phytosphingosine, sphinganine, and sphingosine). Besides these three sphingolipid metabolites, the sphinganine-to-sphingosine ratio and the joint analysis of the three metabolites indicated remarkable diagnostic efficacy in children with IAV pneumonia. This study confirmed significant changes in the characteristics and metabolic profile of the oropharyngeal microbiome in pediatric patients with IAV pneumonia, with high synergy between the two factors. Oropharyngeal sphingolipid metabolites may serve as potential diagnostic biomarkers of IAV pneumonia in children.},
}
@article {pmid36388972,
year = {2022},
author = {Ge, Y and Zadeh, M and Yang, C and Candelario-Jalil, E and Mohamadzadeh, M},
title = {Ischemic Stroke Impacts the Gut Microbiome, Ileal Epithelial and Immune Homeostasis.},
journal = {iScience},
volume = {25},
number = {11},
pages = {105437},
doi = {10.1016/j.isci.2022.105437},
pmid = {36388972},
issn = {2589-0042},
abstract = {Ischemic stroke critically impacts neurovascular homeostasis, potentially resulting in neurological disorders. However, the mechanisms through which stroke-induced inflammation modifies the molecular and metabolic circuits, particularly in ileal epithelial cells (iECs), currently remain elusive. Using multiomic approaches, we illustrated that stroke impaired the ileal microbiome and associated metabolites, leading to increased inflammatory signals and altered metabolites, potentially deteriorating the iEC homeostasis. Bulk transcriptomic and metabolomic profiling demonstrated that stroke enhanced fatty acid oxidation while reducing the tricarboxylic acid (TCA) cycle in iECs within the first day after stroke. Intriguingly, single-cell RNA sequencing analysis revealed that stroke dysregulated cell-type-specific gene responses within iECs and reduced frequencies of goblet and tuft cells. Additionally, stroke augmented interleukin-17A[+] γδ T cells but decreased CD4[+] T cells in the ileum. Collectively, our findings provide a comprehensive overview of stroke-induced intestinal dysbiosis and unveil responsive gene programming within iECs with implications for disease development.},
}
@article {pmid36388879,
year = {2022},
author = {Feng, Y and Wu, C and Huang, X and Huang, X and Peng, L and Guo, R},
title = {Case report: Successful management of Parvimonas micra pneumonia mimicking hematogenous Staphylococcus aureus pneumonia.},
journal = {Frontiers in medicine},
volume = {9},
number = {},
pages = {1017074},
doi = {10.3389/fmed.2022.1017074},
pmid = {36388879},
issn = {2296-858X},
abstract = {Parvimonas micra is an anaerobic Gram-positive coccus frequently found in the oral cavity and gastrointestinal tract, but rarely in the lung. Therefore, pneumonia caused by P. micra is also rare. Although there are some reports of P. micra related pneumonia due to aspiration or blood-borne infection with definite remote infection source, there are no reported cases of hematogenous P. micra pneumonia in healthy adults lacking a remote source of infection. Herein, we described the intact disease of P. micra-related pneumonia mimicking hematogenous Staphylococcus aureus pneumonia in terms of chest imagery and diagnosed via metagenomic next-generation sequencing (mNGS). Interestingly, there was no clear remote pathogenic source identified in the patient. Microbiome analysis revealed dysbiosis of the oral flora possibly related to poor oral hygiene and a long history of smoking. The patient was treated with moxifloxacin for 3 months. Ultimately, computed tomography (CT) of the chest showed total resolution of the lung lesion. Clinicians need to update the etiology of community-acquired pneumonia. When antibiotic therapy is not effective, pathogen examination becomes very important. New methods of pathogen detection such as mNGS should be employed to this end. For the treatment of P. micra pneumonia, no standardized course of treatment was reported. Imaging absorption of lung infections may provide a more objective guidance for the duration of antibiotics in P. micra pneumonia.},
}
@article {pmid36388691,
year = {2022},
author = {Obuya, S and Elkholy, A and Avuthu, N and Behring, M and Bajpai, P and Agarwal, S and Kim, HG and El-Nikhely, N and Akinyi, P and Orwa, J and Afaq, F and Abdalla, M and Michael, A and Farouk, M and Bateman, LB and Fouad, M and Saleh, M and Guda, C and Manne, U and Arafat, W},
title = {A signature of Prevotella copri and Faecalibacterium prausnitzii depletion, and a link with bacterial glutamate degradation in the Kenyan colorectal cancer patients.},
journal = {Journal of gastrointestinal oncology},
volume = {13},
number = {5},
pages = {2282-2292},
doi = {10.21037/jgo-22-116},
pmid = {36388691},
issn = {2078-6891},
abstract = {Background: Colorectal cancer (CRC) is the fifth most diagnosed cancer in Sub-Saharan Africa. In Kenya, CRC incidence rates tripled from 1997 to 2017. In the Moi Teaching and Referral Hospital, Moi University, there has been an increase in CRC cases, notably for younger patients. A suggested pathobiology for this increase is gut microbiome dysbiosis. Since, for the Kenyan CRC patient population, microbiome studies are rare, there is a need for a better understanding of how microbiome dysbiosis influences CRC epidemiology in Kenya. In this single-center study, the focus was on profiling the gut microbiome of Kenyan CRC patients and healthy volunteers and evaluating associations between microbiome profiles and the age of CRC patients.<br><br>Methods: The gut mucosa-associated microbiome of 18 CRC patients and 18 healthy controls were determined by 16S rRNA sequencing and analyzed for alpha and beta diversity, differential abundance, and microbial metabolic profiling.<br><br>Results: Alpha diversity metrics showed no significant differences, but beta diversity metrics showed dissimilarities in the microbial communities between CRC patients and healthy controls. The most underrepresented species in the CRC group were Prevotella copri (P. copri) and Faecalibacterium prausnitzii (F. prausnitzii), although Bacteroides fragilis (B. fragilis) and Prevotella nigrescens were overrepresented (linear discriminant analysis, LDA score >2, P<0.05). Also, for CRC patients, significant metagenomic functional alterations were evident in microbial glutamate metabolic pathways (L-glutamate degradation VIII was enriched, and L-glutamate and L-glutamine biosynthesis were diminished) (P<0.05, log2 Fold Change >1). Moreover, the microbiome composition was different for patients under 40 years of age compared to older patients (LDA score >2, P<0.05).<br><br>Conclusions: Microbiome and microbial metabolic profiles of CRC patients are different from those of healthy individuals. CRC microbiome dysbiosis, particularly P. copri and F. prausnitzii depletion and glutamate metabolic alterations, are evident in Kenyan CRC patients.},
}
@article {pmid36388083,
year = {2022},
author = {Wang, C and Zhao, S and Xu, Y and Sun, W and Feng, Y and Liang, D and Guan, Y},
title = {Integrated Microbiome and Metabolome Analysis Reveals Correlations Between Gut Microbiota Components and Metabolic Profiles in Mice with Methotrexate-Induced Hepatoxicity.},
journal = {Drug design, development and therapy},
volume = {16},
number = {},
pages = {3877-3891},
doi = {10.2147/DDDT.S381667},
pmid = {36388083},
issn = {1177-8881},
abstract = {Purpose: We designed this study to investigate the potential correlations between gut microbiota compositions and hepatic metabolomic disorders in mice with methotrexate (MTX)-induced hepatoxicity.<br><br>Methods: We used MTX to induce hepatoxicity in healthy Kunming mice, and we determined plasma ALT and AST levels and assessed the liver tissue histopathology. We applied an integrated gas chromatography-mass spectrometry (GC-MS) and 16S ribosomal RNA (rRNA) gene sequencing approach to evaluate the effects of MTX on the gut microbiota and hepatic metabolic profiles of mice. We uncovered correlations between the gut microbiota and hepatic metabolomic profiles by calculating the Spearman correlation coefficient.<br><br>Results: MTX caused ALT and AST level elevations and hepatoxicity in our mouse model. MTX disrupted amino acid metabolic pathways (including biosyntheses of valine, leucine, and isoleucine; and arginine; and, metabolism of alanine, aspartate, and glutamate; histidine; beta-alanine; and glycine, serine, and threonine); biosyntheses of aminoacyl-tRNA; and pantothenate, and CoA; and, metabolic pathways of energy, glutathione, and porphyrin; and chlorophyll. In addition, MTX increased the abundances of Staphylococcus, Enterococcus, Collinsella, Streptococcus, and Aerococcus, but decreased the amounts of Lactobacillus, Ruminococcus, norank_f_Muribaculaceae, unclassified_f_Lachnospiraceae, norank_f_Lachnospiraceae, A2, Eubacterium_xylanophilum_group, Phascolarctobacterium, Bifidobacterium, and Faecalibaculum. Our correlation analyses showed that different flora abundance changes including those of Phascolarctobacterium, Faecalibaculum, norank_f_Muribaculaceae, Streptococcus, Enterococcus, Staphylococcus, and Collinsella were associated with liver injury.<br><br>Conclusion: We present evidence supporting the notion that MTX causes hepatoxicity by altering the gut microbiota and hepatic metabolite profiles, our findings provide new venues for the management of MTX-induced hepatoxicity.},
}
@article {pmid36387852,
year = {2022},
author = {Acharya, KD and Friedline, RH and Ward, DV and Graham, ME and Tauer, L and Zheng, D and Hu, X and de Vos, WM and McCormick, BA and Kim, JK and Tetel, MJ},
title = {Differential effects of Akkermansia-enriched fecal microbiota transplant on energy balance in female mice on high-fat diet.},
journal = {Frontiers in endocrinology},
volume = {13},
number = {},
pages = {1010806},
doi = {10.3389/fendo.2022.1010806},
pmid = {36387852},
issn = {1664-2392},
abstract = {Estrogens protect against weight gain and metabolic disruption in women and female rodents. Aberrations in the gut microbiota composition are linked to obesity and metabolic disorders. Furthermore, estrogen-mediated protection against diet-induced metabolic disruption is associated with modifications in gut microbiota. In this study, we tested if estradiol (E2)-mediated protection against obesity and metabolic disorders in female mice is dependent on gut microbiota. Specifically, we tested if fecal microbiota transplantation (FMT) from E2-treated lean female mice, supplemented with or without Akkermansia muciniphila, prevented high fat diet (HFD)-induced body weight gain, fat mass gain, and hyperglycemia in female recipients. FMT from, and cohousing with, E2-treated lean donors was not sufficient to transfer the metabolic benefits to the E2-deficient female recipients. Moreover, FMT from lean donors supplemented with A. muciniphila exacerbated HFD-induced hyperglycemia in E2-deficient recipients, suggesting its detrimental effect on the metabolic health of E2-deficient female rodents fed a HFD. Given that A. muciniphila attenuates HFD-induced metabolic insults in males, the present findings suggest a sex difference in the impact of this microbe on metabolic health.},
}
@article {pmid36387723,
year = {2022},
author = {Gupta, H},
title = {Azithromycin use in Covid- 19: A tale of changing guidelines.},
journal = {Journal of family medicine and primary care},
volume = {11},
number = {7},
pages = {3399-3400},
doi = {10.4103/jfmpc.jfmpc_49_22},
pmid = {36387723},
issn = {2249-4863},
abstract = {It has been more than two years since the arrival of Covid-19 pandemic on world stage. When we look back during landmark events of last two years, several ones stand out. And one of these is utilization and then going out- of- favor of use of an antibiotic - Azithromycin. Pilva- a Croatian pharmaceutical company- headquartered in Zagreb in late 1970s discovered the drug. Then several years of research yielded a product which was highly effective and provided good therapeutic results. As this was a small company having limited resources, it made a licensing agreement with Pfizer to sell the drug at marked geographies. While initial reason of its use in SARS-CoV-2 infection was its supposedly immunomodulatory effect yet randomized controlled trials demonstrated a lack of a beneficial effect for this indication. Therefore, when recollecting our journey with the mutant Coronavirus during last two years, it's necessary to remember that when trying to discover a useful drug for the disease, we had several misses as well. As usual in Medical science, most of the hits have several collateral misses, even though this drug carries with it certain unique features. In the Editorial I chronicle a few such distinguishing features.},
}
@article {pmid36387539,
year = {2022},
author = {Chompre, G and Sambolin, L and Cruz, ML and Sanchez, R and Rodriguez, Y and Rodríguez-Santiago, RE and Yamamura, Y and Appleyard, CB},
title = {A one month high fat diet disrupts the gut microbiome and integrity of the colon inducing adiposity and behavioral despair in male Sprague Dawley rats.},
journal = {Heliyon},
volume = {8},
number = {11},
pages = {e11194},
doi = {10.1016/j.heliyon.2022.e11194},
pmid = {36387539},
issn = {2405-8440},
abstract = {High-fat diet (HFD) is associated with gut microbiome dysfunction and mental disorders. However, the time-dependence as to when this occurs is unclear. We hypothesized that a short-term HFD causes colonic tissue integrity changes resulting in behavioral changes. Rats were fed HFD or low-fat diet (LFD) for a month and gut microbiome, colon, and behavior were evaluated. Behavioral despair was found in the HFD group. Although obesity was absent, the HFD group showed increased percent weight gain, epididymal fat tissue, and leptin expression. Moreover, the HFD group had increased colonic damage, decreased expression of the tight junction proteins, and higher lipopolysaccharides (LPS) in serum. Metagenomic analysis revealed that the HFD group had more Bacteroides and less S24-7 which correlated with the decreased claudin-5. Finally, HFD group showed an increase of microglia percent area, increased astrocytic projections, and decreased phospho-mTOR. In conclusion, HFD consumption in a short period is still sufficient to disrupt gut integrity resulting in LPS infiltration, alterations in the brain, and behavioral despair even in the absence of obesity.},
}
@article {pmid36387384,
year = {2022},
author = {Hankel, J and Sander, S and Muthukumarasamy, U and Strowig, T and Kamphues, J and Jung, K and Visscher, C},
title = {Microbiota of vaccinated and non-vaccinated clinically inconspicuous and conspicuous piglets under natural Lawsonia intracellularis infection.},
journal = {Frontiers in veterinary science},
volume = {9},
number = {},
pages = {1004506},
doi = {10.3389/fvets.2022.1004506},
pmid = {36387384},
issn = {2297-1769},
abstract = {Lawsonia (L.) intracellularis is a widespread, economically important bacterium causing the porcine proliferative enteropathy (PPE). In this study, we evaluated intestinal microbiota of naturally exposed L. intracellularis-positive pigs under standardized conditions. To obtain three independent repetitions, 27 L. intracellularis-infected pigs (19.0 ± 1.50 kg body weight) from one farm were divided into three groups at an age of 7 to 8 weeks (nine pigs/group). Pigs were either vaccinated against L. intracellularis via oral drenching on their 21st day of life (attenuated live vaccine) or non-vaccinated and selected according to clinical findings (pigs without deviating fecal consistency or with moderate to soft fecal consistency). Comparison of the clinically inconspicuous piglets that differed regarding their vaccination status showed fewer significant differences in fecal microbiota composition. The vaccination led to an overall enrichment of bacterial species belonging to the order Clostridiales, while species of the genus Collinsella and Prevotella were decreased. Several bacterial species belonging to the order Bacteroidales, mainly of the family Prevotellacecae, often closely matching Prevotella copri differed significantly between non-vaccinated clinically inconspicuous and conspicuous piglets. Whether those bacterial species play a role in mitigating the severity of an L. intracellularis infection remains to be defined.},
}
@article {pmid36387374,
year = {2022},
author = {Castro, J and Barros, MM and Araújo, D and Campos, AM and Oliveira, R and Silva, S and Almeida, C},
title = {Swine enteric colibacillosis: Current treatment avenues and future directions.},
journal = {Frontiers in veterinary science},
volume = {9},
number = {},
pages = {981207},
doi = {10.3389/fvets.2022.981207},
pmid = {36387374},
issn = {2297-1769},
abstract = {Enteric colibacillosis is a common disease in nursing and weanling pigs. It is caused by the colonization of the small intestine by enterotoxigenic strains of Escherichia coli (ETEC) that make use of specific fimbria or pili to adhere to the absorptive epithelial cells of the jejunum and ileum. Once attached, and when both the immunological systems and the gut microbiota are poorly developed, ETEC produce one or more enterotoxins that can have local and, further on, systemic effects. These enterotoxins cause fluid and electrolytes to be secreted into the intestinal lumen of animals, which results in diarrhea, dehydration, and acidosis. From the diversity of control strategies, antibiotics and zinc oxide are the ones that have contributed more significantly to mitigating post-weaning diarrhea (PWD) economic losses. However, concerns about antibiotic resistance determined the restriction on the use of critically important antimicrobials in food-producing animals and the prohibition of their use as growth promoters. As such, it is important now to begin the transition from these preventive/control measures to other, more sustainable, approaches. This review provides a quick synopsis of the currently approved and available therapies for PWD treatment while presenting an overview of novel antimicrobial strategies that are being explored for the control and treatment of this infection, including, prebiotics, probiotics, synbiotics, organic acids, bacteriophages, spray-dried plasma, antibodies, phytogenic substances, antisense oligonucleotides, and aptamers.},
}
@article {pmid36387363,
year = {2022},
author = {Xia, Y and Feng, Y and Qin, T and Zhao, X and Lu, J and Ma, C},
title = {Characteristics of Vaginal Microbiome in Reproductive-Age Females with HPV Infection in Xinjiang, China.},
journal = {Evidence-based complementary and alternative medicine : eCAM},
volume = {2022},
number = {},
pages = {7332628},
doi = {10.1155/2022/7332628},
pmid = {36387363},
issn = {1741-427X},
abstract = {Objective: We investigated the characteristics of vaginal microbiome in reproductive-age females with HPV infection in Xinjiang, China.<br><br>Methods: A total of 135 females of reproductive age were enrolled. There were 43 healthy HPV-negative females in control group (N group), 58 HPV-positive females in nonlesion group (P1 group), and 34 HPV-positive females in low-grade squamous intraepithelial lesion group (P2 group). DNA was extracted from the vaginal secretions, and V3-V4 regions of bacterial 16S rDNA were amplified and sequenced by NovaSeq. QIIME2 and R software were used to perform diversity analysis of bacteria. PICRUSt2 was used to predict the function of the vaginal microbiota.<br><br>Results: Lactobacillus was the main genus of vaginal microbiota in asymptomatic reproductive-age females with or without HPV in Xinjiang. The diversity of vaginal microbiota in the P1 group was significantly higher than that in the N group, and the proportion of Gardnerella increased significantly. The vaginal microbiota structure of the P2 group was different from the N group, characterized by the decrease of Lactobacillus crispatus and the increase of Shuttleworthia. The function of the inordinate microbiome may play a role in accelerating HPV replication and integration.<br><br>Conclusion: The structure of vaginal microbiota alters under persistent HPV infection in asymptomatic females of reproductive age in Xinjiang. The Gardnerella increase is associated with increased susceptibility to HPV infection, and Lactobacillus iners predominance and Shuttleworthia presence may be a signature of HPV infection with low-grade squamous intraepithelial lesion.},
}
@article {pmid36387258,
year = {2022},
author = {Sun, L and Zhu, Z and Jia, X and Ying, X and Wang, B and Wang, P and Zhang, S and Yu, J},
title = {The difference of human gut microbiome in colorectal cancer with and without metastases.},
journal = {Frontiers in oncology},
volume = {12},
number = {},
pages = {982744},
doi = {10.3389/fonc.2022.982744},
pmid = {36387258},
issn = {2234-943X},
abstract = {Metastasis of colorectal cancer is deemed to be closely related to the changes in the human gut microbiome. The purpose of our study is to distinguish the differences in gut microbiota between colorectal cancer with and without metastases. Firstly, this study recruited colorectal cancer patients who met the established inclusion and exclusion criteria in the Oncology Department of Zhejiang Hospital of Traditional Chinese Medicine from February 2019 to June 2019. Fresh stool samples from healthy volunteers, non-metastatic patients, and metastatic patients were collected for 16S rRNA gene sequencing, to analyze the diversity and abundance of intestinal microorganisms in each group. The results showed that the microbial composition of the control group was more aplenty than the experimental group, while the difference also happened in the Tumor and the metastases group. At the phylum level, the abundance of Bacteroidetes significantly declined in the Tumor and the metastases group, compared with the control group. At the class level, Bacilli increased in experimental groups, while its abundance in the Tumor group was significantly higher than that in the metastases group. At the order level, the Tumor group had the highest abundance of Lactobacillales, followed by the metastases group and the control group had the lowest abundance. Overall, our study showed that the composition of the flora changed with the occurrence of metastasis in colorectal cancer. Therefore, the analysis of gut microbiota can serve as a supplement biological basis for the diagnosis and treatment of metastatic colorectal cancer which may offer the potential to develop non-invasive diagnostic tests.},
}
@article {pmid36387213,
year = {2022},
author = {Rumpold, H and Wolf, D},
title = {Editorial: Current innovations in GI-oncology: Where do we stand?.},
journal = {Frontiers in oncology},
volume = {12},
number = {},
pages = {1048082},
doi = {10.3389/fonc.2022.1048082},
pmid = {36387213},
issn = {2234-943X},
}
@article {pmid36387171,
year = {2022},
author = {Wu, Z and Zhang, S and Li, L and Huang, Z and Huang, D and Hu, Y},
title = {The gut microbiota modulates responses to anti-PD-1 and chemotherapy combination therapy and related adverse events in patients with advanced solid tumors.},
journal = {Frontiers in oncology},
volume = {12},
number = {},
pages = {887383},
doi = {10.3389/fonc.2022.887383},
pmid = {36387171},
issn = {2234-943X},
abstract = {Background: Immune checkpoint inhibitors (ICIs) targeting programmed cell death protein 1 (PD-1) have been widely used in treating different malignancies. Several studies have reported that the gut microbiota modulates the response and adverse events (AEs) to ICIs in melanoma, non-small cell lung cancer (NSCLC), renal cell cancer and hepatocellular carcinoma, but data on other cancer types and ICI combination therapy are limited.<br><br>Methods: Stool samples were collected from patients with cancer who received anti-PD-1 and chemotherapy combination treatment and were analyzed by fecal metagenomic sequencing. The microbiota diversity and composition were compared between the responder (R) and non-responder (NR) groups and the AE vs. the non-AE (NAE) groups. In addition, associated functional genes and metabolic pathways were identified.<br><br>Results: At baseline, the microbiota diversity of the groups was similar, but the genera Parabacteroides, Clostridia bacterium UC5.1_2F7, and Bifidobacterium dentium were enriched in the R group, whereas Bacteroides dorei and 11 species of Nocardia were enriched in the NR group. At 6 weeks, the beta diversity was significantly different between the R and NR groups. Further analysis found that 35 genera, such as Alipes, Parabacteroides, Phascolarctobacterium, Collinsella, Ruminiclostridium, Porphyromonas, and Butyricimonas and several genera of the Fibrobacteraceae family, were frequently distributed in the R group, whereas 17 genera, including Enterococcus, Lachnoclostridium, Hungatella, and Bilophila and several genera of the Pseudonocardiaceae and Beijerinckiaceae families, were more abundant in the NR group. A total of 66 and 52 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs (KOs) were significantly enriched in the R and NR groups, respectively. In addition, pathway analysis revealed functional differences in the gut microbacteria in the R group, including the enrichment of anabolic pathways and DNA damage repair (DDR) pathways. Dynamic comparisons of the bacterial composition at baseline, 6 weeks, and 12 weeks showed that the abundance of Weissella significantly increased in the R group at 6 weeks and the abundance of Fusobacterium and Anaerotruncus significantly increased in the NR group at 12 weeks. Linear discriminant analysis effect size analysis indicated that bacteria of Bacteroidetes, especially Bacteroides, were enriched in the NAE group, whereas flora of Firmcutes, such as Faecalibacterium prausnitzii, Bacteroides fragilis, and Ruminococcus lactaris, were enriched in the AE group.<br><br>Conclusion: Beta diversity and differences in the gut microbiota modulated AEs and the response to anti-PD-1 blockade combined with chemotherapy, by regulating related anabolic and DDR pathways. Dynamic changes in the intestinal microbiome may predict the efficacy of PD-1 inhibitor-based therapy.},
}
@article {pmid36386948,
year = {2022},
author = {Mancin, L and Amatori, S and Caprio, M and Sattin, E and Bertoldi, L and Cenci, L and Sisti, D and Bianco, A and Paoli, A},
title = {Effect of 30 days of ketogenic Mediterranean diet with phytoextracts on athletes' gut microbiome composition.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {979651},
doi = {10.3389/fnut.2022.979651},
pmid = {36386948},
issn = {2296-861X},
abstract = {Background: Recent research suggest that gut microbiome may play a fundamental role in athlete's health and performance. Interestingly, nutrition can affect athletic performance by influencing the gut microbiome composition. Among different dietary patterns, ketogenic diet represents an efficient nutritional approach to get adequate body composition in athletes, however, some concerns have been raised about its potential detrimental effect on gut microbiome. To the best of our knowledge, only one study investigated the effect of ketogenic diet on the gut microbiome in athletes (elite race walkers), whilst no studies are available in a model of mixed endurance/power sport such as soccer. This study aimed to investigate the influence of a ketogenic Mediterranean diet with phytoextracts (KEMEPHY) diet on gut microbiome composition in a cohort of semi-professional soccer players.<br><br>Methods: 16 male soccer players were randomly assigned to KEMEPHY diet (KDP n = 8) or western diet (WD n = 8). Body composition, performance measurements and gut microbiome composition were measured before and after 30 days of intervention by 16S rRNA amplicon sequencing. Alpha-diversity measures and PERMANOVA was used to investigate pre-post differences in the relative abundance of all taxonomic levels (from phylum to genus) and Spearman's correlations was used to investigate associations between microbial composition and macronutrient intake. Linear discriminant analysis was also performed at the different taxonomic levels on the post-intervention data.<br><br>Results: No differences were found between pre and post- dietary intervention for microbial community diversity: no significant effects of time (p = 0.056, ES = 0.486 and p = 0.129, ES = 0.388, respectively for OTUs number and Shannon's ENS), group (p = 0.317, ES = 0.180 and p = 0.809, ES = 0.047) or time × group (p = 0.999, ES = 0.01 and p = 0.230, ES = 0.315). Post-hoc paired Wilcoxon test showed a significant time × group effect for Actinobacteriota (p = 0.021, ES = 0.578), which increased in the WD group (median pre: 1.7%; median post: 2.3%) and decreased in the KEMEPHY group (median pre: 4.3%; median post: 1.7%). At genus level, the linear discriminant analysis in the post intervention differentiated the two groups for Bifidobacterium genus (pertaining to the Actinobacteria phylum), Butyricicoccus and Acidaminococcus genera, all more abundant in the WD group, and for Clostridia UCG-014 (order, family, and genus), Butyricimonas, Odoribacterter genera (pertaining to the Marinifilaceae family), and Ruminococcus genus, all more abundant in the KEMEPHY group.<br><br>Conclusions: Our results demonstrate that 30 days of KEMEPHY intervention, in contrast with previous research on ketogenic diet and gut microbiome, do not modify the overall composition of gut microbiome in a cohort of athletes. KEMEPHY dietary pattern may represent an alternative and safety tool for maintaining and/or regulating the composition of gut microbiome in athletes practicing regular exercise. Due to the fact that not all ketogenic diets are equal, we hypothesized that each version of ketogenic diet, with different kind of nutrients or macronutrients partitioning, may differently affect the human gut microbiome.},
}
@article {pmid36386940,
year = {2022},
author = {Young, W and Maclean, P and Dunstan, K and Ryan, L and Peters, J and Armstrong, K and Anderson, R and Dewhurst, H and van Gendt, M and Dilger, RN and Dekker, J and Haggarty, N and Roy, N},
title = {Lacticaseibacillus rhamnosus HN001 alters the microbiota composition in the cecum but not the feces in a piglet model.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {1002369},
doi = {10.3389/fnut.2022.1002369},
pmid = {36386940},
issn = {2296-861X},
abstract = {The probiotic Lacticaseibacillus rhamnosus strain HN001 has been shown to have several beneficial health effects for both pediatric and maternal groups, including reduced risk of eczema in infants and gestational diabetes and postnatal depression in mothers. While L. rhamnosus HN001 appears to modify immune and gut barrier biomarkers, its mode of action remains to be fully elucidated. To gain insights into the role of HN001 on the infant microbiome, the impacts of L. rhamnosus HN001 supplementation was studied in 10-day old male piglets that were fed either infant formula, or infant formula with L. rhamnosus HN001 at a low (1.3 × 10[5] CFU/ml) or high dose (7.9 × 10[6] CFU/ml) daily for 24 days. The cecal and fecal microbial communities were assessed by shotgun metagenome sequencing and host gene expression in the cecum and colon tissue was assessed by RNA-seq. Piglet fecal samples showed only modest differences between controls and those receiving dietary L. rhamnosus HN001. However, striking differences between the three groups were observed for cecal samples. While total lactobacilli were significantly increased only in the high dose L. rhamnosus HN001 group, both high and low dose groups showed an up to twofold reduction across the Firmicutes phylum and up to fourfold increase in Prevotella compared to controls. Methanobrevibacter was also decreased in HN001 fed piglets. Microbial genes involved in carbohydrate and vitamin metabolism were among those that differed in relative abundance between those with and without L. rhamnosus HN001. Changes in the cecal microbiome were accompanied by increased expression of tight junction pathway genes and decreased autophagy pathway genes in the cecal tissue of piglets fed the higher dose of L. rhamnosus HN001. Our findings showed supplementation with L. rhamnosus HN001 caused substantial changes in the cecal microbiome with likely consequences for key microbial metabolic pathways. Host gene expression changes in the cecum support previous research showing L. rhamnosus HN001 beneficially impacts intestinal barrier function. We show that fecal samples may not adequately reflect microbiome composition higher in the gastrointestinal tract, with the implication that effects of probiotic consumption may be missed by examining only the fecal microbiome.},
}
@article {pmid36386914,
year = {2022},
author = {Mohr, AE and Jasbi, P and Bowes, DA and Dirks, B and Whisner, CM and Arciero, KM and Poe, M and Gu, H and Gumpricht, E and Sweazea, KL and Arciero, PJ},
title = {Exploratory analysis of one versus two-day intermittent fasting protocols on the gut microbiome and plasma metabolome in adults with overweight/obesity.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {1036080},
doi = {10.3389/fnut.2022.1036080},
pmid = {36386914},
issn = {2296-861X},
abstract = {Nutritional interventions are a promising therapeutic option for addressing obesity and cardiometabolic dysfunction. One such option, intermittent fasting (IF), has emerged as a viable alternative to daily caloric restriction and may beneficially modulate body weight regulation and alter the gut microbiome (GM) and plasma metabolome. This secondary analysis of a larger, registered trial (ClinicalTrials.gov ID: NCT04327141) examined the effect of a four-week intervention comparing one vs. two-consecutive days of IF in combination with protein pacing (IF-P; 4-5 meals/day, >30% protein/day) on the GM, the plasma metabolome, and associated clinical outcomes in overweight and obese adults. Participants (n = 20) were randomly assigned to either a diet consisting of one fasting day (total of 36 h) and six low-calorie P days per week (IF1-P, n = 10) or two fasting days (60 h total) and five low-calorie P days per week (IF2-P, n = 10). The fecal microbiome, clinical outcomes, and plasma metabolome were analyzed at baseline (week 0) and after four weeks. There were no significant time or interaction effects for alpha diversity; however, baseline alpha diversity was negatively correlated with percent body fat change after the four-week intervention (p = 0.030). In addition, beta-diversity for both IF groups was altered significantly by time (p = 0.001), with no significant differences between groups. The IF1-P group had a significant increase in abundance of Ruminococcaceae Incertae Sedis and Eubacterium fissicatena group (q ≤ 0.007), while the IF2-P group had a significant increase in abundance of Ruminococcaceae Incertae Sedis and a decrease in Eubacterium ventriosum group (q ≤ 0.005). The plasma metabolite profile of IF2-P participants displayed significant increases in serine, trimethylamine oxide (TMAO), levulinic acid, 3-aminobutyric acid, citrate, isocitrate, and glucuronic acid (q ≤ 0.049) compared to IF1-P. Fecal short-chain fatty acid concentrations did not differ significantly by time or between groups (p ≥ 0.126). Interestingly, gastrointestinal symptoms were significantly reduced for the IF2-P group but not for the IF1-P group. Our results demonstrate that short-term IF modestly influenced the GM community structure and the plasma metabolome, suggesting these protocols could be viable for certain nutritional intervention strategies.},
}
@article {pmid36386790,
year = {2022},
author = {Sabotta, CM and Kwan, SY and Petty, LE and Below, JE and Joon, A and Wei, P and Fisher-Hoch, SP and McCormick, JB and Beretta, L},
title = {Genetic variants associated with circulating liver injury markers in Mexican Americans, a population at risk for non-alcoholic fatty liver disease.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {995488},
doi = {10.3389/fgene.2022.995488},
pmid = {36386790},
issn = {1664-8021},
abstract = {Objective: Mexican Americans are disproportionally affected by non-alcoholic fatty liver disease (NAFLD), liver fibrosis and hepatocellular carcinoma. Noninvasive means to identify those in this population at high risk for these diseases are urgently needed. Approach: The Cameron County Hispanic Cohort (CCHC) is a population-based cohort with high rates of obesity (51%), type 2 diabetes (28%) and NAFLD (49%). In a subgroup of 564 CCHC subjects, we evaluated 339 genetic variants previously reported to be associated with liver injury markers aspartate aminotransferase (AST) and alanine aminotransferase (ALT) in United Kingdom and Japanese cohorts. Results: Association was confirmed for 86 variants. Among them, 27 had higher effect allele frequency in the CCHC than in the United Kingdom and Japanese cohorts, and 16 had stronger associations with AST and ALT than rs738409 (PNPLA3). These included rs17710008 (MYCT1), rs2519093 (ABO), rs1801690 (APOH), rs10409243 (S1PR2), rs1800759 (LOC100507053) and rs2491441 (RGL1), which were also associated with steatosis and/or liver fibrosis measured by vibration-controlled transient elastography. Main contributors to advanced fibrosis risk were rs11240351 (CNTN2), rs1800759 (LOC100507053), rs738409 (PNPLA3) and rs1801690 (APOH), with advanced fibrosis detected in 37.5% of subjects with 3 of these 4 variants [AOR = 11.6 (95% CI) = 3.8-35.3]. AST- and ALT-associated variants implicated distinct pathways (ethanol and galactose degradation versus antigen presentation and B cell development). Finally, 8 variants, including rs62292950 (DNAJC13), were associated with gut microbiome changes. Conclusion: These genotype-phenotype findings may have utility in risk modeling and disease prevention in this high-risk population.},
}
@article {pmid36386777,
year = {2022},
author = {Hammond, TC and Powell, E and Green, SJ and Chlipala, G and Frank, J and Yackzan, AT and Yanckello, LM and Chang, YH and Xing, X and Heil, S and Springer, JE and Pennypacker, K and Stromberg, A and Sawaki, L and Lin, AL},
title = {Functional recovery outcomes following acute stroke is associated with abundance of gut microbiota related to inflammation, butyrate and secondary bile acid.},
journal = {Frontiers in rehabilitation sciences},
volume = {3},
number = {},
pages = {1017180},
doi = {10.3389/fresc.2022.1017180},
pmid = {36386777},
issn = {2673-6861},
abstract = {Accumulating evidence suggests that gut microbes modulate brain plasticity via the bidirectional gut-brain axis and play a role in stroke rehabilitation. However, the microbial species alterations associated with stroke and their correlation with functional outcome measures following acute stroke remain unknown. Here we measure post-stroke gut dysbiosis and how it correlates with gut permeability and cognitive functions in 12 stroke participants, 18 controls with risk factors for stroke, and 12 controls without risk factors. Stool samples were used to measure the microbiome with whole genome shotgun sequencing and leaky gut markers. We genotyped APOE status and measured diet composition and motor, cognitive, and emotional status using NIH Toolbox. We used linear regression methods to identify gut microbial associations with cognitive and emotional assessments. We did not find significance differences between the two control groups. In contrast, the bacteria populations of the Stroke group were statistically dissimilar from the control groups. Relative abundance analysis revealed notable decreases in butyrate-producing microbial taxa, secondary bile acid-producing taxa, and equol-producing taxa. The Stroke group had higher levels of the leaky gut marker alpha-1-antitrypsin in the stool than either of the groups and several taxa including Roseburia species (a butyrate producer) were negatively correlated with alpha-1-antitrypsin. Stroke participants scored lower on memory testing than those in the two control groups. Stroke participants with more Roseburia performed better on the picture vocabulary task; more Bacteroides uniformis (a butyrate producer) and less Escherichia coli (a pro-inflammatory species) reported higher levels of self-efficacy. Intakes of fiber, fruit and vegetable were lower, but sweetened beverages were higher, in the Stroke group compared with controls. Vegetable consumption was correlated with many bacterial changes among the participants, but only the species Clostridium bolteae, a pro-inflammatory species, was significantly associated with stroke. Our findings indicate that stroke is associated with a higher abundance of proinflammatory species and a lower abundance of butyrate producers and secondary bile acid producers. These altered microbial communities are associated with poorer functional performances. Future studies targeting the gut microbiome should be developed to elucidate whether its manipulation could optimize rehabilitation and boost recovery.},
}
@article {pmid36386721,
year = {2022},
author = {Xin, WG and Li, XD and Lin, YC and Jiang, YH and Xu, MY and Zhang, QL and Wang, F and Lin, LB},
title = {Whole genome analysis of host-associated lactobacillus salivarius and the effects on hepatic antioxidant enzymes and gut microorganisms of Sinocyclocheilus grahami.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1014970},
doi = {10.3389/fmicb.2022.1014970},
pmid = {36386721},
issn = {1664-302X},
abstract = {As a fish unique to Yunnan Province in China, Sinocyclocheilus grahami hosts abundant potential probiotic resources in its intestinal tract. However, the genomic characteristics of the probiotic potential bacteria in its intestine and their effects on S. grahami have not yet been established. In this study, we investigated the functional genomics and host response of a strain, Lactobacillus salivarius S01, isolated from the intestine of S. grahami (bred in captivity). The results revealed that the total length of the genome was 1,737,623 bp (GC content, 33.09%), comprised of 1895 genes, including 22 rRNA operons and 78 transfer RNA genes. Three clusters of antibacterial substances related genes were identified using antiSMASH and BAGEL4 database predictions. In addition, manual examination confirmed the presence of functional genes related to stress resistance, adhesion, immunity, and other genes responsible for probiotic potential in the genome of L. salivarius S01. Subsequently, the probiotic effect of L. salivarius S01 was investigated in vivo by feeding S. grahami a diet with bacterial supplementation. The results showed that potential probiotic supplementation increased the activity of antioxidant enzymes (SOD, CAT, and POD) in the hepar and reduced oxidative damage (MDA). Furthermore, the gut microbial community and diversity of S. grahami from different treatment groups were compared using high-throughput sequencing. The diversity index of the gut microbial community in the group supplemented with potential probiotics was higher than that in the control group, indicating that supplementation with potential probiotics increased gut microbial diversity. At the phylum level, the abundance of Proteobacteria decreased with potential probiotic supplementation, while the abundance of Firmicutes, Actinobacteriota, and Bacteroidota increased. At the genus level, there was a decrease in the abundance of the pathogenic bacterium Aeromonas and an increase in the abundance of the potential probiotic bacterium Bifidobacterium. The results of this study suggest that L. salivarius S01 is a promising potential probiotic candidate that provides multiple benefits for the microbiome of S. grahami.},
}
@article {pmid36386713,
year = {2022},
author = {Song, Y and Wen, S and Li, F and Fischer-Tlustos, A and He, Z and Guan, LL and Steele, M},
title = {Metagenomic analysis provides bases on individualized shift of colon microbiome affected by delaying colostrum feeding in neonatal calves.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1035331},
doi = {10.3389/fmicb.2022.1035331},
pmid = {36386713},
issn = {1664-302X},
abstract = {This study investigated the effect of colostrum feeding time on the colon digesta microbiome of 2-day-old dairy calves using whole-genome-based metagenome sequencing, aiming to understand the dynamic changes of the colon microbiome when the colostrum feeding is delayed. In total, 24 male Holstein calves were grouped to different pasteurized colostrum feeding time treatments randomly: TRT0h (45 min after birth, n = 7); TRT6h (6 h after birth, n = 8); and TRT12h (12 h after birth, n = 9). Bacteria, archaea, eukaryotes, and viruses were identified in the colon microbiome, with bacteria (99.20%) being the most predominant domain. Streptococcus, Clostridium, Lactobacillus, Ruminococcus, and Enterococcus were the top five abundant bacteria genera. For colon microbiome functions, 114 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, with nutrients metabolism-related functions "carbohydrate metabolism," "amino acid metabolism," "metabolism of cofactors and vitamins," "metabolism of terpenoids and polyketides," and "metabolism of other amino acids" being the top five secondary level of KEGG hierarchy functions. When colon microbiomes were compared, they were not affected by delaying first colostrum feeding at both taxonomic and functional levels. However, distinct clusters of colon microbiome profiles were shown based on PERMANOVA analysis despite of different colostrum feeding treatment, suggesting the individualized responses. Moreover, the relative abundance of microbial taxa, microbial functions, and differentially expressed genes was compared between the two distinct clusters, and different relationships were observed among host differentially expressed genes, differential levels of microbial taxa, and microbial functions between the two clusters. Our results suggest that the host may play an important role in shaping the colon microbiome of neonatal dairy calves in response to the early life feeding management. Whether the observed colon microbiome shifts affect gut health and function in the long term requires further research.},
}
@article {pmid36386712,
year = {2022},
author = {Kumar, A and Karthikeyan, OP and Joshi, SJ},
title = {Editorial: Insights in microbiotechnology-2021.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1059702},
doi = {10.3389/fmicb.2022.1059702},
pmid = {36386712},
issn = {1664-302X},
}
@article {pmid36386704,
year = {2022},
author = {Medeiros, MM and Ingham, AC and Nanque, LM and Correia, C and Stegger, M and Andersen, PS and Fisker, AB and Benn, CS and Lanaspa, M and Silveira, H and Abrantes, P},
title = {Oral polio revaccination is associated with changes in gut and upper respiratory microbiomes of infants.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1016220},
doi = {10.3389/fmicb.2022.1016220},
pmid = {36386704},
issn = {1664-302X},
abstract = {After the eradication of polio infection, the plan is to phase-out the live-attenuated oral polio vaccine (OPV). Considering the protective non-specific effects (NSE) of OPV on unrelated pathogens, the withdrawal may impact child health negatively. Within a cluster-randomized trial, we carried out 16S rRNA deep sequencing analysis of fecal and nasopharyngeal microbial content of Bissau-Guinean infants aged 4-8 months, before and after 2 months of OPV revaccination (revaccinated infants = 47) vs. no OPV revaccination (control infants = 47). The aim was to address changes in the gut and upper respiratory bacterial microbiotas due to revaccination. Alpha-diversity for both microbiotas increased similarly over time in OPV-revaccinated infants and controls, whereas greater changes over time in the bacterial composition of gut (p adjusted < 0.001) and upper respiratory microbiotas (p adjusted = 0.018) were observed in the former. Taxonomic analysis of gut bacterial microbiota revealed a decrease over time in the median proportion of Bifidobacterium longum for all infants (25-14.3%, p = 0.0006 in OPV-revaccinated infants and 25.3-11.6%, p = 0.01 in controls), compatible with the reported weaning. Also, it showed a restricted increase in the median proportion of Prevotella_9 genus in controls (1.4-7.1%, p = 0.02), whereas in OPV revaccinated infants an increase over time in Prevotellaceae family (7.2-17.4%, p = 0.005) together with a reduction in median proportion of potentially pathogenic/opportunistic genera such as Escherichia/Shigella (5.8-3.4%, p = 0.01) were observed. Taxonomic analysis of upper respiratory bacterial microbiota revealed an increase over time in median proportions of potentially pathogenic/opportunistic genera in controls, such as Streptococcus (2.9-11.8%, p = 0.001 and Hemophilus (11.3-20.5%, p = 0.03), not observed in OPV revaccinated infants. In conclusion, OPV revaccination was associated with a healthier microbiome composition 2 months after revaccination, based on a more abundant and diversified bacterial community of Prevotellaceae and fewer pathogenic/opportunistic organisms. Further information on species-level differentiation and functional analysis of microbiome content are warranted to elucidate the impact of OPV-associated changes in bacterial microbiota on child health.},
}
@article {pmid36386689,
year = {2022},
author = {Ma, P and Sun, C and Liu, M and You, H and Shen, Y and Kang, Y and Sun, Y and Yang, Z and Ma, P and Yang, L and Xue, F},
title = {Metagenomic insights into the rumen epithelial integrity responses to the vitamin B1 supplement under high-concentrate diets treatments.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1008373},
doi = {10.3389/fmicb.2022.1008373},
pmid = {36386689},
issn = {1664-302X},
abstract = {Subacute ruminal acidosis (SARA) becomes the most common nutritional metabolic disease in high-yielding dairy cows and later fatting beef cattle because of the increasing consumption of high-concentrate diets in modern feeding patterns. Our previous research found a certain piece of evidence that adding 180 mg thiamine/kg DMI could increase the rumen pH and regulate the structure of the rumen microbial community in vivo. However, there is still limited experimental data on the effects of SARA on thiamine status, the damage to the structure of rumen epithelial cells, and the underlying mechanism of the epithelium alterations. For this purpose, a total of 18 Angus bulls (average 22.0-months-old) with an average live weight of 567.6 ± 27.4 kg were randomly allocated into a control treatment (CON), a high-concentrate diet treatment (HC), and a high-concentrate diet with the vitamin B1 supplement treatment (HCB). All bulls were conducted with a 7-day adjustment period followed by a 60-day-long main feeding procedure. Results indicated that ADFI and ADG significantly decreased in the HC treatment compared with CON (P < 0.05), while significantly increased after the VB1 supplement (P < 0.05). Besides, ruminal acetate content was significantly downregulated while propionate was significantly upregulated under the HC treatment compared with CON (P < 0.05); however, these alterations showed a completely inverse regulatory effect on the VB1 supplement compared with HC (P < 0.05). These changes causatively induced a significant decrease in the A/P ratio in the HC treatment compared with CON and HCB treatments (P < 0.05). Bacterial communities in the HC treatment could be separated from those in CON through PCoA axes 1 and 2. Meanwhile, the VB1 supplement significantly altered the bacterial communities compared with the HC treatment, except for HCB-3. Furthermore, the HC treatment significantly upregulated the expression of JNK, Bax, Caspase-8, Caspase-3, Caspase-9, and Cyt-C compared with CON, while significantly downregulated the expression of Bcl-2. The VB1 supplement showed a complete converse gene expression compared with HC. In conclusion, the VB1 supplement could effectively attenuate the alterations that occurred when exposed to high-concentrate diets, and help promote production performance through increased fermentability.},
}
@article {pmid36386686,
year = {2022},
author = {Dai, L and Singh, SK and Gong, H and Tang, Y and Peng, Z and Zhang, J and Wu, D and Zhang, H and He, D},
title = {Rhizospheric microbial consortium of Lilium lancifolium Thunb. causes lily root rot under continuous cropping system.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {981615},
doi = {10.3389/fmicb.2022.981615},
pmid = {36386686},
issn = {1664-302X},
abstract = {Tiger lily (Lilium lancifolium Thunb.) is a cash crop with a long history of cultivation in China. Its roots have long been used as a valuable component of Chinese medicine. Continuous cropping, the conventional planting approach for tiger lily, often leads to severe root rot disease, but it is not yet clear how this planting method leads to root rot. In this study, we analyzed the rhizosphere microbiome and predicted microbial protein function in tiger lily planted with the continuous cropping method in three different geological types of soil. In order to explore the specific rhizosphere microbiota triggering root rot disease, tiger lily was compared to maize grown in a similar system, which showed no disease development. An analysis of the chemical elements in the soil revealed that the Pseudomonas and Streptomyces genera, with pathogenic functions, were dominant in the tiger lily rhizosphere. The lower soil pH of tiger lily compared to maize supports the accumulation of pathogenic bacteria in the tiger lily rhizosphere. Meanwhile, we discovered that bacteria of the Flavobacterium genus, with their predicted phosphate transport function, specifically accumulated in the maize rhizosphere. Our findings suggest that Pseudomonas and Streptomyces bacteria may result in continuous cropping-induced root rot disease in tiger lily and that Flavobacterium could serve to protect maize from pathogenic bacteria.},
}
@article {pmid36386682,
year = {2022},
author = {Pan, X and Zhou, Z and Liu, B and Wu, Z},
title = {A novel therapeutic concern: Antibiotic resistance genes in common chronic diseases.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1037389},
doi = {10.3389/fmicb.2022.1037389},
pmid = {36386682},
issn = {1664-302X},
abstract = {Infections caused by multidrug-resistant bacteria carrying antibiotic resistance genes pose a severe threat to global public health and human health. In clinical practice, it has been found that human gut microbiota act as a "reservoir" of antibiotic resistance genes (ARGs) since gut microbiota contain a wide variety of ARGs, and that the structure of the gut microbiome is influenced by the profile of the drug resistance genes present. In addition, ARGs can spread within and between species of the gut microbiome in multiple ways. To better understand gut microbiota ARGs and their effects on patients with chronic diseases, this article reviews the generation of ARGs, common vectors that transmit ARGs, the characteristics of gut microbiota ARGs in common chronic diseases, their impact on prognosis, the current state of treatment for ARGs, and what should be addressed in future research.},
}
@article {pmid36386670,
year = {2022},
author = {Wang, K and Liu, M and Cai, C and Cai, S and Ma, X and Lin, C and Zhu, Q},
title = {The impact of genetic modified Ma bamboo on soil microbiome.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1025786},
doi = {10.3389/fmicb.2022.1025786},
pmid = {36386670},
issn = {1664-302X},
abstract = {Evaluating the potential alteration of microbial communities is a vital step for biosafety of genetic modified plants. Recently, we have produced genetic modified Ma bamboo with increased cold and drought tolerance by anthocyanin accumulation. In this work, we aim to study the potential effects on microbial communities in rhizosphere soils during the cultivation of genetic modified bamboo. Rhizosphere and surrounding soil were collected at 3-month post-transplant. The amplicon (16S rDNA and ITS1) were sequenced for analysis of bacterial and fungal communities. Multiple software and database (Picrust2, FAPROTAX and FUNGulid) were applied to predict and compare the microbial functions involving basic metabolisms, nitrogen usage and presence of plant pathogens. There were no substantial change of the structure and abundance of rhizosphere soil microbial communities between genetic modified and wild type bamboo. For the surrounding soil, the bacterial biota α-diversity increased (chao1: 1,001 ± 80-1,276 ± 84, observed species: 787 ± 52-1,194 ± 137, PD whole tree: 75 ± 4-117 ± 18) and fungal biota α-diversity decreased (chao1: 187 ± 18-145 ± 10) in samples of genetic modified bamboo compared to those of wild type bamboo. The microbiota predicted functions did not change or had no negative alteration between genetic modified and wild type bamboo, in both rhizosphere and surrounding soils. As a conclusion, the growth of genetic modified bamboo had no substantial change on rhizosphere soil microbial communities, while minor alteration on bamboo surrounding soil microbial communities with no harmful effects. Moreover, the genetic modified bamboo had no negative effect on the predicted functions of microbiota in soil.},
}
@article {pmid36386659,
year = {2022},
author = {Chen, L and Sun, M and Xu, D and Gao, Z and Shi, Y and Wang, S and Zhou, Y},
title = {Gut microbiome of captive wolves is more similar to domestic dogs than wild wolves indicated by metagenomics study.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1027188},
doi = {10.3389/fmicb.2022.1027188},
pmid = {36386659},
issn = {1664-302X},
abstract = {Adaptation during the domestication from wolves (Canis lupus) to dogs (Canis lupus familiaris) is a debated ecological topic. Changes in food and environment are major divergences in the domestication of dogs. Gut microbes play an important role in animal adaptation to the food and environmental changes. In this study, shotgun sequencing was performed to compare the species diversity and functional diversity of gut microbes in wild wolves (group CLW, n = 3), captive wolves (group CLC, n = 4), and domestic dogs (group CLF, n = 4). The results found that Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria and Actinobacteria were the most abundant phyla and Bacteroides, Fusobacterium, Prevotella, Megamonas, Paraprevotella, Faecalibacterium, Clostridium were the most abundant genera in the gut of wolves and dogs. Groups CLW, CLC and CLF have shown significant difference in gut microbial species diversity and functional diversity. Bacteroides, Fusobacterium and Faecalibacterium were most abundant genera in groups CLW, CLC and CLF, respectively. Their abundance varied significantly among groups. Compared to the wild wolves, the intestinal microbiol genes of domestic dogs were significantly enriched in the carbohydrate metabolism pathway of KEGG database. One hundred and seventy-seven enzymes were detected with significantly higher abundance in group CLF than that in group CLW, and 49 enzymes showed extremely significant higher abundance in group CLF than that in group CLW (q < 0.01) base on the function abundance annotated in CAZy database. It is noteworthy that there were also significant differences in the abundance of 140 enzymes between groups CLC and CLW (q < 0.05). Clustering analysis based on both the species and the function abundance of intestinal microbiota all found that groups CLC and CLF clustered into one branch, while samples from group CLW clustered into the other branch. This result suggests that captive wolves are more similar to domestic dogs than wild wolves in both species composition and function composition of intestinal microbiota.},
}
@article {pmid36386625,
year = {2022},
author = {Ben Zineb, A and Barkaoui, K and Karray, F and Mhiri, N and Sayadi, S and Mliki, A and Gargouri, M},
title = {Olive agroforestry shapes rhizosphere microbiome networks associated with annual crops and impacts the biomass production under low-rainfed conditions.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {977797},
doi = {10.3389/fmicb.2022.977797},
pmid = {36386625},
issn = {1664-302X},
abstract = {Agroforestry (AF) is a promising land-use system to mitigate water deficiency, particularly in semi-arid areas. However, the belowground microbes associated with crops below trees remain seldom addressed. This study aimed at elucidating the effects of olive AF system intercropped with durum wheat (Dw), barely (Ba), chickpea (Cp), or faba bean (Fb) on crops biomass and their soil-rhizosphere microbial networks as compared to conventional full sun cropping (SC) under rainfed conditions. To test the hypothesis, we compared the prokaryotic and the fungal communities inhabiting the rhizosphere of two cereals and legumes grown either in AF or SC. We determined the most suitable annual crop species in AF under low-rainfed conditions. Moreover, to deepen our understanding of the rhizosphere network dynamics of annual crops under AF and SC systems, we characterized the microbial hubs that are most likely responsible for modifying the microbial community structure and the variability of crop biomass of each species. Herein, we found that cereals produced significantly more above-ground biomass than legumes following in descending order: Ba > Dw > Cp > Fb, suggesting that crop species play a significant role in improving soil water use and that cereals are well-suited to rainfed conditions within both types of agrosystems. The type of agrosystem shapes crop microbiomes with the only marginal influence of host selection. However, more relevant was to unveil those crops recruits specific bacterial and fungal taxa from the olive-belowground communities. Of the selected soil physicochemical properties, organic matter was the principal driver in shaping the soil microbial structure in the AF system. The co-occurrence network analyses indicated that the AF system generates higher ecological stability than the SC system under stressful climate conditions. Furthermore, legumes' rhizosphere microbiome possessed a higher resilient capacity than cereals. We also identified different fungal keystones involved in litter decomposition and drought tolerance within AF systems facing the water-scarce condition and promoting crop production within the SC system. Overall, we showed that AF reduces cereal and legume rhizosphere microbial diversity, enhances network complexity, and leads to more stable beneficial microbial communities, especially in severe drought, thus providing more accurate predictions to preserve soil diversity under unfavorable environmental conditions.},
}
@article {pmid36386613,
year = {2022},
author = {Shafranskaya, D and Kale, V and Finn, R and Lapidus, AL and Korobeynikov, A and Prjibelski, AD},
title = {MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {981458},
doi = {10.3389/fmicb.2022.981458},
pmid = {36386613},
issn = {1664-302X},
abstract = {While metagenome sequencing may provide insights on the genome sequences and composition of microbial communities, metatranscriptome analysis can be useful for studying the functional activity of a microbiome. RNA-Seq data provides the possibility to determine active genes in the community and how their expression levels depend on external conditions. Although the field of metatranscriptomics is relatively young, the number of projects related to metatranscriptome analysis increases every year and the scope of its applications expands. However, there are several problems that complicate metatranscriptome analysis: complexity of microbial communities, wide dynamic range of transcriptome expression and importantly, the lack of high-quality computational methods for assembling meta-RNA sequencing data. These factors deteriorate the contiguity and completeness of metatranscriptome assemblies, therefore affecting further downstream analysis. Here we present MetaGT, a pipeline for de novo assembly of metatranscriptomes, which is based on the idea of combining both metatranscriptomic and metagenomic data sequenced from the same sample. MetaGT assembles metatranscriptomic contigs and fills in missing regions based on their alignments to metagenome assembly. This approach allows to overcome described complexities and obtain complete RNA sequences, and additionally estimate their abundances. Using various publicly available real and simulated datasets, we demonstrate that MetaGT yields significant improvement in coverage and completeness of metatranscriptome assemblies compared to existing methods that do not exploit metagenomic data. The pipeline is implemented in NextFlow and is freely available from https://github.com/ablab/metaGT.},
}
@article {pmid36386066,
year = {2022},
author = {Sharma, N and Dhar, S and De, A and Godse, K and Shankar, DSK and Zawar, V and Girdhar, M and Shah, B},
title = {Use of Bleach Baths for Atopic Dermatitis: An Indian Perspective.},
journal = {Indian journal of dermatology},
volume = {67},
number = {3},
pages = {273-278},
doi = {10.4103/ijd.IJD_536_20},
pmid = {36386066},
issn = {1998-3611},
abstract = {Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disorder affecting 15-20% of children and 1-10% of adults. Staphylococcus aureus (S. aureus) infection is the most frequent complication of AD and is involved in the worsening of the disease. Systemic and topical antibiotics are used in the treatment for AD but there are concerns over increasing resistance. Bleach (sodium hypochlorite, NaOCl) baths are an inexpensive, widely accessible, alternative antibiotic treatment that may not worsen antibiotic resistance. Bleach baths are used as adjunctive treatment in AD patients to treat superinfections, although their mechanism of action is not well understood. Balancing safety concerns with efficacious treatment should be important especially for AD where the majority of patients are in pediatrics age groups. Studies available in PubMed databases were included in this review. Most suggested bleach bath improves clinical symptoms of AD and restores surface microbiome by eradicating bacteria, most notably S. aureus. Some studies have noted that this antimicrobial effect has reduced the need for topical corticosteroids. In addition, bleach seems to have strong anti-inflammatory and antipruritic effects. Overall, bleach baths seem to be safe on human skin, without disrupting the epidermal barrier function. The review concluded, although there are some advantages of use of bleach baths, more studies to investigate long-term efficacy and safety of bleach baths are required before fixing its role in the treatment of AD especially in the context of the Indian scenario.},
}
@article {pmid36385637,
year = {2022},
author = {Natalini, JG and Singh, S and Segal, LN},
title = {The dynamic lung microbiome in health and disease.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {36385637},
issn = {1740-1534},
abstract = {New methods and technologies within the field of lung biology are beginning to shed new light into the microbial world of the respiratory tract. Long considered to be a sterile environment, it is now clear that the human lungs are frequently exposed to live microbes and their by-products. The nature of the lung microbiome is quite distinct from other microbial communities inhabiting our bodies such as those in the gut. Notably, the microbiome of the lung exhibits a low biomass and is dominated by dynamic fluxes of microbial immigration and clearance, resulting in a bacterial burden and microbiome composition that is fluid in nature rather than fixed. As our understanding of the microbial ecology of the lung improves, it is becoming increasingly apparent that certain disease states can disrupt the microbial-host interface and ultimately affect disease pathogenesis. In this Review, we provide an overview of lower airway microbial dynamics in health and disease and discuss future work that is required to uncover novel therapeutic targets to improve lung health.},
}
@article {pmid36385568,
year = {2022},
author = {Zhai, T and Ren, W and Wang, P and Zheng, L},
title = {Lactobacillus rhamnosus GG protects against atherosclerosis by improving ketone body synthesis.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {36385568},
issn = {1432-0614},
support = {82025024//National Science Fund for Distinguished Young Scholars/ ; 2019B1515120074//Key Project of Basic and Applied Basic Research of Guangdong Province/ ; },
abstract = {Atherosclerosis (AS) is a major cause of death and morbidity worldwide. There is an increasing amount of evidence that the gut microbiota plays an important role in disorders associated with lipid metabolism, such as AS, and alterations in the composition of the gut microbiota and its metabolic potential have been identified as contributing factors in the development of AS. Recently, probiotics have attracted great interest for their excellent cholesterol-lowering ability, their capacity to improve vascular endothelial function, and their participation in the remodeling of the intestinal flora to prevent AS. The incidental findings of our other study suggest that probiotic Lactobacillus rhamnosus GG may be associated with slowing the progression of AS. Thus, we delivered strain GG into mice by oral feeding and found that strain GG could effectively inhibit AS plaque generation. We analyzed the differences in gut microbiota composition and the peripheral blood metabolome in mice after oral feeding of strain GG by 16S DNA sequencing and untargeted metabolomics, respectively. The results showed that strain GG changed the composition of the gut microbiota in mice fed a high-fat diet; elevated the abundance of beneficial bacteria, such as Bilophila and Alistipes, and decreased the abundance of harmful bacteria, such as Deltaproteobacteria. The results of enrichment analysis of the gut microbiota and the peripheral blood metabolome both indicated that the antiatherosclerotic effect of strain GG might be associated with the biosynthesis pathway of ketone bodies. In addition, strain GG attenuated endothelial injury and elevated peripheral blood ketone body content in mice but did not significantly affect low-density lipoprotein cholesterol (LDL-C) and total cholesterol (TC) content. In conclusion, our study provides new evidence that strain GG slows the progression of AS, which may be associated with its improvement of the gut microbiome and peripheral blood metabolome, its ability to increase the abundance of beneficial bacteria, and its participation in unsaturated fatty acid and ketone body synthesis and degradation. KEY POINTS: • L. rhamnosus GG attenuated endothelial injury and atherosclerotic plaque formation • L. rhamnosus GG elevated the abundance of beneficial bacteria • L. rhamnosus GG elevated peripheral blood ketone body content in mice.},
}
@article {pmid36385397,
year = {2022},
author = {Schoch, JJ and Gauthier, J and Gharaibeh, RZ and Jobin, C and Bohannon, M and Neu, J and Parker, L},
title = {Skin microbiome sampling in the preterm neonate.},
journal = {Pediatric dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/pde.15158},
pmid = {36385397},
issn = {1525-1470},
support = {1KL2TROO1429/TR/NCATS NIH HHS/United States ; //Pediatric Dermatology Research Alliance/ ; //Society for Pediatric Dermatology/ ; },
abstract = {Despite advances in our understanding of the human microbiome, there exist significant knowledge gaps in our understanding of the skin microbiome of the preterm neonate. Herein, we describe skin microbiome sampling of six preterm neonates at multiple timepoints, and compare the skin microbiome samples to environmental (crib/isolette swabs) and negative controls. Samples of the same type (skin, crib, control) were more similar than when compared by week or by patient.},
}
@article {pmid36385263,
year = {2022},
author = {Kim, JW and Jung, H and Baek, IP and Nam, Y and Kang, J and Chung, MK and Park, JB and Lee, J and Kwok, SK and Kim, WU and Park, SH and Ju, JH},
title = {Differential effects of periodontal microbiome on the rheumatoid factor induction during rheumatoid arthritis pathogenesis.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {19636},
pmid = {36385263},
issn = {2045-2322},
support = {2019R1G1A1100421//National Research Foundation of Korea/ ; 2019R1A2027588//National Research Foundation of Korea/ ; },
abstract = {Association between exposure to periodontal bacteria and development of autoantibodies related to rheumatoid arthritis (RA) has been widely accepted; however, direct causal relationship between periodontal bacteria and rheumatoid factor (RF) is currently not fully understood. We investigated whether periodontal bacteria could affect RF status. Patients with preclinical, new-onset, or chronic RA underwent periodontal examination, and investigation of subgingival microbiome via 16S rRNA sequencing. Degree of arthritis and RF induction was examined in collagen-induced arthritis (CIA) mice that were orally inoculated with different periodontal bacteria species. Subsequently, single-cell RNA sequencing analysis of the mouse spleen cells was performed. Patients with preclinical RA showed an increased abundance of the Porphyromonadacae family in the subgingival microbiome compared to those with new-onset or chronic RA, despite comparable periodontitis severity among them. Notably, a distinct subgingival microbial community was found between patients with high-positive RF and those with negative or low-positive RF (p=0.022). Oral infections with the periodontal pathogens P. gingivalis and Treponema denticola in CIA mice similarly enhanced arthritis score, but resulted in different levels of RF induction. Genes related to B cell receptor signaling, B cell proliferation, activation, and differentiation, and CD4[+] T cell costimulation and cytokine production were involved in the differential induction of RF in mice exposed to different bacteria. In summary, periodontal microbiome might shape RF status by affecting the humoral immune response during RA pathogenesis.},
}
@article {pmid36385260,
year = {2022},
author = {Sousa, JMG and Louvado, A and Coelho, FJRC and Oliveira, V and Oliveira, H and Cleary, DFR and Gomes, NCM},
title = {In vitro study of the modulatory effects of heat-killed bacterial biomass on aquaculture bacterioplankton communities.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {19699},
pmid = {36385260},
issn = {2045-2322},
support = {UIDP/50017/2020+UIDB/50017/2020+LA/P/0094/2020//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/ ; PTDC/BIA-MIC/6473/2014-POCI-01-0145-FEDER-016531//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; },
abstract = {Recent studies have shown that the addition of non-viable microbial biomass or their components (postbiotics) to fish feed can modulate the gut microbiome and positively influence fish health in aquaculture systems. However, no information was hitherto available on the use of non-viable microbial biomass to manipulate aquaculture bacterioplankton communities. To fill this gap, here we used an in vitro model to assess the effects of heat-killed biomasses of an antagonistic strain Pseudoalteromonas rubra SubTr2 and a non-antagonist strain Escherichia coli DH5α on bacterioplankton communities of a recirculating aquaculture system (RAS). Our results showed that these biomasses can have generalist and species-specific effects on aquaculture bacterioplankton structure and function. In addition, they enriched the abundance of bacterial predators, reduced bacterial load and potentially influenced nutrient cycling and pathogen development in aquaculture water. Despite its preliminary nature, for the first time, this study showed that heat-killed microbial biomass has potential application as an in situ modulator of bacterioplankton in aquaculture systems.},
}
@article {pmid36384808,
year = {2022},
author = {Park, J and Davis, K and Lajoie, G and Parfrey, LW},
title = {Alternative approaches to identify core bacteria in Fucus distichus microbiome and assess their distribution and host-specificity.},
journal = {Environmental microbiome},
volume = {17},
number = {1},
pages = {55},
pmid = {36384808},
issn = {2524-6372},
support = {2021-03160//NSERC Discovery/ ; },
abstract = {BACKGROUND: Identifying meaningful ecological associations between host and components of the microbiome is challenging. This is especially true for hosts such as marine macroalgae where the taxonomic composition of the microbiome is highly diverse and variable in space and time. Identifying core taxa is one way forward but there are many methods and thresholds in use. This study leverages a large dataset of microbial communities associated with the widespread brown macroalga, Fucus distichus, across sites and years on one island in British Columbia, Canada. We compare three different methodological approaches to identify core taxa at the amplicon sequence variant (ASV) level from this dataset: (1) frequency analysis of taxa on F. distichus performed over the whole dataset, (2) indicator species analysis (IndVal) over the whole dataset that identifies frequent taxa that are enriched on F. distichus in comparison to the local environment, and (3) a two-step IndVal method that identifies taxa that are consistently enriched on F. distichus across sites and time points. We then investigated a F. distichus time-series dataset to see if those core taxa are seasonally consistent on another remote island in British Columbia, Canada. We then evaluate host-specificity of the identified F. distichus core ASVs using comparative data from 32 other macroalgal species sampled at one of the sites.<br><br>RESULTS: We show that a handful of core ASVs are consistently identified by both frequency analysis and IndVal approaches with alternative definitions, although no ASVs were always present on F. distichus and IndVal identified a diverse array of F. distichus indicator taxa across sites on Calvert Island in multiple years. Frequency analysis captured a broader suit of taxa, while IndVal was better at identifying host-specific microbes. Finally, two-step IndVal identified hundreds of indicator ASVs for particular sites/timepoints but only 12 that were indicators in a majority (> 6 out of 11) of sites/timepoints. Ten of these ASVs were also indicators on Quadra Island, 250 km away. Many F. distichus-core ASVs are generally found on multiple macroalgal species, while a few ASVs are highly specific to F. distichus.<br><br>CONCLUSIONS: Different methodological approaches with variable set thresholds influence core identification, but a handful of core taxa are apparently identifiable as they are widespread and temporally associated with F. distichus and enriched in comparison to the environment. Moreover, we show that many of these core ASVs of F. distichus are found on multiple macroalgal hosts, indicating that most occupy a macroalgal generalist niche rather than forming highly specialized associations with F. distichus. Further studies should test whether macroalgal generalists or specialists are more likely to engage in biologically important exchanges with host.},
}
@article {pmid36384753,
year = {2022},
author = {van Bommel, MHD and Pijnenborg, JMA and van der Putten, LJM and Bulten, J and Snijders, MPLM and Küsters-Vandevelde, HVN and Sweegers, S and Vos, MC and Ligtenberg, MJL and Eijkelenboom, A and de Hullu, JA and Reijnen, C},
title = {Diagnostic accuracy of mutational analysis along the Müllerian tract to detect ovarian cancer.},
journal = {International journal of gynecological cancer : official journal of the International Gynecological Cancer Society},
volume = {},
number = {},
pages = {},
doi = {10.1136/ijgc-2022-003911},
pmid = {36384753},
issn = {1525-1438},
abstract = {OBJECTIVE: Ovarian cancer is known for its poor prognosis, which is mainly due to the lack of early symptoms and adequate screening options. In this study we evaluated whether mutational analysis in cervicovaginal and endometrial samples could assist in the detection of ovarian cancer.<br><br>METHODS: In this prospective multicenter study, we included patients surgically treated for either (suspicion of) ovarian cancer or for a benign gynecological condition (control group). A cervicovaginal self-sample, a Papanicolaou (Pap) smear, a pipelle endometrial biopsy, and the surgical specimen were analyzed for (potentially) pathogenic variants in eight genes (ARID1A, CTNNB1, KRAS, MTOR, PIK3CA, POLE, PTEN, and TP53) using single-molecule molecular inversion probes. Sensitivity and specificity were calculated to assess diagnostic accuracy.<br><br>RESULTS: Based on surgical histology, our dataset comprised 29 patients with ovarian cancer and 32 controls. In 83% of the patients with ovarian cancer, somatic (potentially) pathogenic variants could be detected in the final surgical specimen, of which 71% included at least a TP53 variant. In 52% of the ovarian cancer patients, such variants could be detected in either the self-sample, Pap smear, or pipelle. The Pap smear yielded the highest diagnostic accuracy with 26% sensitivity (95% CI 10% to 48%). Overall diagnostic accuracy was low and was not improved when including TP53 variants only.<br><br>CONCLUSIONS: Mutational analysis in cervicovaginal and endometrial samples has limited accuracy in the detection of ovarian cancer. Future research with cytologic samples analyzed on methylation status or the vaginal microbiome may be relevant.},
}
@article {pmid36384698,
year = {2022},
author = {Chandel, A and Mann, R and Kaur, J and Tannenbaum, I and Norton, S and Edwards, J and Spangenberg, G and Sawbridge, T},
title = {Australian native Glycine clandestina seed microbiota hosts a more diverse bacterial community than the domesticated soybean Glycine max.},
journal = {Environmental microbiome},
volume = {17},
number = {1},
pages = {56},
pmid = {36384698},
issn = {2524-6372},
abstract = {BACKGROUND: Plant microbiome composition has been demonstrated to change during the domestication of wild plants and it is suggested that this has resulted in loss of plant beneficial microbes. Recently, the seed microbiome of native plants was demonstrated to harbour a more diverse microbiota and shared a common core microbiome with modern cultivars. In this study the composition of the seed-associated bacteria of Glycine clandestina is compared to seed-associated bacteria of Glycine max (soybean).<br><br>RESULTS: The seed microbiome of the native legume Glycine clandestina (crop wild relative; cwr) was more diverse than that of the domesticated Glycine max and was dominated by the bacterial class Gammaproteobacteria. Both the plant species (cwr vs domesticated) and individual seed accessions were identified as the main driver for this diversity and composition of the microbiota of all Glycine seed lots, with the effect of factor "plant species" exceeded that of "geographical location". A core microbiome was identified between the two Glycine species. A high percentage of the Glycine microbiome was unculturable [G. clandestina (80.8%) and G. max (75.5%)] with only bacteria of a high relative abundance being culturable under the conditions of this study.<br><br>CONCLUSION: Our results provided novel insights into the structure and diversity of the native Glycine clandestina seed microbiome and how it compares to that of the domesticated crop Glycine max. Beyond that, it also increased our knowledge of the key microbial taxa associated with the core Glycine spp. microbiome, both wild and domesticated. The investigation of this commonality and diversity is a valuable and essential tool in understanding the use of native Glycine spp. for the discovery of new microbes that would be of benefit to domesticated Glycine max cultivars or any other economically important crops. This study has isolated microbes from a crop wild relative that are now available for testing in G. max for beneficial phenotypes.},
}
@article {pmid36384582,
year = {2022},
author = {Khesali Aghtaei, H and Püttker, S and Maus, I and Heyer, R and Huang, L and Sczyrba, A and Reichl, U and Benndorf, D},
title = {Adaptation of a microbial community to demand-oriented biological methanation.},
journal = {Biotechnology for biofuels and bioproducts},
volume = {15},
number = {1},
pages = {125},
pmid = {36384582},
issn = {2731-3654},
support = {031A532B, 031A533A, 031A533B, 031A534A, 031A535A, 031A537A, 031A537B, 031A537C, 031A537D, 031A538A, 031L0103//Bundesministerium für Bildung und Forschung/ ; 031A532B, 031A533A, 031A533B, 031A534A, 031A535A, 031A537A, 031A537B, 031A537C, 031A537D, 031A538A, 031L0103//Bundesministerium für Bildung und Forschung/ ; 031A532B, 031A533A, 031A533B, 031A534A, 031A535A, 031A537A, 031A537B, 031A537C, 031A537D, 031A538A, 031L0103//Bundesministerium für Bildung und Forschung/ ; 031A532B, 031A533A, 031A533B, 031A534A, 031A535A, 031A537A, 031A537B, 031A537C, 031A537D, 031A538A, 031L0103//Bundesministerium für Bildung und Forschung/ ; 031A532B, 031A533A, 031A533B, 031A534A, 031A535A, 031A537A, 031A537B, 031A537C, 031A537D, 031A538A, 031L0103//Bundesministerium für Bildung und Forschung/ ; },
abstract = {BACKGROUND: Biological conversion of the surplus of renewable electricity and carbon dioxide (CO2) from biogas plants to biomethane (CH4) could support energy storage and strengthen the power grid. Biological methanation (BM) is linked closely to the activity of biogas-producing Bacteria and methanogenic Archaea. During reactor operations, the microbiome is often subject to various changes, e.g., substrate limitation or pH-shifts, whereby the microorganisms are challenged to adapt to the new conditions. In this study, various process parameters including pH value, CH4 production rate, conversion yields and final gas composition were monitored for a hydrogenotrophic-adapted microbial community cultivated in a laboratory-scale BM reactor. To investigate the robustness of the BM process regarding power oscillations, the biogas microbiome was exposed to five hydrogen (H2)-feeding regimes lasting several days.<br><br>RESULTS: Applying various "on-off" H2-feeding regimes, the CH4 production rate recovered quickly, demonstrating a significant resilience of the microbial community. Analyses of the taxonomic composition of the microbiome revealed a high abundance of the bacterial phyla Firmicutes, Bacteroidota and Thermotogota followed by hydrogenotrophic Archaea of the phylum Methanobacteriota. Homo-acetogenic and heterotrophic fermenting Bacteria formed a complex food web with methanogens. The abundance of the methanogenic Archaea roughly doubled during discontinuous H2-feeding, which was related mainly to an increase in acetoclastic Methanothrix species. Results also suggested that Bacteria feeding on methanogens could reduce overall CH4 production. On the other hand, using inactive biomass as a substrate could support the growth of methanogenic Archaea. During the BM process, the additional production of H2 by fermenting Bacteria seemed to support the maintenance of hydrogenotrophic methanogens at non-H2-feeding phases. Besides the elusive role of Methanothrix during the H2-feeding phases, acetate consumption and pH maintenance at the non-feeding phase can be assigned to this species.<br><br>CONCLUSIONS: Taken together, the high adaptive potential of microbial communities contributes to the robustness of BM processes during discontinuous H2-feeding and supports the commercial use of BM processes for energy storage. Discontinuous feeding strategies could be used to enrich methanogenic Archaea during the establishment of a microbial community for BM. Both findings could contribute to design and improve BM processes from lab to pilot scale.},
}
@article {pmid36384569,
year = {2022},
author = {Alamer, A and Jones, R and Drinnan, M and Simpson, AJ and Griffin, M and Patterson, JM and Althuwaybi, A and Ward, C and Forrest, IA},
title = {Oropharyngeal swallowing physiology and safety in patients with Idiopathic Pulmonary Fibrosis: a consecutive descriptive case series.},
journal = {BMC pulmonary medicine},
volume = {22},
number = {1},
pages = {422},
pmid = {36384569},
issn = {1471-2466},
support = {KTP 008821//an aero digestive approach for lung fibrosis' from Innovate UK/ ; KTP 008821//an aero digestive approach for lung fibrosis' from Innovate UK/ ; KTP 008821//an aero digestive approach for lung fibrosis' from Innovate UK/ ; KTP 008821//an aero digestive approach for lung fibrosis' from Innovate UK/ ; KTP 008821//an aero digestive approach for lung fibrosis' from Innovate UK/ ; IPFPSG12-7//British Lung Foundation/ ; IPFPSG12-7//British Lung Foundation/ ; IPFPSG12-7//British Lung Foundation/ ; },
abstract = {INTRODUCTION: Dysphagia occurs in multiple respiratory pathophysiologies, increasing the risk of pulmonary complications secondary to aspiration. Reflux associated aspiration and a dysregulated lung microbiome is implicated in Idiopathic Pulmonary Fibrosis (IPF), but swallowing dysfunction has not been described. We aimed to explore oropharyngeal swallowing in IPF patients, without known swallowing dysfunction.<br><br>METHODS: Fourteen consecutive outpatients with a secure diagnosis of IPF were recruited and the 10-item Eating Assessment Tool (Eat 10) used to assess patient perception of swallowing difficulty. Oropharyngeal swallowing was assessed in ten patients using Videofluoroscopy Swallow Studies (VFSS). The studies were rated using validated scales: Penetration-Aspiration Scale (PAS); standardised Modified Barium Swallow Impairment Profile (MBSImP).<br><br>RESULTS: EAT-10 scores indicated frank swallowing difficulty in 4/14 patients. Videofluoroscopy Studies showed that 3/10 patients had airway penetration, and one aspirated liquid without a cough response. Median MBSImp for oral impairment was 5, range [3-7] and pharyngeal impairment 4, range [1-14] indicating, overall mild alteration to swallowing physiology.<br><br>CONCLUSION: We conclude that people with IPF can show a range of swallowing dysfunction, including aspiration into an unprotected airway. To our knowledge, this is the first report on swallowing physiology and safety in IPF. We believe a proportion of this group may be at risk of aspiration. Further work is indicated to fully explore swallowing in this vulnerable group.},
}
@article {pmid36384523,
year = {2022},
author = {Xu, K and Cai, J and Xing, J and Li, X and Wu, B and Zhu, Z and Zhang, Z},
title = {Broad-spectrum antibiotics associated gut microbiome disturbance impairs T cell immunity and promotes lung cancer metastasis: a retrospective study.},
journal = {BMC cancer},
volume = {22},
number = {1},
pages = {1182},
pmid = {36384523},
issn = {1471-2407},
abstract = {BACKGROUND: Gut microbiome has been linked to a regulatory role in cancer progression. However, whether broad-spectrum antibiotics (ATB) associated gut microbiome dysbiosis contributes to an impaired T cell immune function, and ultimately promotes lung cancer metastasis is not well known.<br><br>METHODS: In this study, a retrospective analysis was performed in a cohort of 263 patients initially diagnosed with non-small cell lung cancer (NSCLC) patients, including the ATB group (patients with broad-spectrum antibiotics treatment) (n = 124), and non-ATB group (n = 139) as control. ATB patients were prescribed ATB for over 5 days within 30 days prior to the collection of blood and fecal specimens and followed surgical treatment or first-line therapy. T cell immune function and metastasis-free survival (MFS) were evaluated between the two groups. Gut microbiota was evaluated by 16S rDNA sequencing. The predictive value of T cell immunity for MFS was evaluated by ROC analysis and Cox regression analysis.<br><br>RESULTS: Our results suggest that broad-spectrum antibiotics (ATB) impair T cell immune function in patients with either early-stage or advanced NSCLC, which likely contribute to the promotion of lung cancer metastasis. Results of the survival analysis show that metastasis-free survival (MFS) is significantly shorter in the ATB patients than that in the non-ATB patients with stage III NSCLC. The 16S rDNA sequencing shows that ATB administration contributes to a significant dysbiosis of the composition and diversity of gut microbiota. Moreover, ROC analysis results of CD4 (AUC 0.642, p = 0.011), CD8 (AUC was 0.729, p < 0.001), CD16 + 56 + (AUC 0.643, p = 0.003), and the combination of CD4, CD8 and CD16 + 56+ (AUC 0.810, p < 0.001), or Cox regression analysis results of CD4 (HR 0.206, p < 0.001), CD8 (HR 0.555, p = 0.009), which is likely regulated by ATB administration, have significantly predictive values for MFS.<br><br>CONCLUSION: These results provide evidence of gut microbiome disturbance due to ATB administration is involved in the regulation of T cell immunity, and their predictive value for the tumor metastasis in lung cancer patients. Thus, gut microbiota may serve as a therapeutic target for lung cancer. Consequently, caution should be exercised before the long-term administration of broad-spectrum antibiotics in cancer patients.},
}
@article {pmid36384379,
year = {2022},
author = {Shajiei, A and Liu, L and Seinen, J and Dieperink, W and Hammerschmidt, S and Maarten van Dijl, J and Harmsen, HJM},
title = {Specific associations between fungi and bacteria in broncho-alveolar aspirates from mechanically ventilated intensive care unit patients.},
journal = {Virulence},
volume = {13},
number = {1},
pages = {2022-2031},
doi = {10.1080/21505594.2022.2146568},
pmid = {36384379},
issn = {2150-5608},
abstract = {The detection of fungi in the human respiratory tract may represent contamination, colonization or a respiratory infection. To develop effective management strategies, a more accurate and comprehensive understanding of the lung fungal microbiome is required. Therefore, the objective of the present study was to define the "mycobiome" of mechanically ventilated patients admitted to an intensive care unit (ICU) using broncho-alveolar aspirate ("sputum") samples and correlate this with clinical parameters and the bacterial microbiota. To this end, the mycobiome of 33 sputum samples was analyzed by Internal Transcribed Spacer2 (ITS2) amplicon sequencing of the ribosomal operons. The results show that in the investigated sputa of mechanically ventilated patients Candida spp. were most frequently detected, independent of pneumonia or antimicrobial therapy. The presence of Candida excluded in most cases the presence of Malassezia, which was the second most-frequently encountered fungus. Moreover, a hierarchical clustering of the sequence data indicated a patient-specific mycobiome. Fungi detected by culturing (Candida and Aspergillus) were also detected through ITS2 sequencing, but other yeasts and fungi were only detectable by sequencing. While Candida showed no correlations with identified bacterial groups, the presence of Malassezia and Rhodotorula correlated with oral bacteria associated with periodontal disease. Likewise, Cladosporium correlated with other oral bacteria, whereas Saccharomyces correlated more specifically with dental plaque bacteria and Alternaria with the nasal-throat-resident bacteria Neisseria, Haemophilus and Moraxella. In conclusion, ITS2 sequencing of sputum samples uncovered patient-specific lung mycobiomes, which were only partially detectable by culturing, and which could be correlated to specific nasal-oral-pharyngeal niches.},
}
@article {pmid36384132,
year = {2022},
author = {LaCourse, KD and Zepeda-Rivera, M and Kempchinsky, AG and Baryiames, A and Minot, SS and Johnston, CD and Bullman, S},
title = {The cancer chemotherapeutic 5-fluorouracil is a potent Fusobacterium nucleatum inhibitor and its activity is modified by intratumoral microbiota.},
journal = {Cell reports},
volume = {41},
number = {7},
pages = {111625},
doi = {10.1016/j.celrep.2022.111625},
pmid = {36384132},
issn = {2211-1247},
abstract = {Fusobacterium nucleatum (Fn) is a dominant bacterial species in colorectal cancer (CRC) tissue that is associated with cancer progression and poorer patient prognosis. Following a small-molecule inhibitor screen of 1,846 bioactive compounds against a Fn CRC isolate, we find that 15% of inhibitors are antineoplastic agents including fluoropyrimidines. Validation of these findings reveals that 5-fluorouracil (5-FU), a first-line CRC chemotherapeutic, is a potent inhibitor of Fn CRC isolates. We also identify members of the intratumoral microbiota, including Escherichia coli, that are resistant to 5-FU. Further, CRC E. coli isolates can modify 5-FU and relieve 5-FU toxicity toward otherwise-sensitive Fn and human CRC epithelial cells. Lastly, we demonstrate that ex vivo patient CRC tumor microbiota undergo community disruption after 5-FU exposure and have the potential to deplete 5-FU levels, reducing local drug efficacy. Together, these observations argue for further investigation into the role of the CRC intratumoral microbiota in patient response to chemotherapy.},
}
@article {pmid36384106,
year = {2022},
author = {Bootz-Maoz, H and Pearl, A and Melzer, E and Malnick, S and Sharon, E and Bennet, Y and Tsentsarevsky, R and Abuchatzera, S and Amidror, S and Aretz, E and Azriel, S and Gam Ze Letova, C and Naama, M and Shoval, I and Yaron, O and Karako-Lampert, S and Bel, S and Yissachar, N},
title = {Diet-induced modifications to human microbiome reshape colonic homeostasis in irritable bowel syndrome.},
journal = {Cell reports},
volume = {41},
number = {7},
pages = {111657},
doi = {10.1016/j.celrep.2022.111657},
pmid = {36384106},
issn = {2211-1247},
abstract = {Changes in microbiome composition are associated with a wide array of human diseases, turning the human microbiota into an attractive target for therapeutic intervention. Yet, clinical translation of these findings requires the establishment of causative connections between specific microbial taxa and their functional impact on host tissues. Here, we infuse gut organ cultures with longitudinal microbiota samples collected from therapy-naive patients with irritable bowel syndrome (IBS) under a low-fermentable oligo-, di-, mono-saccharides and polyols (FODMAP) diet. We show that post-diet microbiota regulates intestinal expression of inflammatory and neuro-muscular gene sets. Specifically, we identify Bifidobacterium adolescentis as a diet-sensitive pathobiont that alters tight junction integrity and disrupts gut barrier functions. Collectively, we present a pathway discovery platform for mechanistic dissection and identification of functional diet-host-microbiota modules. Our data support the hypothesis that the gut microbiota mediates the beneficial effects of a low-FODMAP diet and reinforce the potential feasibility of microbiome-based therapies in IBS.},
}
@article {pmid36384089,
year = {2022},
author = {Zhou, CB and Fang, JY},
title = {Cross communication of diet-microbiome-immune interactions in cancer immunotherapy.},
journal = {Cell reports. Medicine},
volume = {3},
number = {11},
pages = {100806},
doi = {10.1016/j.xcrm.2022.100806},
pmid = {36384089},
issn = {2666-3791},
abstract = {Simpson et al. have highlighted a diet-driven microbiome community, which paves the way for landmark therapeutic avenues for facilitating efficacy and minimizing immune-related adverse events during neoadjuvant immune checkpoint inhibitor treatment in melanoma patients. This innovative attempt inspires application of the diet-microbiome-immune interaction axis to maximize clinical benefits.},
}
@article {pmid36380060,
year = {2022},
author = {Bilenduke, E and Sterrett, JD and Ranby, KW and Borges, VF and Grigsby, J and Carr, AL and Kilbourn, K and Lowry, CA},
title = {Impacts of breast cancer and chemotherapy on gut microbiome, cognitive functioning, and mood relative to healthy controls.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {19547},
pmid = {36380060},
issn = {2045-2322},
abstract = {Women diagnosed with breast cancer undergoing chemotherapy experience cognitive impairment, symptoms of anxiety and depression, and physical side effects including disruption in the diversity and community composition of the gut microbiome. To date, there is limited research exploring the associations among these specific challenges. The present cross-sectional study explored the associations of self-reported cognitive functioning, depression, and anxiety symptoms, and gut microbiome diversity and community composition in women who were diagnosed with and undergoing chemotherapy treatment for breast cancer (BC) compared to cancer-free healthy controls (HC). The BC group displayed higher rates of cognitive dysfunction (p < 0.001) and depressive symptoms (p < 0.05) relative to HC. There was a significant difference in microbiome community composition between BC and HC, particularly characterized by a decreased relative abundance of the mucin-degrading genus Akkermansia in BC compared to HC (p < 0.05). Association models identified significant associations among group, cognitive, depression, and microbiome variables (p < 0.001). Overall, the study identified that BC participants experienced significant differences in self-reported cognitive functioning, self-reported depression symptoms, microbiome community composition, and mucin-degrading bacteria of the gut-mucosal barrier, relative to HC. The present study is consistent with the hypothesis that gut microbiome community composition impacts a woman's experience with breast cancer and treatment suggesting that microbiome-based interventions have potential for improving quality of life outcomes in individuals with breast cancer.},
}
@article {pmid36379940,
year = {2022},
author = {Zhang, T and Zhang, W and Feng, C and Kwok, LY and He, Q and Sun, Z},
title = {Stronger gut microbiome modulatory effects by postbiotics than probiotics in a mouse colitis model.},
journal = {NPJ science of food},
volume = {6},
number = {1},
pages = {53},
pmid = {36379940},
issn = {2396-8370},
support = {2020ZD12//Natural Science Foundation of Inner Mongolia (Inner Mongolian Natural Science Foundation)/ ; 31972083//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32001711//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Probiotics are increasingly used as adjunctive therapy to manage gastrointestinal diseases, such as ulcerative colitis. However, probiotic use has posed some safety concerns. Thus, postbiotics are proposed as alternatives to probiotics in clinical applications. However, no study has directly compared the clinical benefits of probiotics and postbiotics. This study compared the beneficial effect of postbiotics and probiotics derived from the strain, Bifidobacterium adolescentis B8598, in a dextran sulfate sodium (DSS)-induced experimental colitis mouse model. Four groups of mice (n = 7 per group) were included in this work: Control (received water plus saline), DSS (received DSS without postbiotic/probiotic), Postbiotic (received DSS plus postbiotic), and Probiotic (received DSS plus probiotic). Our results showed that intragastric administration of both probiotic and postbiotic ameliorated colitis, reflected by decreased histology scores in Postbiotic and Probiotic groups compared with DSS group (P < 0.05). The fecal microbiota alpha diversity was not significantly affected by DSS-, postbiotic, or probiotic treatment. However, the postbiotic treatment showed stronger effects on modulating the fecal microbiota beta diversity, composition, and metagenomic potential than the probiotic treatment. Overall, our findings suggested that probiotics and postbiotics had similar ability to improve disease phenotype but had distinct ability to regulate the gut microbiota and metabolic pathways in the context of ulcerative colitis. In view of the smaller safety concern of postbiotics compared with probiotics and its stronger modulatory effect on the host gut microbiota, we propose that postbiotics are to be considered for use as next-generation biotherapeutics in managing ulcerative colitis or even other diseases.},
}
@article {pmid36383683,
year = {2022},
author = {Schwabkey, ZI and Wiesnoski, DH and Chang, CC and Tsai, WB and Pham, D and Ahmed, SS and Hayase, T and Ortega Turrubiates, MR and El-Himri, RK and Sanchez, CA and Hayase, E and Frenk Oquendo, AC and Miyama, T and Halsey, TM and Heckel, BE and Brown, AN and Jin, Y and Raybaud, M and Prasad, R and Flores, I and McDaniel, L and Chapa, V and Lorenzi, PL and Warmoes, MO and Tan, L and Swennes, AG and Fowler, S and Conner, M and McHugh, K and Graf, T and Jensen, VB and Peterson, CB and Do, KA and Zhang, L and Shi, Y and Wang, Y and Galloway-Pena, JR and Okhuysen, PC and Daniel-MacDougall, CR and Shono, Y and Burgos da Silva, M and Peled, JU and van den Brink, MRM and Ajami, N and Wargo, JA and Reddy, P and Valdivia, RH and Davey, L and Rondon, G and Srour, SA and Mehta, RS and Alousi, AM and Shpall, EJ and Champlin, RE and Shelburne, SA and Molldrem, JJ and Jamal, MA and Karmouch, JL and Jenq, RR},
title = {Diet-derived metabolites and mucus link the gut microbiome to fever after cytotoxic cancer treatment.},
journal = {Science translational medicine},
volume = {14},
number = {671},
pages = {eabo3445},
doi = {10.1126/scitranslmed.abo3445},
pmid = {36383683},
issn = {1946-6242},
abstract = {Not all patients with cancer and severe neutropenia develop fever, and the fecal microbiome may play a role. In a single-center study of patients undergoing hematopoietic cell transplant (n = 119), the fecal microbiome was characterized at onset of severe neutropenia. A total of 63 patients (53%) developed a subsequent fever, and their fecal microbiome displayed increased relative abundances of Akkermansia muciniphila, a species of mucin-degrading bacteria (P = 0.006, corrected for multiple comparisons). Two therapies that induce neutropenia, irradiation and melphalan, similarly expanded A. muciniphila and additionally thinned the colonic mucus layer in mice. Caloric restriction of unirradiated mice also expanded A. muciniphila and thinned the colonic mucus layer. Antibiotic treatment to eradicate A. muciniphila before caloric restriction preserved colonic mucus, whereas A. muciniphila reintroduction restored mucus thinning. Caloric restriction of unirradiated mice raised colonic luminal pH and reduced acetate, propionate, and butyrate. Culturing A. muciniphila in vitro with propionate reduced utilization of mucin as well as of fucose. Treating irradiated mice with an antibiotic targeting A. muciniphila or propionate preserved the mucus layer, suppressed translocation of flagellin, reduced inflammatory cytokines in the colon, and improved thermoregulation. These results suggest that diet, metabolites, and colonic mucus link the microbiome to neutropenic fever and may guide future microbiome-based preventive strategies.},
}
@article {pmid36383522,
year = {2022},
author = {DiLegge, MJ and Manter, DK and Vivanco, JM},
title = {Soil microbiome disruption reveals specific and general plant-bacterial relationships in three agroecosystem soils.},
journal = {PloS one},
volume = {17},
number = {11},
pages = {e0277529},
doi = {10.1371/journal.pone.0277529},
pmid = {36383522},
issn = {1932-6203},
abstract = {Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogens, often resulting in increased crop growth. However, little is known about the effect of soil microbiome disruption on non-pathogenic members of the soil microbiome. Here, we applied soil microbiome disruption in the form of moist-heat sterilization (autoclaving) to reduce populations of naturally occurring soil microbiota. The disruption was applied to analyze bacterial community rearrangement mediated by four crops (corn, beet, lettuce, and tomato) grown in three historically distinct agroecosystem soils (conventional, organic, and diseased). Applying the soil disruption enhanced plant influence on rhizosphere bacterial colonization, and significantly different bacterial communities were detected between the tested crops. Furthermore, bacterial genera showed significant abundance increases in ways both unique-to and shared-by each tested crop. As an example, corn uniquely promoted abundances of Pseudomonas and Sporocytophaga, regardless of the disrupted soil in which it was grown. Whereas the promotion of Bosea, Dyadobacter and Luteoliobacter was shared by all four crops when grown in disrupted soils. In summary, soil disruption followed by crop introduction amplified the plant colonization of potential beneficial bacterial genera in the rhizosphere.},
}
@article {pmid36383360,
year = {2022},
author = {Wu, F and Lei, H and Chen, G and Chen, C and Song, Y and Cao, Z and Zhang, C and Zhang, C and Zhou, J and Lu, Y and Zhang, L},
title = {Multiomics Analyses Reveal That Long-Term Intake of Hesperetin-7-O-glucoside Modulates the Gut Microbiota and Bile Acid Metabolism in Mice.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.2c05053},
pmid = {36383360},
issn = {1520-5118},
abstract = {Hesperetin-7-O-glucoside (Hes-7-G) is a typical flavonoid monoglucoside, which can be generated from hesperidin with the removal of rhamnose by hydrolysis. Untargeted and targeted metabolomics together with 16S rRNA gene sequencing were employed to explore the exact absorption site of Hes-7-G and its beneficial effect in mice. Intestinal [1]H nuclear magnetic resonance (NMR)-based metabolomics screening showed that Hes-7-G is mainly metabolized in the small intestine of mice, especially the ileum segment. Quantification analysis of bile acids (BAs) in the liver, intestinal tract, feces, and serum of mice suggests that Hes-7-G intake accelerates the processes of biosynthesis and excretion of BAs, thus promoting digestion and lowing hepatic cholesterol and triglyceride. 16S rRNA gene sequencing reveals that Hes-7-G significantly elevates the diversity of the gut microbiota in mice, especially those bacteria associated with BA secondary metabolism. These results demonstrated that long-term dietary Hes-7-G plays beneficial roles in health by modulating the gut bacteria and BA metabolism in mice.},
}
@article {pmid36383025,
year = {2022},
author = {Ugarcina Perovic, S and Ksiezarek, M and Rocha, J and Cappelli, EA and Sousa, M and Ribeiro, TG and Grosso, F and Peixe, L},
title = {Urinary Microbiome of Reproductive-Age Asymptomatic European Women.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0130822},
doi = {10.1128/spectrum.01308-22},
pmid = {36383025},
issn = {2165-0497},
abstract = {The knowledge of bacterial species diversity within the female urinary microbiome (FUM) is essential for understanding the role of the FUM in urinary tract health and disease. This study aimed to characterize the bacterial species diversity of the FUM of asymptomatic reproductive-age European women by combining extended culturomics and long-read sequencing of the near-full-length 16S rRNA gene. A total of 297 bacterial species (median of 53 species/sample) were identified, yet only 22% of the species were detected by both culture and sequencing methods. Recently recognized Gardnerella, Lactobacillus, and Limosilactobacillus species and 5 new putative Corynebacterium species were identified by culturomics, while anaerobic species (e.g., 11 Peptoniphilus spp.) were mostly detected by amplicon sequencing. Notably, there was not a single species common to all samples, although members of the genus Lactobacillus were detected in all. Lactobacillus crispatus, Lactobacillus iners, and Lactobacillus mulieris were observed in high relative abundance in several samples, as well as other species (e.g., Streptococcus agalactiae, Fannyhessea vaginae, Gardnerella vaginalis, Gardnerella swidsinskii), while low-abundance members (e.g., Finegoldia magna) were often more prevalent. A moderate correlation (Mantel test; r = 0.5) between community structure types captured by culturomics and amplicon sequencing was observed, highlighting the benefit of combining both methodologies. This study provided a detailed FUM structure at the species level, which is critical to unveil the potential relationship between specific microbiome members and urinary diseases/disorders. Moreover, the different capacity to characterize microbiome profiles of culturomic and amplicon sequencing is described, providing valuable insights for further urinary microbiome studies. IMPORTANCE The bacterial species diversity within the female urinary microbiome (FUM) has been insufficiently characterized. This study demonstrated that complementarity between optimized culture-dependent and -independent approaches is highly beneficial for comprehensive FUM species profiling by detecting higher FUM species diversity than previously reported, including identification of unreported species belonging to the genera Lactobacillus, Limosilactobacillus, and Latilactobacillus and putative novel Corynebacterium species. Although some species were present in high relative abundance, low-abundance members were more prevalent. FUM classification into community structure types demonstrated high interindividual differences in urinary microbiome composition among asymptomatic women. We also report moderate correlation between culture-dependent and -independent derived data-highlighting drawbacks of each methodological approach. Our findings suggest that FUM bacterial diversity reported from previous studies may be underestimated. Finally, our results contribute to the fundamental knowledge of the FUM required for further exploration of the urinary microbiome role in urinary tract diseases.},
}
@article {pmid36383004,
year = {2022},
author = {Brown, AL and Sharp, K and Apprill, A},
title = {Reshuffling of the Coral Microbiome during Dormancy.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0139122},
doi = {10.1128/aem.01391-22},
pmid = {36383004},
issn = {1098-5336},
abstract = {Quiescence, or dormancy, is a response to stressful conditions in which an organism slows or halts physiological functioning. Although most species that undergo dormancy maintain complex microbiomes, there is little known about how dormancy influences and is influenced by the host's microbiome, including in the temperate coral Astrangia poculata. Northern populations of A. poculata undergo winter quiescence. Here, we characterized wild A. poculata microbiomes in a high-resolution sampling time series before, during, and after quiescence using 16S rRNA gene sequencing on active (RNA) and present (DNA) microbiomes. We observed a restructuring of the coral microbiome during quiescence that persisted after reemergence. Upon entering quiescence, corals shed copiotrophic microbes, including putative pathogens, suggesting a removal of these taxa as corals cease normal functioning. During and after quiescence, bacteria and archaea associated with nitrification were enriched, suggesting that the quiescent microbiome may replace essential functions through supplying nitrate to corals and/or microbes. Overall, this study demonstrates that key microbial groups related to quiescence in A. poculata may play a role in the onset or emergence from dormancy and long-term regulation of the microbiome composition. The predictability of dormancy in A. poculata provides an ideal natural manipulation system to further identify factors that regulate host-microbial associations. IMPORTANCE Using a high-resolution sampling time series, this study is the first to demonstrate a persistent microbial community shift with quiescence (dormancy) in a marine organism, the temperate coral Astrangia poculata. Furthermore, during this period of community turnover, there is a shedding of putative pathogens and copiotrophs and an enhancement of the ammonia-oxidizing bacteria (Nitrosococcales) and archaea ("Candidatus Nitrosopumilus"). Our results suggest that quiescence represents an important period during which the coral microbiome can reset, shedding opportunistic microbes and enriching for the reestablishment of beneficial associates, including those that may contribute nitrate while the coral animal is not actively feeding. We suggest that this work provides foundational understanding of the interplay of microbes and the host's dormancy response in marine organisms.},
}
@article {pmid36382735,
year = {2022},
author = {Yu, J and Yin, Y and Yu, Y and Cheng, M and Zhang, S and Jiang, S and Dong, M},
title = {Effect of concomitant antibiotics use on patient outcomes and adverse effects in patients treated with ICIs.},
journal = {Immunopharmacology and immunotoxicology},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/08923973.2022.2145966},
pmid = {36382735},
issn = {1532-2513},
abstract = {Background: Immune checkpoint inhibitors (ICIs) such as PD-1/PD-L1/CTLA-4 inhibitors have brought new opportunities for the cure of cancer patients and have been widely used and which are the most successful cancer immunotherapy drug in recent years. Gut microbiome and metabolites exert a critical regulatory function in cancer immunotherapy of ICIs, which can be affected by antibiotics intervention. However, inflammatory infections caused by impaired immune function in tumor patients often require antibiotic treatment.Objective: In this review, we briefly discussed the correlation between antibiotics and ICIs treatment to evaluate the impact of antibiotics on cancer progression.Methods: By searches of PubMed, we collected the data such as progression-free survival time (PFS) and overall survival time (OS) in patients with non-small cell lung cancer (NSCLC), kidney cancer, Melanoma, colorectal cancer, and other tumors.Results: Antibiotics have a negative effect on the prolongation of survival in cancer patients treated with ICIs. This may depend on the patient's cancer type and the type of ICIs and antibiotics they have used.Conclusions: Antibiotics may reduce the effectiveness of immunotherapy by depleting the body's microbiome. Therefore, paying attention to the changes in the level of microorganisms in cancer patients, while making more individualized and precise improvements in treatment regimens, may bring new opportunities to improve the efficacy of immunotherapy.},
}
@article {pmid36382631,
year = {2022},
author = {Rossini, V and Tolosa-Enguis, V and Frances-Cuesta, C and Sanz, Y},
title = {Gut microbiome and anti-viral immunity in COVID-19.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/10408398.2022.2143476},
pmid = {36382631},
issn = {1549-7852},
abstract = {SARS-CoV-2 mainly affects the respiratory system, but the gastrointestinal tract is also a target. Prolonged gut disorders, in COVID-19 patients, were correlated with decreased richness and diversity of the gut microbiota, immune deregulation and delayed viral clearance. Although there are no definitive conclusions, ample evidence would suggest that the gut microbiome composition and function play a role in COVID-19 progression. Microbiome modulation strategies for population stratification and management of COVID-19 infection are under investigation, representing an area of interest in the ongoing pandemic. In this review, we present the existing data related to the interaction between gut microbes and the host's immune response to SARS-CoV-2 and discuss the implications for current disease management and readiness to face future pandemics.},
}
@article {pmid36382433,
year = {2022},
author = {Martinez, SS and Stebliankin, V and Hernandez, J and Martin, H and Tamargo, J and Rodriguez, JB and Teeman, C and Johnson, A and Seminario, L and Campa, A and Narasimhan, G and Baum, MK},
title = {Multiomic analysis reveals microbiome-related relationships between cocaine use and metabolites.},
journal = {AIDS (London, England)},
volume = {36},
number = {15},
pages = {2089-2099},
pmid = {36382433},
issn = {1473-5571},
abstract = {OBJECTIVE: Over 19 million individuals globally have a cocaine use disorder, a significant public health crisis. Cocaine has also been associated with a pro-inflammatory state and recently with imbalances in the intestinal microbiota as compared to nonuse. The objective of this pilot study was to characterize the gut microbiota and plasma metabolites in people with HIV (PWH) who use cocaine compared with those who do not.<br><br>DESIGN: Cross-sectional study.<br><br>METHODS: A pilot study in PWH was conducted on 25 cocaine users and 25 cocaine nonusers from the Miami Adult Studies on HIV cohort. Stool samples and blood plasma were collected. Bacterial composition was characterized using 16S rRNA sequencing. Metabolomics in plasma were determined using gas and liquid chromatography/mass spectrometry.<br><br>RESULTS: The relative abundances of the Lachnopspira genus, Oscillospira genus, Bifidobacterium adolescentis species, and Euryarchaeota phylum were significantly higher in the cocaine- using PWH compared to cocaine-nonusing PWH. Cocaine-use was associated with higher levels of several metabolites: products of dopamine catabolism (3-methoxytyrosine and 3-methoxytyramine sulfate), phenylacetate, benzoate, butyrate, and butyrylglycine.<br><br>CONCLUSIONS: Cocaine use was associated with higher abundances of taxa and metabolites known to be associated with pathogenic states that include gastrointestinal conditions. Understanding key intestinal bacterial functional pathways that are altered due to cocaine use in PWH will provide a better understanding of the relationships between the host intestinal microbiome and potentially provide novel treatments to improve health.},
}
@article {pmid36382399,
year = {2022},
author = {Chen, IA and Chu, K and Palaniappan, K and Ratner, A and Huang, J and Huntemann, M and Hajek, P and Ritter, SJ and Webb, C and Wu, D and Varghese, NJ and Reddy, TBK and Mukherjee, S and Ovchinnikova, G and Nolan, M and Seshadri, R and Roux, S and Visel, A and Woyke, T and Eloe-Fadrosh, EA and Kyrpides, NC and Ivanova, NN},
title = {The IMG/M data management and analysis system v.7: content updates and new features.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkac976},
pmid = {36382399},
issn = {1362-4962},
support = {//U.S. Department of Energy Joint Genome Institute/ ; //DOE Office of Science User Facility/ ; DE-AC02-05CH11231//Office of Science of the U.S. Department of Energy/ ; //National Energy Research Scientific Computing Center/ ; },
abstract = {The Integrated Microbial Genomes &amp; Microbiomes system (IMG/M: https://img.jgi.doe.gov/m/) at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to provide support for users to perform comparative analysis of isolate and single cell genomes, metagenomes, and metatranscriptomes. In addition to datasets produced by the JGI, IMG v.7 also includes datasets imported from public sources such as NCBI Genbank, SRA, and the DOE National Microbiome Data Collaborative (NMDC), or submitted by external users. In the past couple years, we have continued our effort to help the user community by improving the annotation pipeline, upgrading the contents with new reference database versions, and adding new analysis functionalities such as advanced scaffold search, Average Nucleotide Identity (ANI) for high-quality metagenome bins, new cassette search, improved gene neighborhood display, and improvements to metatranscriptome data display and analysis. We also extended the collaboration and integration efforts with other DOE-funded projects such as NMDC and DOE Biology Knowledgebase (KBase).},
}
@article {pmid36382383,
year = {2022},
author = {Couture, G and Luthria, DL and Chen, Y and Bacalzo, NP and Tareq, FS and Harnly, J and Phillips, KM and Pehrsson, PR and McKillop, K and Fukagawa, NK and Lebrilla, CB},
title = {Multi-Glycomic Characterization of Fiber from AOAC Methods Defines the Carbohydrate Structures.},
journal = {Journal of agricultural and food chemistry},
volume = {70},
number = {45},
pages = {14559-14570},
doi = {10.1021/acs.jafc.2c06191},
pmid = {36382383},
issn = {1520-5118},
abstract = {Dietary fiber has long been known to be an essential component of a healthy diet, and recent investigations into the gut microbiome-health paradigm have identified fiber as a prime determinant in this interaction. Further, fiber is now known to impact the gut microbiome in a structure-specific manner, conferring differential bioactivities to these specific structures. However, current analytical methods for food carbohydrate analysis do not capture this important structural information. To address this need, we utilized rapid-throughput LC-MS methods to develop a novel analytical pipeline to determine the structural composition of soluble and insoluble fiber fractions from two AOAC methods (991.43 and 2017.16) at the total monosaccharide, glycosidic linkage, and free saccharide level. Two foods were chosen for this proof-of-concept study: oats and potato starch. For oats, both AOAC methods gave similar results. Insoluble fiber was found to be comprised of linkages corresponding to β-glucan, arabinoxylan, xyloglucan, and mannan, while soluble fiber was found to be mostly β-glucan, with small amounts of arabinogalactan. For raw potato starch, each AOAC method gave markedly different results in the soluble fiber fractions. These observed differences are attributable to the resistant starch content of potato starch and the different starch digestion conditions used in each method. Together, these tools are a means to obtain the complex structures present within dietary fiber while retaining "classical" determinations such as soluble and insoluble fiber. These efforts will provide an analytical framework to connect gravimetric fiber determinations with their constituent structures to better inform gut microbiome and clinical nutrition studies.},
}
@article {pmid36382203,
year = {2022},
author = {Ny, V and Needham, T and Ceacero, F},
title = {Potential benefits of amino acid supplementation for cervid performance and nutritional ecology, with special focus on lysine and methionine: A review.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {11},
number = {},
pages = {391-401},
pmid = {36382203},
issn = {2405-6383},
abstract = {Deer farming is a thriving industry for venison, velvet antlers, trophy hunting, and other by-products. Feeding and nutrition are important factors for improving production performance, especially dietary protein and amino acids (AAs), as they are the main components of all tissues. Only a few studies on AA supplementation (Lys, Met, Arg) have been performed on cervids, which show positive effects on weight gain, ADG, feed-:gain ratio, plasma AAs, carcass weight, dressing percentage, yield of high-quality muscles, storage of internal fat during winter, DM and CP digestibility, plasma protein- and fat-related metabolite concentrations, antler burr perimeter, weight, length and mineralisation, velvet antler yield, rumen volatile fatty acids, and microbiome composition. All these effects are relevant for supporting the production of cervids products, from venison to velvet or trophy antlers, as well as their general performance and well-being of captive-bred cervids. The current available information suggests that AA supplementation can be especially interesting for animals fed low protein rations, and growing animals, but should be avoided in high rations and during winter, since it may promote the accumulation of internal fat. Potential effects on milk production and the concentrations of different hormones involved in the regulation of the antler cycle should be further explored.},
}
@article {pmid36382178,
year = {2022},
author = {Nakamura, Y and Suzuki, S and Murakami, S and Nishimoto, Y and Higashi, K and Watarai, N and Umetsu, J and Ishii, C and Ito, Y and Mori, Y and Kohno, M and Yamada, T and Fukuda, S},
title = {Integrated gut microbiome and metabolome analyses identified fecal biomarkers for bowel movement regulation by Bifidobacterium longum BB536 supplementation: A RCT.},
journal = {Computational and structural biotechnology journal},
volume = {20},
number = {},
pages = {5847-5858},
pmid = {36382178},
issn = {2001-0370},
abstract = {Background: Bifidobacterium longum BB536 supplementation can be used to regulate bowel movements in various people, including healthy subjects and patients with irritable bowel syndrome (IBS); however, individuals vary in their responses to B. longum BB536 treatment. One putative factor is the gut microbiota; recent studies have reported that the gut microbiota mediates the effects of diet or drugs on the host. Here, we investigated intestinal features, such as the microbiome and metabolome, related to B. longum BB536 effectiveness in increasing bowel movement frequency.<br><br>Results: A randomized, double-blind controlled crossover trial was conducted with 24 adults who mainly tended to be constipated. The subjects received a two-week dietary intervention consisting of B. longum BB536 in acid-resistant seamless capsules or similarly encapsulated starch powder as the placebo control. Bowel movement frequency was recorded daily, and fecal samples were collected at several time points, and analyzed by metabologenomic approach that consists of an integrated analysis of metabolome data obtained using mass spectrometry and microbiome data obtained using high-throughput sequencing. There were differences among subjects in B. longum intake-induced bowel movement frequency. The responders were predicted by machine learning based on the microbiome and metabolome features of the fecal samples collected before B. longum intake. The abundances of eight bacterial genera were significantly different between responders and nonresponders.<br><br>Conclusions: Intestinal microbiome and metabolome profiles might be utilized as potential markers of improved bowel movement after B. longum BB536 supplementation. These findings have implications for the development of personalized probiotic treatments.},
}
@article {pmid36382086,
year = {2022},
author = {Cortez, NE and Rodriguez Lanzi, C and Hong, BV and Xu, J and Wang, F and Chen, S and Ramsey, JJ and Pontifex, MG and Müller, M and Vauzour, D and Vahmani, P and Hwang, CI and Matsukuma, K and Mackenzie, GG},
title = {A ketogenic diet in combination with gemcitabine increases survival in pancreatic cancer KPC mice.},
journal = {Cancer research communications},
volume = {2},
number = {9},
pages = {951-965},
pmid = {36382086},
issn = {2767-9764},
support = {P30 CA093373/CA/NCI NIH HHS/United States ; },
abstract = {Pancreatic ductal adenocarcinoma (PDAC) continues to be a major health problem. A ketogenic diet (KD), characterized by a very low carbohydrate and high fat composition, has gained attention for its anti-tumor potential. We evaluated the effect and mechanisms of feeding a strict KD alone or in combination with gemcitabine in the autochthonous LSL-Kras[G12D/+]; LSL-Trp53 [R172H/+]; Pdx1-Cre (KPC) mouse model. For this purpose, both male and female pancreatic tumor-bearing KPC mice were allocated to a control diet (CD; %kcal: 70% carb, 14% protein, 16% fat), a KD (%kcal: 14% protein, 1% carb, 85% fat), a CD + gemcitabine (CG), or a KD + gemcitabine (KG) group. Mice fed a KD alone or in combination with gemcitabine showed significantly increased blood β-hydroxybutyrate levels compared to mice fed a CD or CG. KPC mice fed a KG had a significant increase in overall median survival compared to KPC mice fed a CD (increased overall median survival by 42%). Interestingly, when the data was disaggregated by sex, the effect of a KG was significant in female KPC mice (60% increase in median overall survival), but not in male KPC mice (28% increase in median overall survival). Mechanistically, the enhanced survival response to a KD combined with gemcitabine was multifactorial, including inhibition of ERK and AKT pathways, regulation of fatty acid metabolism and the modulation of the gut microbiota. In summary, a KD in combination with gemcitabine appears beneficial as a treatment strategy in PDAC in KPC mice, deserving further clinical evaluation.},
}
@article {pmid36381928,
year = {2022},
author = {Alsaeedi, SM and Aggarwal, S},
title = {The Holistic Review on Occurrence, Biology, Diagnosis, and Treatment of Oral Squamous Cell Carcinoma.},
journal = {Cureus},
volume = {14},
number = {10},
pages = {e30226},
pmid = {36381928},
issn = {2168-8184},
abstract = {A prevalent head and neck cancer type is oral squamous cell carcinoma (OSCC). It is widespread and associated with a high death rate of around 50% in some regions of the world. We discuss the likelihood of developing OSCC and the impact of age in this review. Prior to examining the vast array of diagnostic indicators, a brief explanation of the biology of the disease is addressed. Finally, the therapeutic strategies for OSCC are listed. The complete literature for this study was compiled by searching Google Scholar and PubMed using the terms "OSCC," "oral squamous cell carcinoma," "diagnosis of OSCC," "oral cancer," and "biomarkers and OSCC." The research finds that OSCC has several critical parameters with a lot of room for additional in-depth study.},
}
@article {pmid36381851,
year = {2022},
author = {Naik, SS and Ramphall, S and Rijal, S and Prakash, V and Ekladios, H and Mulayamkuzhiyil Saju, J and Mandal, N and Kham, NI and Shahid, R and Venugopal, S},
title = {Association of Gut Microbial Dysbiosis and Hypertension: A Systematic Review.},
journal = {Cureus},
volume = {14},
number = {10},
pages = {e29927},
pmid = {36381851},
issn = {2168-8184},
abstract = {Hypertension (HTN) is one of the most prevalent and dangerous cardiovascular diseases worldwide. Recently, its direct or indirect association with gut dysbiosis has been an interest of study for many. It also includes the metabolomic and functional gene changes in hypertensives compared with healthy individuals. This systematic review aims to study quantitative and qualitative interactions between the two and re-defining the heart-gut axis. We have strictly followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), 2020, guidelines. We conducted an in-depth search of databases such as PubMed, PubMed Central (PMC), Medline, and ScienceDirect to find relevant studies for our topic of interest. After the final quality check, we included eight articles in the systematic review. A significant difference in richness and diversity in gut microbiota was observed in hypertensive patients compared with healthy controls. There was an increased abundance of many bacteria such as Catabacter, Robinsoleilla, Serratia, Enterobacteriaceae, Ruminococcus torques, Parasutterella, Escherichia, Shigella, and Klebsiella, while a decreased abundance of Sporobacter, Roseburia hominis, Romboutsia spp., and Roseburia. Alteration of the composition also varied based on diet, age, ethnicity, and severity of HTN. Short-chain fatty acids (SCFAs)-producing bacteria are found to be on the lower side in hypertensives owing to the protective property of SCFAs against inflammation, especially butyric acid. From the perspective of metabolomic changes, harmful metabolites for cardiovascular health such as intestinal fatty acid binding protein (I-FABP), lipopolysaccharides (LPSs), zonulin, sphingomyelins, acylcarnitines, and trimethylamine N-oxide (TMAO) were found to be increased in hypertensives. Changes in these biomarkers further establish the relation between gut epithelial health and high blood pressure (BP). Participants affected by diseases have an overall lower rate of acquiring new genes, which results in a low richness of genes in them compared with healthy individuals. There is increased expression of the choline utilization (cutC) gene and reduced expression of genes associated with biosynthesis and transport of amino acids in high-BP participants. The unique changes in the composition of the microbiota, functional changes in genes, and metabolome collectively help for a better understanding of the pathogenesis of HTN and also suggest the gut as a promising new therapeutic target for HTN. To establish a further causal relationship between the two, more research is required.},
}
@article {pmid36381829,
year = {2022},
author = {Nassar, ST and Tasha, T and Desai, A and Bajgain, A and Ali, A and Dutta, C and Pasha, K and Paul, S and Abbas, MS and Venugopal, S},
title = {Fecal Microbiota Transplantation Role in the Treatment of Alzheimer's Disease: A Systematic Review.},
journal = {Cureus},
volume = {14},
number = {10},
pages = {e29968},
pmid = {36381829},
issn = {2168-8184},
abstract = {Alzheimer's, a neurodegenerative disease that starts slowly and worsens progressively, is the leading cause of dementia worldwide. Recent studies have linked the brain with the gut and its microbiota through the microbiota-gut-brain axis, opening the door for gut-modifying agents (e.g., prebiotics and probiotics) to influence our brain's cognitive function. This review aims to identify and summarize the effects of fecal microbiota transplantation (FMT) as a gut-microbiota-modifying agent on the progressive symptoms of Alzheimer's disease (AD). This systematic review is based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines. A systematic search was done using Google Scholar, PubMed, PubMed Central, and ScienceDirect databases in June 2022. The predefined criteria upon which the studies were selected are English language, past 10 years of narrative reviews, observational studies, case reports, and animal studies involving Alzheimer's subjects as no previous meta-analysis or systematic reviews were done on this subject. Later, a quality assessment was done using the available assessment tool based on each study type. The initial search generated 4,302 studies, yielding 13 studies to be included in the final selection: 1 cohort, 2 case reports, 2 animal studies, and 8 narrative reviews. Our results showed that FMT positively affected AD subjects (whether mice or humans). In humans, the FMT effect was measured by the Mini-Mental State Examination (MMSE), showing improvement in Alzheimer's symptoms of mood, memory, and cognition. However, randomized and nonrandomized clinical trials are essential for more conclusive results.},
}
@article {pmid36381370,
year = {2022},
author = {Beker, BM and Colombo, I and Gonzalez-Torres, H and Musso, CG},
title = {Decreasing microbiota-derived uremic toxins to improve CKD outcomes.},
journal = {Clinical kidney journal},
volume = {15},
number = {12},
pages = {2214-2219},
pmid = {36381370},
issn = {2048-8505},
abstract = {Chronic kidney disease (CKD) is set to become the fifth-leading global cause of death by 2040. This illustrates the many unknowns regarding its pathogenesis and therapy. A key unknown relates to the therapeutic impact of the interaction between CKD and the gut microbiome. The normal gut microbiome is essential for body homeostasis. There is evidence for multiple interactions between the microbiota and CKD-its causes, comorbidities and therapeutic interventions-that are only starting to be unraveled. Thus uremic retention products, such as urea itself, modify the gut microbiota biology and both dietary and drug prescriptions modify the composition and function of the microbiota. Conversely, the microbiota may influence the progression and manifestations of CKD through the production of biologically active compounds (e.g. short-chain fatty acids such as butyrate and crotonate) and precursors of uremic toxins. The present review addresses these issues and their relevance for novel therapeutic approaches ranging from dietary interventions to prebiotics, probiotics, synbiotics and postbiotics, to the prevention of the absorption of microbial metabolites and to increased clearance of uremic toxins of bacterial origin through optimized dialysis techniques or blockade of tubular cell transporters.},
}
@article {pmid36381318,
year = {2022},
author = {Himbert, C and Stephens, WZ and Gigic, B and Hardikar, S and Holowatyj, AN and Lin, T and Ose, J and Swanson, E and Ashworth, A and Warby, CA and Peoples, AR and Nix, D and Jedrzkiewicz, J and Bronner, M and Pickron, B and Scaife, C and Cohan, JN and Schrotz-King, P and Habermann, N and Boehm, J and Hullar, M and Figueiredo, JC and Toriola, AT and Siegel, EM and Li, CI and Ulrich, AB and Shibata, D and Boucher, K and Huang, LC and Schneider, M and Round, JL and Ulrich, CM},
title = {Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients.},
journal = {American journal of cancer research},
volume = {12},
number = {10},
pages = {4789-4801},
pmid = {36381318},
issn = {2156-6976},
abstract = {Associations of energy balance components, including physical activity and obesity, with colorectal cancer risk and mortality are well established. However, the gut microbiome has not been investigated as underlying mechanism. We investigated associations of physical activity, BMI, and combinations of physical activity/BMI with gut microbiome diversity and differential abundances among colorectal cancer patients. N=179 patients with colorectal cancer (stages I-IV) were included in the study. Pre-surgery stool samples were used to perform 16S rRNA gene sequencing (Illumina). Physical activity (MET hrs/wk) during the year before diagnosis was assessed by questionnaire and participants were classified as being active vs. inactive based on guidelines. BMI at baseline was abstracted from medical records. Patients were classified into four combinations of physical activity levels/BMI. Lower gut microbial diversity was observed among 'inactive' vs. 'active' patients (Shannon: P=0.01, Simpson: P=0.03), 'obese' vs. 'normal weight' patients (Shannon, Simpson, and Observed species: P=0.02, respectively), and 'overweight/obese/inactive' vs. 'normal weight/active' patients (Shannon: P=0.02, Observed species: P=0.04). Results differed by sex and tumor site. Two phyla and 12 genera (Actinobacteria and Fusobacteria, Adlercreutzia, Anaerococcus, Clostridium, Eubacterium, Mogibacteriaceae, Olsenella, Peptinophilus, Pyramidobacter, RFN20, Ruminococcus, Succinivibrio, Succiniclasticum) were differentially abundant across physical activity and BMI groups. This is the first evidence for associations of physical activity with gut microbiome diversity and abundances, directly among colorectal cancer patients. Our results indicate that physical activity may offset gut microbiome dysbiosis due to obesity. Alterations in gut microbiota may contribute mechanistically to the energy balance-colorectal cancer link and impact clinical outcomes.},
}
@article {pmid36381066,
year = {2023},
author = {Wang, Z and Wang, W and Xu, S and Ding, J and Zeng, X and Liu, H and Wang, F},
title = {Diets enriched with finely ground wheat bran alter digesta passage rate and composition of the gut microbiome in sows.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {12},
number = {},
pages = {32-41},
pmid = {36381066},
issn = {2405-6383},
abstract = {We investigated the effects of finely ground wheat bran on the nutrient digestibility, digesta passage rate, and gut microbiota structure in sows. A 3 × 3 Latin square design with 3 test periods and 3 experimental diets was used. Six non-pregnant sows (parity: 5 to 7) were randomly assigned to 3 experimental diets with 2 replicates per treatment in each period. Each period lasted 19 d (12 d for adaptation and 7 d for experiment). The experimental diets included (a) a basal corn and soybean meal diet (CON), (b) a basal diet with 20% coarse wheat bran (CWB; particle size: 605 μm), and (c) a basal diet with 20% fine wheat bran (FWB; particle size: 438 μm). The results demonstrated that the apparent total tract digestibility of neutral detergent fiber, acid detergent fiber and energy were reduced (P < 0.05) in the FWB and CWB groups compared with those in the CON group. Viscosity of digesta increased (P < 0.001) in FWB-fed sows. The passage rate of digesta from the mouth to the ileum decreased (P < 0.001) in FWB-fed sows. Peptide YY (PYY) concentration increased (P = 0.01) in FWB-fed sows after 30 min of feeding. In the FWB group, the relative abundance of Lactobacillaceae at the family level increased (P < 0.05) in the ileal digesta. At the class level, the relative abundance of Clostridia in feces decreased (P < 0.05) in FWB-fed sows. FWB enhanced the concentration of butyrate in feces compared with CON and CWB (P = 0.04). These results suggest that dietary supplementation with finely ground wheat bran reduces the passage rate of digesta, increases the abundance of beneficial microorganisms, and elevates the concentration of short-chain fatty acids and PYY in sows. These findings indicate that the addition of finely-ground wheat bran to the diets of sows is more effective than using coarse wheat bran for improving their satiety and intestinal microbial composition.},
}
@article {pmid36380339,
year = {2022},
author = {Haque, MM and Yerex, K and Kelekis-Cholakis, A and Duan, K},
title = {Advances in novel therapeutic approaches for periodontal diseases.},
journal = {BMC oral health},
volume = {22},
number = {1},
pages = {492},
pmid = {36380339},
issn = {1472-6831},
support = {RGPIN-05864-2019//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Periodontal diseases are pathological processes resulting from infections and inflammation affecting the periodontium or the tissue surrounding and supporting the teeth. Pathogenic bacteria living in complex biofilms initiate and perpetuate this disease in susceptible hosts. In some cases, broad-spectrum antibiotic therapy has been a treatment of choice to control bacterial infection. However, increasing antibiotic resistance among periodontal pathogens has become a significant challenge when treating periodontal diseases. Thanks to the improved understanding of the pathogenesis of periodontal disease, which involves the host immune response, and the importance of the human microbiome, the primary goal of periodontal therapy has shifted, in recent years, to the restoration of homeostasis in oral microbiota and its harmonious balance with the host periodontal tissues. This shift in therapeutic goals and the drug resistance challenge call for alternative approaches to antibiotic therapy that indiscriminately eliminate harmful or beneficial bacteria. In this review, we summarize the recent advancement of alternative methods and new compounds that offer promising potential for the treatment and prevention of periodontal disease. Agents that target biofilm formation, bacterial quorum-sensing systems and other virulence factors have been reviewed. New and exciting microbiome approaches, such as oral microbiota replacement therapy and probiotic therapy for periodontal disease, are also discussed.},
}
@article {pmid36379514,
year = {2022},
author = {Ahn, JS and Kang, MJ and Seo, Y and Kim, HS},
title = {Intestinal organoids as advanced modeling platforms to study the role of host-microbiome interaction in homeostasis and disease.},
journal = {BMB reports},
volume = {},
number = {},
pages = {},
pmid = {36379514},
issn = {1976-670X},
abstract = {After birth, animals are colonized by a diverse community of microorganisms. The digestive tract is known to contain the largest number of microbiome in the body. With emergence of the gut-brain axis, the importance of gut microbiome and its metabolites in host health has been extensively studied in recent years. The establishment of organoid culture systems has contributed to studying intestinal pathophysiology by replacing current limited models. Owing to their architectural and functional complexity similar to a real organ, co-culture of intestinal organoids with gut microbiome can provide mechanistic insights into the detrimental role of pathobiont and the homeostatic function of commensal symbiont. Here organoid-based bacterial co-culture techniques for modeling host-microbe interactions are reviewed. This review also summarizes representative studies that explore impact of enteric microorganisms on intestinal organoids to provide a better understanding of host-microbe interaction in the context of homeostasis and disease.},
}
@article {pmid36379333,
year = {2022},
author = {Singh, KS and Paul, D and Gupta, A and Dhotre, D and Klawonn, F and Shouche, Y},
title = {Indian sewage microbiome has unique community characteristics and potential for population-level disease predictions.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {160178},
doi = {10.1016/j.scitotenv.2022.160178},
pmid = {36379333},
issn = {1879-1026},
abstract = {Sewage wastewater pollutes water and poses a public health issue but it could also prove useful in certain research domains. Sewage is a complex niche relevant for research concerning 'one-health', human health, pollution and antibiotic resistance. Indian gut microbiome is also understudied due to sampling constraints and sewage could be used to explore it. Ostensibly, Indian sewage needs to be studied and here, we performed a cross-sectional pan-India sewage sampling to generate the first comprehensive Indian sewage microbiome. Indian sewage showed predominance of Burkholderiaceae, Rhodocyclaceae, Veillonellaceae, Prevotellaceae, etc. and has high representation of gut microbes. The identified gut microbes have overrepresentation of Veillonellaceae, Rikenellaceae, Streptococcaceae, and Bacillaceae. Imputed metagenomics of sewage microbiome indicated dominance of transport, motility, peptidases, amino acid metabolism, and antibiotic resistance genes. Microbiome-disease associations drawn using simple decision tree and random forest analysis identified specific microbes as potential predictors of diabetes and obesity in a city. Altogether, we generated the first Indian sewage microbiome and our non-invasive, high-throughput workflow could be emulated for future research, wastewater-based epidemiology and designing policies concerning public health.},
}
@article {pmid36379254,
year = {2022},
author = {Wu, Z and Hu, T and Merits, A and He, Y and Wang, M and Jia, R and Zhu, D and Liu, M and Zhao, X and Yang, Q and Wu, Y and Zhang, S and Huang, J and Mao, S and Ou, X and Gao, Q and Sun, D and Liu, Y and Zhang, L and Yu, Y and Cheng, A and Chen, S},
title = {Toll-like receptor 4 and lipopolysaccharide from commensal microbes regulate Tembusu virus infection.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {102699},
doi = {10.1016/j.jbc.2022.102699},
pmid = {36379254},
issn = {1083-351X},
abstract = {Unlike most flaviviruses transmitted by arthropods, Tembusu virus (TMUV) is still active during winter and causes outbreaks in some areas, indicating vector-independent spread of the virus. Gastrointestinal transmission might be one of the possible routes of vector-free transmission, which also means that the virus has to interact with more intestinal bacteria. Here, we found evidence that TMUV indeed can transmit through the digestive tract. Interestingly, using an established TMUV disease model by oral gavage combined with an antibiotic treatment, we revealed that a decrease in intestinal bacteria significantly reduced local TMUV proliferation in the intestine, revealing that the bacterial microbiome is important in TMUV infection. We found that lipopolysaccharide (LPS) present in the outer membrane of Gram-negative bacteria enhanced TMUV proliferation by promoting its attachment. Toll-like receptor 4 (TLR4), a cell surface receptor, can transmit signal from LPS. We confirmed co-localization of TLR4 with TMUV envelope (E) protein as well as their interaction in infected cells. Coherently, TMUV infection of susceptible cells was inhibited by an anti-TLR4 antibody, purified soluble TLR4 protein, and knockdown of TLR4 expression. LPS-enhanced TMUV proliferation could also be blocked by a TLR4 inhibitor. Meanwhile, pre-treatment of duck primary cells with TMUV significantly impaired LPS-induced IL6 production. Collectively, our study provides first insights into vector-free transmission mechanisms of flaviviruses.},
}
@article {pmid36379022,
year = {2022},
author = {Liu, Z and Zhao, J and Lu, K and Wang, Z and Yin, L and Zheng, H and Wang, X and Mao, L and Xing, B},
title = {Biodegradation of Graphene Oxide by Insects (Tenebrio molitor Larvae): Role of the Gut Microbiome and Enzymes.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.2c03342},
pmid = {36379022},
issn = {1520-5851},
abstract = {Biodegradation of graphene materials is critical for understanding their environmental process and fate. Thus, biodegradation and mineralization of graphene oxide (GO) by an insect (yellow mealworms, Tenebrio molitor larvae) were investigated. Twenty mealworms could eat up a piece of GO film (1.5 × 1.5 cm) in 15 days. The ingested GO film underwent degradation, and the residual GO sheets were observed in the frass. Raman imaging confirmed that the residual GO (ID/IG, 1.16) was more defective than the pristine GO film (ID/IG, 0.95). [14]C analysis showed that GO sheets were partially mineralized into CO2 (0.26%) and assimilated into biomass compositions (e.g., lipid and protein) (0.36%). Gut microbes and extracellular enzymes in yellow mealworms played crucial roles in GO degradation, and the predominant gut microbes for GO biodegradation were identified as Enterobacteriaceae bacteria (e.g., Escherichia-Shigella sp.). Two biodegradation products belonging to hydroxylated or carboxylated aromatic compounds were formed with the assistance of electrons and hydroxyl radicals in mealworm guts. These findings are useful for better understanding the environmental and biological fate of graphene materials.},
}
@article {pmid36378822,
year = {2022},
author = {Wang, Y and Wang, J and Yu, D and Zou, J and Zhang, C and Yan, H and Ye, X and Chen, Y},
title = {Microbial Community Structure of Colostrum in Women with Antibiotic Exposure Immediately After Delivery.},
journal = {Breastfeeding medicine : the official journal of the Academy of Breastfeeding Medicine},
volume = {17},
number = {11},
pages = {940-946},
doi = {10.1089/bfm.2022.0140},
pmid = {36378822},
issn = {1556-8342},
abstract = {Background: The microbial community in human milk is associated with many maternal and neonatal factors. This study aimed to investigate the effect of antibiotic exposure on the microbial community structure of colostrum. Methods: Twenty women with antibiotic treatment immediately after delivery and 10 age-matched control women were enrolled at the Guangdong Women and Children Hospital. Colostrum samples were collected within postpartum 30 hours. The V4 variable region of the bacterial 16S rRNA gene was sequenced to characterize the microbial profile using Illumina MiSeq platform. Results: Phyla Proteobacteria and Firmicutes were the predominant bacteria in colostrum samples. The core and abundant genera in colostrum included Streptococcus, Staphylococcus, and Pseudomonas. Compared with the control group, principal coordinate analysis based on the Bray-Curtis distance showed a significant difference in milk microbial community in women with antibiotic exposure, accompanied by a significantly lower alpha diversity and a different microbial ecological network. Furthermore, the relative abundances of genera Actinomyces, Anaerobacter, and Clostridium_sensu_stricto significantly decreased after antibiotic treatment. Conclusions: This study provided evidence of alterations in the colostrum microbial community with antibiotic exposure, improving our understanding of the effects of antibiotic treatment on the milk microbiome.},
}
@article {pmid36378698,
year = {2022},
author = {Kopchak, OO and Hrytsenko, OY and Pulyk, OR},
title = {PECULIARITIES OF THE GUT MICROBIOTA IN PATIENTS WITH MIGRAINE COMPARING TO HEALTHY INDIVIDUALS.},
journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)},
volume = {75},
number = {9 pt 2},
pages = {2218-2221},
doi = {10.36740/WLek202209207},
pmid = {36378698},
issn = {0043-5147},
abstract = {OBJECTIVE: The aim: Analyze the gut microbiome state in patients with migraine (M) and healthy individuals, to assess possible correlations between the detected changes in patients with migraine and the frequency, intensity of headaches, psycho-emotional state of the patients, and their quality of life.<br><br>PATIENTS AND METHODS: Materials and methods: 100 objects were enrolled, divided into 2 groups: main - patients with M and control - healthy volunteers. Investigation of the intestinal microbiome was performed by chromato-mass spectrometry. For M patients the following scales were used: Visual Analogue Scale (VAS), Migraine Disability Assessment (MIDAS), Back Depression Inventory (BDI).<br><br>RESULTS: Results: In main group increased amount of Alcaligenes spp (p = 0.0061), Clostridium coccoides (p = 0.0021), Clostridium propionicum (p = 0.0287), Eggerthella lenta (p = 0.0138), Pseudonocardia spp (p = 0.0210), Rhodococcus spp (p = 0.0164), Candida spp (p = 0.0079), Micromycetes spp (campesterol) (p = 0.0011) were found. Patients with M had a raised amount of Herpes simplex (p = 0.0305) and endotoxin level (p = 0.0459). Differences in gut microorganisms in both groups were significant. In patients with M negative correlations were observed between Alcaligenes spp ammount and BDI score (r = -0.6226, p =0.007), VAS score (r = -0.489, p = 0.046), headache frequency (r = -0.487, p = 0.046); between the levels of Clostridium coccoides and MIDAS score (r =-0.51, p = 0.035), BDI score (r = -0.54, p = 0.025) and positive correlation between Eggerthella lenta level and VAS score (r =0.4830, p=0.049).<br><br>CONCLUSION: Conclusions: Correlations between changes of gut microbiome and M are promising for further research.},
}
@article {pmid36378489,
year = {2022},
author = {Gupta, VK and Bakshi, U and Chang, D and Lee, AR and Davis, JM and Chandrasekaran, S and Jin, YS and Freeman, MF and Sung, J},
title = {TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0092522},
doi = {10.1128/msystems.00925-22},
pmid = {36378489},
issn = {2379-5077},
abstract = {Biosynthetic gene clusters (BGCs) in microbial genomes encode bioactive secondary metabolites (SMs), which can play important roles in microbe-microbe and host-microbe interactions. Given the biological significance of SMs and the current profound interest in the metabolic functions of microbiomes, the unbiased identification of BGCs from high-throughput metagenomic data could offer novel insights into the complex chemical ecology of microbial communities. Currently available tools for predicting BGCs from shotgun metagenomes have several limitations, including the need for computationally demanding read assembly, predicting a narrow breadth of BGC classes, and not providing the SM product. To overcome these limitations, we developed taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC), a command-line tool for predicting experimentally characterized BGCs (and inferring their known SMs) in metagenomes by first pinpointing the microbial species likely to harbor them. We benchmarked TaxiBGC on various simulated metagenomes, showing that our taxonomy-guided approach could predict BGCs with much-improved performance (mean F1 score, 0.56; mean PPV score, 0.80) compared with directly identifying BGCs by mapping sequencing reads onto the BGC genes (mean F1 score, 0.49; mean PPV score, 0.41). Next, by applying TaxiBGC on 2,650 metagenomes from the Human Microbiome Project and various case-control gut microbiome studies, we were able to associate BGCs (and their SMs) with different human body sites and with multiple diseases, including Crohn's disease and liver cirrhosis. In all, TaxiBGC provides an in silico platform to predict experimentally characterized BGCs and their SM production potential in metagenomic data while demonstrating important advantages over existing techniques. IMPORTANCE Currently available bioinformatics tools to identify BGCs from metagenomic sequencing data are limited in their predictive capability or ease of use to even computationally oriented researchers. We present an automated computational pipeline called TaxiBGC, which predicts experimentally characterized BGCs (and infers their known SMs) in shotgun metagenomes by first considering the microbial species source. Through rigorous benchmarking techniques on simulated metagenomes, we show that TaxiBGC provides a significant advantage over existing methods. When demonstrating TaxiBGC on thousands of human microbiome samples, we associate BGCs encoding bacteriocins with different human body sites and diseases, thereby elucidating a possible novel role of this antibiotic class in maintaining the stability of microbial ecosystems throughout the human body. Furthermore, we report for the first time gut microbial BGC associations shared among multiple pathologies. Ultimately, we expect our tool to facilitate future investigations into the chemical ecology of microbial communities across diverse niches and pathologies.},
}
@article {pmid36378136,
year = {2022},
author = {Lai, J and Zhuo, X and Yin, K and Jiang, F and Liu, L and Xu, X and Liu, H and Wang, J and Zhao, J and Xu, W and Yang, S and Guo, H and Yuan, X and Lin, X and Qi, F and Fu, G},
title = {Potential mechanism of pyrotinib-induced diarrhea was explored by gut microbiome and ileum metabolomics.},
journal = {Anti-cancer drugs},
volume = {},
number = {},
pages = {},
doi = {10.1097/CAD.0000000000001440},
pmid = {36378136},
issn = {1473-5741},
abstract = {BACKGROUND: Pyrotinib is a novel epidermal growth factor receptor/human epidermal growth factor receptor-2 (HER2) tyrosine kinase inhibitor that exhibited clinical efficacy in patients with HER2-positive breast cancer and HER2-mutant/amplified lung cancer. However, severe diarrhea adverse responses preclude its practical use. At present, the mechanism of pyrotinib-induced diarrhea is unknown and needs further study.<br><br>METHODS: First, to develop a suitable and reproducible animal model, we compared the effects of different doses of pyrotinib (20, 40, 60 and 80 mg/kg) in Wistar rats. Second, we used this model to examine the intestinal toxicity of pyrotinib. Finally, the mechanism underlying pyrotinib-induced diarrhea was fully studied using gut microbiome and host intestinal tissue metabolomics profiling.<br><br>RESULTS: Reproducible diarrhea occurred in rats when they were given an 80 mg/kg daily dose of pyrotinib. Using the pyrotinib-induced model, we observed that Lachnospiraceae and Acidaminococcaceae decreased in the pyrotinib groups, whereas Enterobacteriaceae, Helicobacteraceae and Clostridiaceae increased at the family level by 16S rRNA gene sequence. Multiple bioinformatics methods revealed that glycocholic acid, ursodeoxycholic acid and cyclic AMP increased in the pyrotinib groups, whereas kynurenic acid decreased, which may be related to the pathogenesis of pyrotinib-induced diarrhea. Additionally, pyrotinib-induced diarrhea may be associated with a number of metabolic changes mediated by the gut microbiome, such as Primary bile acid biosynthesis.<br><br>CONCLUSION: We reported the establishment of a reproducible pyrotinib-induced animal model for the first time. Furthermore, we concluded from this experiment that gut microbiome imbalance and changes in related metabolites are significant contributors to pyrotinib-induced diarrhea.},
}
@article {pmid36378114,
year = {2022},
author = {Bongers, KS and Chanderraj, R and Woods, RJ and McDonald, RA and Adame, MD and Falkowski, NR and Brown, CA and Baker, JM and Winner, KM and Fergle, DJ and Hinkle, KJ and Standke, AK and Vendrov, KC and Young, VB and Stringer, KA and Sjoding, MW and Dickson, RP},
title = {The Gut Microbiome Modulates Body Temperature Both in Sepsis and Health.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202201-0161OC},
pmid = {36378114},
issn = {1535-4970},
abstract = {RATIONALE: Among patients with sepsis, variation in temperature trajectories predicts clinical outcomes. In healthy individuals, normal body temperature is variable and has decreased consistently since the 1860s. The biologic underpinnings of this temperature variation in disease and health are unknown.<br><br>OBJECTIVES: To establish and interrogate the role of the gut microbiome in calibrating body temperature.<br><br>METHODS: We performed a series of translational analyses and experiments to determine whether and how variation in gut microbiota explains variation in body temperature in sepsis and in health. We studied patient temperature trajectories using electronic medical record data. We characterized gut microbiota in hospitalized patients using 16S ribosomal RNA gene sequencing. We modeled sepsis using intraperitoneal lipopolysaccharide in mice and modulated the microbiome using antibiotics, germ-free, and gnotobiotic animals.<br><br>MEASUREMENTS AND MAIN RESULTS: Consistent with prior work, we identified four temperature trajectories in patients hospitalized with sepsis that predicted clinical outcomes. In a separate cohort of 116 hospitalized patients, we found that composition of patients' gut microbiota at admission predicted their temperature trajectories. Compared with conventional mice, germ-free mice had reduced temperature loss during experimental sepsis. Among conventional mice, heterogeneity of temperature response in sepsis was strongly explained by variation in gut microbiota. Healthy germ-free and antibiotic-treated mice both had lower basal body temperatures when compared to controls. The Lachnospiraceae family was consistently associated with temperature trajectories in hospitalized patients, experimental sepsis, and antibiotic-treated mice.<br><br>CONCLUSIONS: The gut microbiome is a key modulator of body temperature variation both in health and critical illness, and is thus a major, understudied target for modulating physiologic heterogeneity in sepsis.},
}
@article {pmid36377936,
year = {2022},
author = {Chen, J and Li, Z and Wang, X and Fan, B and Deng, F and D Yu, H and Ze, X and Zhu, L and Yin, Y and Chen, Y and Zhao, J and Yang, Y and Wang, X},
title = {Isomaltooligosaccharides Sustain the Growth of Prevotella Both In Vitro and in Animal Models.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0262121},
doi = {10.1128/spectrum.02621-21},
pmid = {36377936},
issn = {2165-0497},
abstract = {The human digestive tract is colonized by trillions of bacterial cells that play important roles in human health and diseases. It is well known that dietary habits are associated with human microbiota enterotypes. However, the factors that determine the enterotype still remain elusive. In this study, it was first examined, via in vitro batch fermentation, how different carbohydrates affect the Bacteroides and Prevotella enterotypes. Among the 11 substrates (fructo-, galacto-, xylo-, manno-, and isomalto-oligosaccharides [IMO] and lactulose, raffinose, starch, inulin [INU], mannitol, and xylitol) tested, IMO, INU, and starch were found to sustain the growth of Prevotella through batch fermentation. The development of the Prevotella and Bacteroides enterotypes was further simulated in chemostats using fecal samples. IMO coupled with faster dilution rates and lower pH were required to sustain the growth of Prevotella copri in the chemostat based on 16S rRNA gene and metagenomic sequencing. Meanwhile, starch with relatively lower dilution rates and higher pH was required to support the development of the Bacteroides enterotype. Amylo-α-1,6-glucosidase, pectin, and xylan lyases were the carbohydrate-active enzymes associated with the Prevotella enterotype. The Bacteroides enterotype was associated with more diversified carbohydrate-active enzymes. Consistently, since honey contains high isomaltose content, mice fed IMO and honey displayed an increased relative abundance of Prevotella in the colon. In conclusion, both in vitro systems and a mouse model were used to demonstrate that IMO maintains the Prevotella enterotype. This result provides insight into the nutritional requirements underlying gut enterotype formation. IMPORTANCE The Prevotella enterotype type is a human traditional enterotype with high dietary fiber intake, which is related to healthy ageing and Parkinson's disease development. Manipulations of the dwelled gut microbes by dietary isomalto-oligosaccharides efficiently sustained Prevotella type enterotypes, indicating that it can be used in the improvement of elderly health by increasing the gut transit time.},
}
@article {pmid36377933,
year = {2022},
author = {Clokie, BGJ and Elsheshtawy, A and Albalat, A and Nylund, A and Beveridge, A and Payne, CJ and MacKenzie, S},
title = {Optimization of Low-Biomass Sample Collection and Quantitative PCR-Based Titration Impact 16S rRNA Microbiome Resolution.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0225522},
doi = {10.1128/spectrum.02255-22},
pmid = {36377933},
issn = {2165-0497},
abstract = {The major aquatic interface between host and environment in teleost finfish species is the gill. The diversity of this infraclass, high complexity of the organ, and its direct exposure to the surrounding environment make it an ideal candidate for furthering our understanding of the intertwined relationships between host and microbiome. Capturing the structure and diversity of bacterial communities from this low-biomass, inhibitor-rich tissue can, however, prove challenging. Lessons learned in doing so are directly applicable to similar sample types in other areas of microbiology. Through the development of a quantitative PCR assay for both host material and 16S rRNA genes, we tested and developed a robust method for low-biomass sample collection which minimized host DNA contamination. Quantification of 16S rRNA facilitated not only the screening of samples prior to costly library construction and sequencing but also the production of equicopy libraries based on 16S rRNA gene copies. A significant increase in diversity of bacteria captured was achieved, providing greater information on the true structure of the microbial community. Such findings offer important information for determining functional processes. Results were confirmed across fresh, brackish, and marine environs with four different fish species, with results showing broad homology between samples, demonstrating the robustness of the approach. Evidence presented is widely applicable to samples similar in composition, such as sputum or mucus, or those that are challenging due to the inherent inclusion of inhibitors. IMPORTANCE The interaction between the fish gill and surrounding bacteria-rich water provides an intriguing model for examining the interaction between the fish, free-floating bacteria, and the bacterial microbiome on the gill surface. Samples that are inherently low in bacteria, or that have components that inhibit the ability to produce libraries that identify the components of microbial communities, present significant challenges. Gill samples present both of these types of challenges. We developed methods for quantifying both the bacterial and host DNA material and established a sampling method which both reduced inhibitor content and maximized bacterial diversity. By quantifying and normalizing bacteria prior to library construction, we showed significant improvements with regards to the fidelity of the final data. Our results support wide-ranging applications for analyzing samples of similar composition, such as mucus and sputum, in other microbiological spheres.},
}
@article {pmid36377901,
year = {2022},
author = {Wicaksono, WA and Egamberdieva, D and Berg, C and Mora, M and Kusstatscher, P and Cernava, T and Berg, G},
title = {Function-Based Rhizosphere Assembly along a Gradient of Desiccation in the Former Aral Sea.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0073922},
doi = {10.1128/msystems.00739-22},
pmid = {36377901},
issn = {2379-5077},
abstract = {The desiccation of the Aral Sea represents one of the largest human-made environmental regional disasters. The salt- and toxin-enriched dried-out basin provides a natural laboratory for studying ecosystem functioning and rhizosphere assembly under extreme anthropogenic conditions. Here, we investigated the prokaryotic rhizosphere communities of the native pioneer plant Suaeda acuminata (C.A.Mey.) Moq. in comparison to bulk soil across a gradient of desiccation (5, 10, and 40 years) by metagenome and amplicon sequencing combined with quantitative PCR (qPCR) analyses. The rhizosphere effect was evident due to significantly higher bacterial abundances but less diversity in the rhizosphere compared to bulk soil. Interestingly, in the highest salinity (5 years of desiccation), rhizosphere functions were mainly provided by archaeal communities. Along the desiccation gradient, we observed a significant change in the rhizosphere microbiota, which was reflected by (i) a decreasing archaeon-bacterium ratio, (ii) replacement of halophilic archaea by specific plant-associated bacteria, i.e., Alphaproteobacteria and Actinobacteria, and (iii) an adaptation of specific, potentially plant-beneficial biosynthetic pathways. In general, both bacteria and archaea were found to be involved in carbon cycling and fixation, as well as methane and nitrogen metabolism. Analysis of metagenome-assembled genomes (MAGs) showed specific signatures for production of osmoprotectants, assimilatory nitrate reduction, and transport system induction. Our results provide evidence that rhizosphere assembly by cofiltering specific taxa with distinct traits is a mechanism which allows plants to thrive under extreme conditions. Overall, our findings highlight a function-based rhizosphere assembly, the importance of plant-microbe interactions in salinated soils, and their exploitation potential for ecosystem restoration approaches. IMPORTANCE The desertification of the Aral Sea basin in Uzbekistan and Kazakhstan represents one of the most serious anthropogenic environmental disasters of the last century. Since the 1960s, the world's fourth-largest inland body of water has been constantly shrinking, which has resulted in an extreme increase of salinity accompanied by accumulation of many hazardous and carcinogenic substances, as well as heavy metals, in the dried-out basin. Here, we investigated bacterial and archaeal communities in the rhizosphere of pioneer plants by combining classic molecular methods with amplicon sequencing as well as metagenomics for functional insights. By implementing a desiccation gradient, we observed (i) remarkable differences in the archaeon-bacterium ratio of plant rhizosphere samples, (ii) replacement of archaeal indicator taxa during succession, and (iii) the presence of specific, potentially plant-beneficial biosynthetic pathways in archaea present during the early stages. In addition, our results provide hitherto-undescribed insights into the functional redundancy between plant-associated archaea and bacteria.},
}
@article {pmid36377768,
year = {2022},
author = {Sun, Q and Vega, NM and Cervantes, B and Mancuso, CP and Mao, N and Taylor, MN and Collins, JJ and Khalil, AS and Gore, J and Lu, TK},
title = {Enhancing nutritional niche and host defenses by modifying the gut microbiome.},
journal = {Molecular systems biology},
volume = {18},
number = {11},
pages = {e9933},
doi = {10.15252/msb.20209933},
pmid = {36377768},
issn = {1744-4292},
support = {HR0011-15-C-0091//DOD ¦ Defense Advanced Research Projects Agency (DARPA)/ ; },
abstract = {The gut microbiome is essential for processing complex food compounds and synthesizing nutrients that the host cannot digest or produce, respectively. New model systems are needed to study how the metabolic capacity provided by the gut microbiome impacts the nutritional status of the host, and to explore possibilities for altering host metabolic capacity via the microbiome. Here, we colonized the nematode Caenorhabditis elegans gut with cellulolytic bacteria that enabled C. elegans to utilize cellulose, an otherwise indigestible substrate, as a carbon source. Cellulolytic bacteria as a community component in the worm gut can also support additional bacterial species with specialized roles, which we demonstrate by using Lactobacillus plantarum to protect C. elegans against Salmonella enterica infection. This work shows that engineered microbiome communities can be used to endow host organisms with novel functions, such as the ability to utilize alternate nutrient sources or to better fight pathogenic bacteria.},
}
@article {pmid36377756,
year = {2022},
author = {Wang, X and Wang, H and Su, X and Zhang, J and Bai, J and Zeng, J and Li, H},
title = {Dynamic changes of gut bacterial communities present in larvae of Anoplophora glabripennies collected at different developmental stages.},
journal = {Archives of insect biochemistry and physiology},
volume = {},
number = {},
pages = {e21978},
doi = {10.1002/arch.21978},
pmid = {36377756},
issn = {1520-6327},
support = {YJ2021017//Special Project for Introduced Talents of Hebei Agricultural University/ ; 32171799//National Natural Science Foundation of China/ ; },
abstract = {The Asian long-horned beetle, Anoplophora glabripennies (Motschulsky), is a destructive wood-boring pest that is capable of killing healthy trees. Gut bacteria in the larvae of the wood-boring pest is essential for the fitness of hosts. However, little is known about the structure of the intestinal microbiome of A. glabripennies during larval development. Here, we used Illumina MiSeq high-throughput sequencing technology to analyze the larval intestinal bacterial communities of A. glabripennies at the stages of newly hatched larvae, 1st instar larvae and 4th instar larvae. Significant differences were found in larval gut microbial community structure at different larvae developmental stages. Different dominant genus was detected during larval development. Acinetobacter were dominant in the newly hatched larvae, Enterobacter and Raoultella in the 1st instar larvae, and Enterococcus and Gibbsiella in the 4th instar larvae. The microbial richness in the newly hatched larvae was higher than those in the 1st and 4th instar larvae. Many important functions of the intestinal microbiome were predicted, for example, fermentation and chemoheterotrophy functions that may play an important role in insect growth and development was detected in the bacteria at all tested stages. However, some specific functions are found to be associated with different development stages. Our study provides a theoretical basis for investigating the function of the intestinal symbiosis bacteria of A. glabripennies.},
}
@article {pmid36377583,
year = {2022},
author = {Marín-Tello, C and Jintaridth, P and Sanchez, F and González, C and Zelada-Castillo, L and Vásquez-Arqueros, A and Guevara-Vásquez, A and Vieira, A},
title = {Epigenetic regulation by metabolites from the gut microbiome.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-8},
doi = {10.3920/BM2022.0006},
pmid = {36377583},
issn = {1876-2891},
abstract = {The gut microbiome can metabolise food components, such as dietary fibres and various phytochemicals; and the microbiome can also synthesise some nutrients, for example B vitamins. The metabolites produced by bacteria and other micro-organisms in the colon can have implications for health and disease risk. Some of these metabolites are epigenetically active, and can contribute to changes in the chemical modification and structure of chromatin by affecting the activity and expression of epigenetically-active enzymes, for example histone deacetylases and DNA methyltransferases. The epigenetic activity of such gut microbiome metabolites is reviewed herein.},
}
@article {pmid36377581,
year = {2022},
author = {Amamoto, R and Shimamoto, K and Suwa, T and Park, S and Matsumoto, H and Shimizu, K and Katto, M and Makino, H and Matsubara, S and Aoyagi, Y},
title = {Relationships between dietary diversity and gut microbial diversity in the elderly.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-12},
doi = {10.3920/BM2022.0054},
pmid = {36377581},
issn = {1876-2891},
abstract = {Diet is considered as a major driver of gut microbiota composition. However, little is known about the relationship between overall dietary balance and gut microbiota, especially in the elderly. Here, using the Quantitative Index for Dietary Diversity (QUANTIDD), we analysed the relationships between dietary diversity and gut microbiota diversity in 445 Japanese subjects aged 65-90 years. We also examined the effect of age by comparing the young-old group aged 65 to 74 years (<75 years group; n=246) and the old-old group aged 75 years and older (≥75 years group; n=199). QUANTIDD showed significant positive relationships with Pielou's evenness and Shannon indices, two α-diversity indices related to the uniformity of species distribution. This suggests that a more diverse diet is associated with a more uniform abundance of various bacterial groups, rather than a greater variety of gut bacteria. QUANTIDD also showed significant positive associations with the abundance of Anaerostipes, Eubacterium eligens group, and Eubacterium ventriosum group, which produce short-chain fatty acids (SCFAs) and are beneficial to health. Negative association was found with the abundance of Ruminococcus gnavus group, which produces inflammatory polysaccharides. Positive associations between QUANTIDD and α-diversity indices or the abundance of specific bacterial groups were identified among all subjects and in the <75 years group, but not in the ≥75 years group. Our results suggest that dietary diversity contributes to the diversity of the gut microbiota and increases the abundance of SCFAs-producing bacteria, but only up to a certain age. These findings help to understand the complex relationship between diet and gut microbiota, and provide hints for specific dietary interventions to promote beneficial gut microbiota in the elderly.},
}
@article {pmid36377577,
year = {2022},
author = {Gao, K and Chen, CL and Ke, XQ and Yu, YX and Chen, S and Liu, GC and Wang, HF and Li, YJ},
title = {Ingestion of Lactobacillus helveticus WHH1889 improves depressive and anxiety symptoms induced by chronic unpredictable mild stress in mice.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-16},
doi = {10.3920/BM2022.0052},
pmid = {36377577},
issn = {1876-2891},
abstract = {Emerging evidence indicates that the alterations in the gut microbiota-brain axis (GBA), which is the bilateral connection between the gut microbial communities and brain function, are involved in several mental illnesses, including depression. Certain probiotic strains have been revealed to improve depressive behaviours and the dysregulation of 5-hydroxytryptamine (5-HT) metabolism in depression. Here we evaluated the potential antidepressant effects of Lactobacillus helveticus strains using an in vitro enterochromaffin cell model (RIN14B). The L. helveticus strain WHH1889 was shown to significantly promote the level of 5-hydroxytryptamine (5-HTP, 5-HT precursor) and the gene expression of tryptophan hydroxylase 1 (Tph1), which is the key synthetase in the 5-HT biosynthesis in RIN14B cells. Ingestion of 0.2 ml WHH1889 (1´10[9] cfu/ml) in a chronic unpredictable mild stress (CUMS) mouse model of depression for five weeks normalised depressive and anxiety-like behaviours in the forced swim test, tail suspension test, sucrose preference test, and open field test. Meanwhile, the CUMS-induced elevated level of serum corticosterone and declined levels of hippocampal 5-HT and 5-HTP were reversed by WHH1889. Furthermore, the disturbances of the gut microbiome composition with reduced microbial diversity were also improved by WHH1889, accompanied by the increased colonic 5-HTP level and Tph1 gene expression. In summary, these findings indicate that WHH1889 exerts antidepressant-like effects on CUMS mice, which is associated with the modulations of the 5-HT/5-HTP metabolism and gut microbiome composition. Therefore, ingestion of the L. helveticus strain WHH1889 with antidepressant potentials may become an encouraging therapeutic option in the treatment of depression.},
}
@article {pmid36377505,
year = {2022},
author = {Wang, L and Zhang, S and Huang, Y and You, W and Zhou, Y and Chen, W and Sun, Y and Yi, W and Sun, H and Xie, J and Zhu, X and Zheng, Q and Shan, T},
title = {CLA improves the lipo-nutritional quality of pork and regulates the gut microbiota in Heigai pigs.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d2fo02549c},
pmid = {36377505},
issn = {2042-650X},
abstract = {Conjugated linoleic acid (CLA) is a potential nutritional strategy to regulate meat quality in pigs and produce high-quality pork. However, the effects of CLA on nutritional quality, lipid dynamics, microbiota, and their metabolites in the gut of pigs remain unclear. Our study explored the effects of CLA on lipo-nutritional quality based on a Heigai pig model and investigated the regulatory mechanism using an integrated analysis of multiple omics. A total of 58 Heigai finishing pigs (body weight: 85.58 ± 10.39 kg) were randomly divided into 2 treatments and fed diets containing 1% soyabean oil and 1% CLA for 40 days. 1% CLA significantly decreased the backfat thickness (P < 0.05) and increased the intramuscular fat (IMF) content (P < 0.05). The expression of lipid metabolism-related genes was significantly changed (P < 0.05) and lipidome analysis showed the alternations of lipid dynamics in the longissimus dorsi muscle (LDM). In addition, based on the microbiome and metabolomic analyses, the relative abundances of Parabacteroides, Bacteroides, and Lachnospiraceae_UCG-010 increased and CLA changed the metabolome profiles and the short-chain fatty acid (SCFA) composition in the gut, which were significantly increased (P < 0.05). Additionally, Pearson's correlation analysis indicated that differential microbial genera and SCFAs induced by CLA had tight correlations with the backfat thickness, IMF content and lipids in the LDM. CLA enhances the lipid accumulation and metabolism in muscle and these changes are associated with the production and functions of the differential bacteria and SCFAs in the gut of pigs.},
}
@article {pmid36376984,
year = {2022},
author = {Attard, TM and Septer, S and Lawson, CE and Attard, MI and Lee, STM and Umar, S},
title = {Microbiome insights into pediatric familial adenomatous polyposis.},
journal = {Orphanet journal of rare diseases},
volume = {17},
number = {1},
pages = {416},
pmid = {36376984},
issn = {1750-1172},
abstract = {BACKGROUND: Individuals with familial adenomatous polyposis (FAP) harbor numerous polyps with inevitable early progression to colon cancer. Complex microbiotic-tumor microenvironment perturbations suggest a dysbiotic relationship between polyp and microbiome. In this study, we performed comprehensive analyses of stool and tissue microbiome of pediatric FAP subjects and compared with unaffected cohabiting relatives through 16S V4 region amplicon sequencing and machine learning platforms.<br><br>RESULTS: Within our FAP and control patient population, Firmicutes and Bacteroidetes were the predominant phyla in the tissue and stool samples, while Proteobacteria dominated the polyp/non-polyp mucosa. A decline in Faecalibacterium in polyps contrasted with a decline in Bacteroides in the FAP stool. The alpha- and beta-diversity indices differed significantly within the polyp/non-polyp groups, with a concurrent shift towards lower diversity in polyps. In a limited 3-year longitudinal study, the relative abundance of Proteobacteria and Fusobacteria was higher in polyps compared to non-polyp and stool specimens over time. Through machine learning, we discovered that Archaeon_enrichment_culture_clone_A13, Micrococcus_luteus, and Eubacterium_hallii in stool and PL-11B10, S1-80, and Blastocatellaceae in tissues were significantly different between patients with and without polyps.<br><br>CONCLUSIONS: Detection of certain bacterial concentrations within stool or biopsied polyps could serve as adjuncts to current screening modalities to help identify higher-risk patients.},
}
@article {pmid36376937,
year = {2022},
author = {Liang, X and Fu, Y and Cao, WT and Wang, Z and Zhang, K and Jiang, Z and Jia, X and Liu, CY and Lin, HR and Zhong, H and Miao, Z and Gou, W and Shuai, M and Huang, Y and Chen, S and Zhang, B and Chen, YM and Zheng, JS},
title = {Gut microbiome, cognitive function and brain structure: a multi-omics integration analysis.},
journal = {Translational neurodegeneration},
volume = {11},
number = {1},
pages = {49},
pmid = {36376937},
issn = {2047-9158},
support = {82073529//the National Natural Science Foundation of China/ ; 81903316//the National Natural Science Foundation of China/ ; 81773416//the National Natural Science Foundation of China/ ; 82103826//the National Natural Science Foundation of China/ ; 2019R52039//Zhejiang Provincial Ten Thousand Plan for Young Top Talents/ ; R01-HD30880//Foundation for the National Institutes of Health/ ; DK056350//Foundation for the National Institutes of Health/ ; R24 HD050924/HD/NICHD NIH HHS/United States ; R01-HD38700//Foundation for the National Institutes of Health/ ; R01-DK104371/DK/NIDDK NIH HHS/United States ; },
abstract = {BACKGROUND: Microbiome-gut-brain axis may be involved in the progression of age-related cognitive impairment and relevant brain structure changes, but evidence from large human cohorts is lacking. This study was aimed to investigate the associations of gut microbiome with cognitive impairment and brain structure based on multi-omics from three independent populations.<br><br>METHODS: We included 1430 participants from the Guangzhou Nutrition and Health Study (GNHS) with both gut microbiome and cognitive assessment data available as a discovery cohort, of whom 272 individuals provided fecal samples twice before cognitive assessment. We selected 208 individuals with baseline microbiome data for brain magnetic resonance imaging during the follow-up visit. Fecal 16S rRNA and shotgun metagenomic sequencing, targeted serum metabolomics, and cytokine measurements were performed in the GNHS. The validation analyses were conducted in an Alzheimer's disease case-control study (replication study 1, n = 90) and another community-based cohort (replication study 2, n = 1300) with cross-sectional dataset.<br><br>RESULTS: We found protective associations of specific gut microbial genera (Odoribacter, Butyricimonas, and Bacteroides) with cognitive impairment in both the discovery cohort and the replication study 1. Result of Bacteroides was further validated in the replication study 2. Odoribacter was positively associated with hippocampal volume (β, 0.16; 95% CI 0.06-0.26, P = 0.002), which might be mediated by acetic acids. Increased intra-individual alterations in gut microbial composition were found in participants with cognitive impairment. We also identified several serum metabolites and inflammation-associated metagenomic species and pathways linked to impaired cognition.<br><br>CONCLUSIONS: Our findings reveal that specific gut microbial features are closely associated with cognitive impairment and decreased hippocampal volume, which may play an important role in dementia development.},
}
@article {pmid36376913,
year = {2022},
author = {Mukhtar, I and Anwar, H and Iftikhar, A and Hashem, HE and Ali, Q and Siddique, F},
title = {Human targeted phenobarbital presents a poor substrate of gut microbiome deciphering new drug targets beyond pharmacokinetic curbs.},
journal = {BMC pharmacology &amp; toxicology},
volume = {23},
number = {1},
pages = {85},
pmid = {36376913},
issn = {2050-6511},
abstract = {BACKGROUND: The gut microbiome, a new organ of the body, can potentially alter the pharmacokinetics of orally administered drugs through microbial enzymes. However, absorption of orally administered non-antibiotic drugs by the gut microbiome, during drug-microbiome interaction, is barely addressed. Structural homology studies confirm similar membrane transport proteins in gut epithelial cells and the gut microbiome of the host that may compete for drug substrates with the host itself for its absorbance. Therefore, it is hypothesized that orally administered human targeted phenobarbital may interact and/or be uptake by the gut microbiome during its transit through the small intestine.<br><br>METHODS: In the current in vivo study, thirty-six male Wistar albino rats were divided into six groups including one control and 5 treatment groups, each having an equal number of rats (n = 6). Phenobarbital was administered orally (single dose of 15 mg/kg bw) to treatment groups. Animals were subsequently sacrificed to harvest microbial mass pallets residing in the small intestine after 2, 3, 4, 5, and 6 h of phenobarbital administration. Phenobarbital absorbance by the microbiome in the microbial lysate was estimated through RP-HPLC-UV at a wavelength of 207 nm.<br><br>RESULTS: Maximum phenobarbital absorbance (149.0 ± 5.93 µg) and drug absorbance per milligram of microbial mass (1.19 ± 0.05 µg) were found significantly higher at 4 h of post-administration in comparison to other groups. Percent dose recovery of phenobarbital was 5.73 ± 0.19% at 4 h while the maximum intestinal transit time was 5 h till the drug was absorbed by the microbes. Such results pronounce the idea of the existence of structural homology between membrane transporters of the gut microbiome and intestinal enterocytes of the host that may competitively absorb orally administered phenobarbital during transit in the small intestine. The docking studies revealed that the phenobarbital is a poor substrate for the gut microbiome.<br><br>CONCLUSION: Gut microbiome may competitively absorb the non-antibiotics such as phenobarbital as novel substrates due to the presence of structurally homologous transporting proteins as in enterocytes. This phenomenon suggests the microbiome as a potential candidate that can significantly alter the pharmacokinetics of drugs.},
}
@article {pmid36376804,
year = {2022},
author = {Cheng, X and Zhang, Y and Li, Y and Wu, Q and Wu, J and Park, SK and Guo, C and Lu, J},
title = {Meta-analysis of 16S rRNA microbial data identified alterations of the gut microbiota in COVID-19 patients during the acute and recovery phases.},
journal = {BMC microbiology},
volume = {22},
number = {1},
pages = {274},
pmid = {36376804},
issn = {1471-2180},
abstract = {BACKGROUND: Dozens of studies have demonstrated gut dysbiosis in COVID-19 patients during the acute and recovery phases. However, a consensus on the specific COVID-19 associated bacteria is missing. In this study, we performed a meta-analysis to explore whether robust and reproducible alterations in the gut microbiota of COVID-19 patients exist across different populations.<br><br>METHODS: A systematic review was conducted for studies published prior to May 2022 in electronic databases. After review, we included 16 studies that comparing the gut microbiota in COVID-19 patients to those of controls. The 16S rRNA sequence data of these studies were then re-analyzed using a standardized workflow and synthesized by meta-analysis.<br><br>RESULTS: We found that gut bacterial diversity of COVID-19 patients in both the acute and recovery phases was consistently lower than non-COVID-19 individuals. Microbial differential abundance analysis showed depletion of anti-inflammatory butyrate-producing bacteria and enrichment of taxa with pro-inflammatory properties in COVID-19 patients during the acute phase compared to non-COVID-19 individuals. Analysis of microbial communities showed that the gut microbiota of COVID-19 recovered patients were still in unhealthy ecostates.<br><br>CONCLUSIONS: Our results provided a comprehensive synthesis to better understand gut microbial perturbations associated with COVID-19 and identified underlying biomarkers for microbiome-based diagnostics and therapeutics.},
}
@article {pmid36376701,
year = {2022},
author = {Wen, X and Ye, X and Yang, X and Jiang, R and Qian, C and Wang, X},
title = {The crosstalk between intestinal bacterial microbiota and immune cells in colorectal cancer progression.},
journal = {Clinical &amp; translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico},
volume = {},
number = {},
pages = {},
pmid = {36376701},
issn = {1699-3055},
abstract = {Different types of cells that are involved in tumor immunity play a significant part in antitumor therapy. The intestinal microbiota consist of the trillions of diverse microorganisms that inhabit the gastrointestinal tract. Recently, much emphasis has been paid to the link between these symbionts and colorectal cancer (CRC). This association might be anything from oncogenesis and cancer development to resistance or susceptibility to chemotherapeutic medicines. Cancer patients have a significantly different microbial composition in their guts compared to healthy persons. The microbiome may play a role in the development and development of cancer through the modulation of tumor immunosurveillance, as shown by these studies; however, the specific processes underlying this role are still poorly understood. This review focuses on the relationship between the intestinal bacterial microbiota and immune cells to determine how the commensal microbiome influences the initiation and development of CRC.},
}
@article {pmid36376576,
year = {2022},
author = {Piovezani Ramos, G and Camilleri, M},
title = {Current and Future Therapeutic Options for Irritable Bowel Syndrome with Diarrhea and Functional Diarrhea.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {36376576},
issn = {1573-2568},
abstract = {Irritable bowel syndrome with diarrhea and functional diarrhea are disorders of gut-brain interaction presenting with chronic diarrhea; they have significant impact on quality of life. The two conditions may exist as a continuum and their treatment may overlap. Response to first-line therapy with antispasmodics and anti-diarrheal agents is variable, leaving several patients with suboptimal symptom control and need for alternative therapeutic options. Our aim was to discuss current pharmacologic options and explore alternative therapeutic approaches and future perspectives for symptom management in irritable bowel syndrome with diarrhea and functional diarrhea. We conducted a search of PubMed, Cochrane, clinicaltrial.gov, major meeting abstracts for publications on current, alternative, and emerging drugs for irritable bowel syndrome with diarrhea and functional diarrhea. Currently approved therapeutic options for patients with first-line refractory irritable bowel syndrome with diarrhea and functional diarrhea include serotonin-3 receptor antagonists, eluxadoline and rifaximin. Despite their proven efficacy, cost and availability worldwide impact their utilization. One-third of patients with disorders of gut-brain interaction with diarrhea have bile acid diarrhea and may benefit from drugs targeting bile acid synthesis and excretion. Further understanding of underlying pathophysiology of irritable bowel syndrome with diarrhea and functional diarrhea related to bile acid metabolism, gastrointestinal transit, and microbiome has led to evaluation of novel therapeutic approaches, including fecal microbiota transplantation and enterobacterial "crapsules". These opportunities to treat disorders of gut-brain interaction with diarrhea should be followed with formal studies utilizing large samples of well-characterized patients at baseline and validated response outcomes as endpoints for regulatory approval.},
}
@article {pmid36376318,
year = {2022},
author = {Wallen, ZD and Demirkan, A and Twa, G and Cohen, G and Dean, MN and Standaert, DG and Sampson, TR and Payami, H},
title = {Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {6958},
pmid = {36376318},
issn = {2041-1723},
support = {PF-SF-JFA-830658//Parkinson&apos;s Foundation (Parkinson&apos;s Foundation, Inc.)/ ; W81XWH1810508//United States Department of Defense | United States Army | Army Medical Command | Medical Research and Materiel Command (U.S. Army Medical Research and Materiel Command)/ ; },
abstract = {Parkinson's disease (PD) may start in the gut and spread to the brain. To investigate the role of gut microbiome, we conducted a large-scale study, at high taxonomic resolution, using uniform standardized methods from start to end. We enrolled 490 PD and 234 control individuals, conducted deep shotgun sequencing of fecal DNA, followed by metagenome-wide association studies requiring significance by two methods (ANCOM-BC and MaAsLin2) to declare disease association, network analysis to identify polymicrobial clusters, and functional profiling. Here we show that over 30% of species, genes and pathways tested have altered abundances in PD, depicting a widespread dysbiosis. PD-associated species form polymicrobial clusters that grow or shrink together, and some compete. PD microbiome is disease permissive, evidenced by overabundance of pathogens and immunogenic components, dysregulated neuroactive signaling, preponderance of molecules that induce alpha-synuclein pathology, and over-production of toxicants; with the reduction in anti-inflammatory and neuroprotective factors limiting the capacity to recover. We validate, in human PD, findings that were observed in experimental models; reconcile and resolve human PD microbiome literature; and provide a broad foundation with a wealth of concrete testable hypotheses to discern the role of the gut microbiome in PD.},
}
@article {pmid36375468,
year = {2022},
author = {Perler, BK and Friedman, ES and Wu, GD},
title = {The Role of the Gut Microbiota in the Relationship Between Diet and Human Health.},
journal = {Annual review of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-physiol-031522-092054},
pmid = {36375468},
issn = {1545-1585},
abstract = {The interplay between diet, the gut microbiome, and host health is complex. Diets associated with health have many similarities: high fiber, unsaturated fatty acids, and polyphenols while being low in saturated fats, sodium, and refined carbohydrates. Over the past several decades, dietary patterns have changed significantly in Westernized nations with the increased consumption of calorically dense ultraprocessed foods low in fiber and high in saturated fats, salt, and refined carbohydrates, leading to numerous negative health consequences including obesity, metabolic syndrome, and cardiovascular disease. The gut microbiota is an environmental factor that interacts with diet and may also have an impact on health outcomes, many of which involve metabolites produced by the microbiota from dietary components that can impact the host. This review focuses on our current understanding of the complex relationship between diet, the gut microbiota, and host health, with examples of how diet can support health, increase an individual's risk for disease, and be used as a therapy for specific diseases. Expected final online publication date for the Annual Review of Physiology, Volume 85 is February 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}
@article {pmid36375230,
year = {2022},
author = {Gao, Y and Liu, X and Pan, M and Zeng, D and Zhou, X and Tsunoda, M and Zhang, Y and Xie, X and Wang, R and Hu, W and Li, L and Yang, H and Song, Y},
title = {Integrated untargeted fecal metabolomics and gut microbiota strategy for screening potential biomarkers associated with schizophrenia.},
journal = {Journal of psychiatric research},
volume = {156},
number = {},
pages = {628-638},
doi = {10.1016/j.jpsychires.2022.10.072},
pmid = {36375230},
issn = {1879-1379},
abstract = {Schizophrenia (SZ) is a serious neurodevelopmental disorder. As the etiology of SZ is complex and the pathogenesis is not thoroughly understood, the diagnosis of different subtypes still depends on the subjective judgment of doctors. Therefore, there is an urgent need to develop early objective laboratory diagnostic biomarkers to screen different subtypes of patients as early as possible, and to implement targeted prevention and precision medicine to reduce the risk of SZ and improve patients' quality of life. In this study, untargeted metabolomics and 16S rDNA sequencing were used to analyze the differences in metabolites and gut microflora among 28 patients with two types of schizophrenia and 11 healthy subjects. The results showed that the metabolome and sequencing data could effectively discriminate among paranoid schizophrenia patients, undifferentiated schizophrenia patients and healthy controls. We obtained 65 metabolites and 76 microorganisms with significant changes, and fecal metabolite composition was significantly correlated with the differential genera (|r|>0.5), indicating that there was a regulatory relationship between the gut microbiota and the host metabolites. The gut microbiome, as an objective and measurable index, showed good diagnostic value for distinguishing schizophrenia patients from healthy people, especially with a combination of several differential microorganisms, which had the best diagnostic effect (AUC>0.9). Our results are conducive to understanding the complicated metabolic changes in SZ patients and providing valuable information for the clinical diagnosis of SZ.},
}
@article {pmid36374551,
year = {2022},
author = {Rhee, MS and Alqam, ML and Jones, BC and Phadungpojna, S and Day, D and Hitchcock, TM},
title = {Characterization of a live Cutibacterium acnes subspecies defendens strain XYCM42 and clinical assessment as a topical regimen for general skin health and cosmesis.},
journal = {Journal of cosmetic dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jocd.15510},
pmid = {36374551},
issn = {1473-2165},
support = {//Crown Laboratories Inc/ ; },
abstract = {BACKGROUND: When formulating topical products to treat skin diseases and addressing general skin health and cosmesis, most of the focus has traditionally been placed on how any given ingredient may impact the structure, function, and health of human skin elements. However, recent research is beginning to highlight the importance of the skin microbiome in relation to certain skin conditions and general cosmesis. Cutibacterium acnes is one of the most prolific skin-specific bacterial species. Research has shown that the species is divided into subspecies, some of which are thought to be beneficial to the skin. This paper aims to determine the efficacy of strainXYCM42, a C. acnes subspecies defendens derived strain designed to improve the health and appearance of the skin.<br><br>METHODS: In vitro studies were performed on human keratinocyte and fibroblast monolayers, human peripheral blood mononuclear cells (PBMC), and skin explants to elucidate the effects of live XYCM42 cells and their ferment on human skin cells and tissues. Subsequently, clinical studies were performed using XYCM42-based topical regimens designed to deliver and support the engraftment of live XYCM42 cells onto subjects' skin. Two studies were performed, a 3-week pilot study (n = 10) and a 8-week pivotal study (n = 121). In the latter, 32 subjects were enrolled for an in-clinic portion for efficacy evaluation, with clinic visits occurring at Baseline, Week 1, Week 4, and Week 8.<br><br>RESULTS: In vitro data suggest that XYCM42 and its ferment filtrate have potential to provide benefits to the skin via antioxidant, anti-inflammatory, and select antimicrobial activities. Clinical observation demonstrated that a XYCM42-containing regimen supports a healthy skin environment, promotes increased skin hydration, decreases erythema, calms the skin, and regulates sebum production.<br><br>CONCLUSION: These studies provide further evidence that specific strains of C. acnes, such as XYCM42, have a more beneficial function regarding skin health and appearance than was previously thought. Appropriate use of formulations derived from symbiotic strains within the skin microbiome can support the development of novel, beneficial topicals.},
}
@article {pmid36374479,
year = {2022},
author = {Szemraj, M and Lisiecki, P and Glajzner, P and Szewczyk, EM},
title = {Vancomycin heteroresistance among methicillin-resistant clinical isolates S. haemolyticus, S. hominis, S. simulans, and S. warneri.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {36374479},
issn = {1678-4405},
support = {502-03/3-012-03/ 503-31-011//Uniwersytet Medyczny w Lodzi/ ; },
abstract = {Besides being an essential part of the skin microbiome, coagulase-negative staphylococci are the etiological factors of serious infections. The aim of the study was to evaluate the heteroresistance to vancomycin and the potential antimicrobial efficacy of teicoplanin and daptomycin against the multiresistant strains of S. haemolyticus, S. hominis, S. warneri, and S. simulans. The study covered 80 clinical coagulase-negative staphylococci. Teicoplanin, vancomycin, and daptomycin MICs for the tested strains were determined according to EUCAST recommendation. The vanA and vanB genes were searched. The brain heart infusion screen agar method detected vancomycin heteroresistance. The population analysis profile method and analysis of autolytic activity were applied for the strains growing on BHI containing 4 mg/L vancomycin. Seven S. haemolyticus, two S. hominis, and two S. warneri strains presented a heterogeneous resistance to vancomycin. Their subpopulations were able to grow on a medium containing 4-12 mg/L of vancomycin. Monitoring heteroresistance to peptide antibiotics, which are often the last resort in staphylococcal infections, is essential due to the severe crisis in antibiotic therapy and the lack of alternatives to treat infections with multiresistant strains. Our work highlights the selection of resistant strains and the need for more careful use of peptide antibiotics.},
}
@article {pmid36373409,
year = {2022},
author = {Nakayasu, M and Takamatsu, K and Yazaki, K and Sugiyama, A},
title = {Plant specialized metabolites in the rhizosphere of tomatoes: secretion and effects on microorganisms.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbac181},
pmid = {36373409},
issn = {1347-6947},
abstract = {Plants interact with microorganisms in the phyllosphere and rhizosphere. Here the roots exude plant specialized metabolites (PSM) that have diverse biological and ecological functions. Recent reports have shown that these PSMs influence the rhizosphere microbiome, which is essential for the plant's growth and health. This review summarizes several specialized metabolites secreted into the rhizosphere of the tomato plant (Solanum lycopersicum), which is an important model species for plant research and a commercial crop. In this review, we focused on the effects of such plant metabolites on plant-microbe interactions. We also reviewed recent studies on improving the growth of tomatoes by analyzing and reconstructing the rhizosphere microbiome and discussed the challenges to be addressed in establishing sustainable agriculture.},
}
@article {pmid36250560,
year = {2022},
author = {Coller, HA},
title = {Highlighting recent impactful publications in Physiological Genomics.},
journal = {Physiological genomics},
volume = {54},
number = {11},
pages = {455-456},
doi = {10.1152/physiolgenomics.00148.2022},
pmid = {36250560},
issn = {1531-2267},
}
@article {pmid36373270,
year = {2022},
author = {DeWolf, EI and Brock, MT and Calder, WJ and Kliebenstein, DJ and Katz, E and Li, B and Morrison, HG and Maïgnien, L and Weinig, C},
title = {The rhizosphere microbiome and host plant glucosinolates exhibit feedback cycles in Brassica rapa.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16782},
pmid = {36373270},
issn = {1365-294X},
abstract = {The rhizosphere microbiome influences many aspects of plant fitness, including production of secondary compounds and defense against insect herbivores. Plants also modulate the composition of the microbial community in the rhizosphere via secretion of root exudates. We tested both the effect of the rhizosphere microbiome on plant traits, and host plant effects on rhizosphere microbes using recombinant inbred lines (RILs) of Brassica rapa that differ in production of glucosinolates (GLS), secondary metabolites that contribute to defense against insect herbivores. First, we investigated the effect of genetic variation in GLS production on the composition of the rhizosphere microbiome. Using a Bayesian Dirichlet-multinomial regression model (DMBVS), we identified both negative and positive associations between bacteria from 6 genera and the concentration of 5 GLS compounds produced in plant roots. Additionally, we tested the effects of microbial inoculation (an intact vs. disrupted soil microbiome) on GLS production and insect damage in these RILs. We found a significant microbial treatment × genotype interaction, in which total GLS was higher in the intact relative to the disrupted microbiome treatment in some RILs. However, despite differences in GLS production between microbial treatments, we observed no difference in insect damage between treatments. Together, these results provide evidence for a full feedback cycle of plant-microbe interactions mediated by GLS, i.e. GLS compounds produced by the host plant "feed-down" to influence rhizosphere microbial community and rhizosphere microbes "feed-up" to influence GLS production.},
}
@article {pmid36357685,
year = {2022},
author = {Diener, C and Dai, CL and Wilmanski, T and Baloni, P and Smith, B and Rappaport, N and Hood, L and Magis, AT and Gibbons, SM},
title = {Genome-microbiome interplay provides insight into the determinants of the human blood metabolome.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {36357685},
issn = {2522-5812},
support = {R01DK133468//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Variation in the blood metabolome is intimately related to human health. However, few details are known about the interplay between genetics and the microbiome in explaining this variation on a metabolite-by-metabolite level. Here, we perform analyses of variance for each of 930 blood metabolites robustly detected across a cohort of 1,569 individuals with paired genomic and microbiome data while controlling for a number of relevant covariates. We find that 595 (64%) of these blood metabolites are significantly associated with either host genetics or the gut microbiome, with 69% of these associations driven solely by the microbiome, 15% driven solely by genetics and 16% under hybrid genome-microbiome control. Additionally, interaction effects, where a metabolite-microbe association is specific to a particular genetic background, are quite common, albeit with modest effect sizes. This knowledge will help to guide targeted interventions designed to alter the composition of the human blood metabolome.},
}
@article {pmid36357577,
year = {2022},
author = {Krukowski, H and Valkenburg, S and Madella, AM and Garssen, J and van Bergenhenegouwen, J and Overbeek, SA and Huys, GRB and Raes, J and Glorieux, G},
title = {Gut microbiome studies in CKD: opportunities, pitfalls and therapeutic potential.},
journal = {Nature reviews. Nephrology},
volume = {},
number = {},
pages = {},
pmid = {36357577},
issn = {1759-507X},
abstract = {Interest in gut microbiome dysbiosis and its potential association with the development and progression of chronic kidney disease (CKD) has increased substantially in the past 6 years. In parallel, the microbiome field has matured considerably as the importance of host-related and environmental factors is increasingly recognized. Past research output in the context of CKD insufficiently considered the myriad confounding factors that are characteristic of the disease. Gut microbiota-derived metabolites remain an interesting therapeutic target to decrease uraemic (cardio)toxicity. However, future studies on the effect of dietary and biotic interventions will require harmonization of relevant readouts to enable an in-depth understanding of the underlying beneficial mechanisms. High-quality standards throughout the entire microbiome analysis workflow are also of utmost importance to obtain reliable and reproducible results. Importantly, investigating the relative composition and abundance of gut bacteria, and their potential association with plasma uraemic toxins levels is not sufficient. As in other fields, the time has come to move towards in-depth quantitative and functional exploration of the patient's gut microbiome by relying on confounder-controlled quantitative microbial profiling, shotgun metagenomics and in vitro simulations of microorganism-microorganism and host-microorganism interactions. This step is crucial to enable the rational selection and monitoring of dietary and biotic intervention strategies that can be deployed as a personalized intervention in CKD.},
}
@article {pmid36357461,
year = {2022},
author = {Moneda, APC and de Carvalho, LAL and Teheran-Sierra, LG and Funnicelli, MIG and Pinheiro, DG},
title = {Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {19174},
pmid = {36357461},
issn = {2045-2322},
support = {145962/2019-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico , Brasil/ ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2017/09008-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
mesh = {Rhizosphere ; *Saccharum/genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Plant Roots/microbiology ; *Microbiota/genetics ; Edible Grain/genetics ; },
abstract = {Sugarcane (Saccharum spp.) represents a crop of great economic importance, remarkably relevant in the food industry and energy supply chains from renewable sources. However, its conventional cultivation involves the intensive use of fertilizers, pesticides, and other agrochemical agents whose detrimental effects on the environment are notorious. Alternative systems, such as organic farming, have been presented as an environmentally friendly way of production. Still, the outcomes of different cropping systems on the microbiota associated with sugarcane-whose role in its health and growth is crucial-remain underexplored. Thus, we studied the rhizospheric microbiota of two adjacent sugarcane fields, which differ in terms of the type of farming system. For this, we used the sequencing of taxonomic markers of prokaryotes (gene 16S rRNA, subregions V3-V4) and fungi (Internal transcribed spacer 2) and evaluated the changes caused by the systems. Our results show a well-conserved microbiota composition among farming systems in the highest taxonomic ranks, such as phylum, class, and order. Also, both systems showed very similar alpha diversity indices and shared core taxa with growth-promoting capacities, such as bacteria from the Bacillus and Bradyrhizobium genera and the fungal genus Trichoderma. However, the composition at more specific levels denotes differences, such as the separation of the samples concerning beta diversity and the identification of 74 differentially abundant taxa between the systems. Of these, 60 were fungal taxa, indicating that this microbiota quota is more susceptible to changes caused by farming systems. The analysis of co-occurrence networks also showed the formation of peripheral sub-networks associated with the treatments-especially in fungi-and the presence of keystone taxa in terms of their ability to mediate relationships between other members of microbial communities. Considering that both crop fields used the same cultivar and had almost identical soil properties, we conclude that the observed findings are effects of the activities intrinsic to each system and can contribute to a better understanding of the effects of farming practices on the plant microbiome.},
}
@article {pmid36357393,
year = {2022},
author = {Su, Q and Liu, Q and Lau, RI and Zhang, J and Xu, Z and Yeoh, YK and Leung, TWH and Tang, W and Zhang, L and Liang, JQY and Yau, YK and Zheng, J and Liu, C and Zhang, M and Cheung, CP and Ching, JYL and Tun, HM and Yu, J and Chan, FKL and Ng, SC},
title = {Faecal microbiome-based machine learning for multi-class disease diagnosis.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {6818},
pmid = {36357393},
issn = {2041-1723},
mesh = {Humans ; *COVID-19/diagnosis ; Feces ; Machine Learning ; *Microbiota ; },
abstract = {Systemic characterisation of the human faecal microbiome provides the opportunity to develop non-invasive approaches in the diagnosis of a major human disease. However, shared microbial signatures across different diseases make accurate diagnosis challenging in single-disease models. Herein, we present a machine-learning multi-class model using faecal metagenomic dataset of 2,320 individuals with nine well-characterised phenotypes, including colorectal cancer, colorectal adenomas, Crohn's disease, ulcerative colitis, irritable bowel syndrome, obesity, cardiovascular disease, post-acute COVID-19 syndrome and healthy individuals. Our processed data covers 325 microbial species derived from 14.3 terabytes of sequence. The trained model achieves an area under the receiver operating characteristic curve (AUROC) of 0.90 to 0.99 (Interquartile range, IQR, 0.91-0.94) in predicting different diseases in the independent test set, with a sensitivity of 0.81 to 0.95 (IQR, 0.87-0.93) at a specificity of 0.76 to 0.98 (IQR 0.83-0.95). Metagenomic analysis from public datasets of 1,597 samples across different populations observes comparable predictions with AUROC of 0.69 to 0.91 (IQR 0.79-0.87). Correlation of the top 50 microbial species with disease phenotypes identifies 363 significant associations (FDR < 0.05). This microbiome-based multi-disease model has potential clinical application in disease diagnostics and treatment response monitoring and warrants further exploration.},
}
@article {pmid36357382,
year = {2022},
author = {Liu, Y and Elworth, RAL and Jochum, MD and Aagaard, KM and Treangen, TJ},
title = {De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {6799},
pmid = {36357382},
issn = {2041-1723},
support = {P01-AI152999//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; W911NF-17-2-0089//ODNI | Intelligence Advanced Research Projects Activity (IARPA)/ ; },
mesh = {Humans ; Biomass ; *Microbiota/genetics ; Metagenomics/methods ; Metagenome ; Specimen Handling ; },
abstract = {Computational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant to human health and disease. However, contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low-biomass environments. Contamination from DNA extraction kits or sampling lab environments leaves taxonomic "bread crumbs" across multiple distinct sample types. Here we describe Squeegee, a de novo contamination detection tool that is based upon this principle, allowing the detection of microbial contaminants when negative controls are unavailable. On the low-biomass samples, we compare Squeegee predictions to experimental negative control data and show that Squeegee accurately recovers putative contaminants. We analyze samples of varying biomass from the Human Microbiome Project and identify likely, previously unreported kit contamination. Collectively, our results highlight that Squeegee can identify microbial contaminants with high precision and thus represents a computational approach for contaminant detection when negative controls are unavailable.},
}
@article {pmid36357381,
year = {2022},
author = {Liu, Q and Su, Q and Zhang, F and Tun, HM and Mak, JWY and Lui, GC and Ng, SSS and Ching, JYL and Li, A and Lu, W and Liu, C and Cheung, CP and Hui, DSC and Chan, PKS and Chan, FKL and Ng, SC},
title = {Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {6806},
pmid = {36357381},
issn = {2041-1723},
support = {InnoHk//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health Care and Promotion Fund (HCPF)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *COVID-19 ; Metagenomics/methods ; Feces/microbiology ; },
abstract = {Our knowledge of the role of the gut microbiome in acute coronavirus disease 2019 (COVID-19) and post-acute COVID-19 is rapidly increasing, whereas little is known regarding the contribution of multi-kingdom microbiota and host-microbial interactions to COVID-19 severity and consequences. Herein, we perform an integrated analysis using 296 fecal metagenomes, 79 fecal metabolomics, viral load in 1378 respiratory tract samples, and clinical features of 133 COVID-19 patients prospectively followed for up to 6 months. Metagenomic-based clustering identifies two robust ecological clusters (hereafter referred to as Clusters 1 and 2), of which Cluster 1 is significantly associated with severe COVID-19 and the development of post-acute COVID-19 syndrome. Significant differences between clusters could be explained by both multi-kingdom ecological drivers (bacteria, fungi, and viruses) and host factors with a good predictive value and an area under the curve (AUC) of 0.98. A model combining host and microbial factors could predict the duration of respiratory viral shedding with 82.1% accuracy (error ± 3 days). These results highlight the potential utility of host phenotype and multi-kingdom microbiota profiling as a prognostic tool for patients with COVID-19.},
}
@article {pmid36357242,
year = {2022},
author = {Wildner, G},
title = {Antigenic mimicry - The key to autoimmunity in immune privileged organs.},
journal = {Journal of autoimmunity},
volume = {},
number = {},
pages = {102942},
doi = {10.1016/j.jaut.2022.102942},
pmid = {36357242},
issn = {1095-9157},
abstract = {The eye and the brain are the best investigated immune privileged sites for T cell mediated autoimmune diseases, with several experimental animal models in multiple species like experimental autoimmune encephalomyelitis (EAE) and experimental autoimmune uveitis (EAU). It was difficult to explain autoimmunity to antigens which are sequestered behind blood-organ barriers since those barriers can only be passed by already activated lymphocytes. Antigen-specific lymphocytes must therefore be activated outside of the immune privileged target organs by crossreactivity of immune receptors to similar antigens, designated as "antigenic mimicry". Crossreactivity as the basic mechanism for antigenic mimicry is generally important for the immune recognition of a huge variety of different antigens with a comparably restricted number of T cell receptors and antibodies. Here, various T cell mimotopes are discussed that can induce autoimmune diseases or immune tolerance or both. Mimotopes are antigenic epitopes with similarity to different, unrelated antigens that are not distinguished by T cell receptors. Finally, the role of the microbiome is touched briefly, it is suspected to provide many mimotopes for T cell responses that, however, are very difficult to define due to the enormous size, and individual variability of our microbiome and virome.},
}
@article {pmid36372415,
year = {2022},
author = {Matsumoto, H},
title = {[PATHOPHYSIOLOGY OF ASTHMA].},
journal = {Arerugi = [Allergy]},
volume = {71},
number = {9},
pages = {1065-1071},
doi = {10.15036/arerugi.71.1065},
pmid = {36372415},
issn = {0021-4884},
}
@article {pmid36372041,
year = {2022},
author = {Nguyen, UT and Kalan, LR},
title = {Forgotten fungi: the importance of the skin mycobiome.},
journal = {Current opinion in microbiology},
volume = {70},
number = {},
pages = {102235},
doi = {10.1016/j.mib.2022.102235},
pmid = {36372041},
issn = {1879-0364},
abstract = {The mosaic ecosystems of microbes that live on our skin encompass not only bacteria but also fungi, microeukaryotes, and viruses. As the second most prevalent group, unique fungal communities are found across the dry, moist, and oily microenvironments of human skin, and alterations of these communities are largely driven by changes in skin physiology throughout an individual's lifespan. Fungi have also been associated with infection and dermatological disorders, resulting from the disrupted balance between fungal-bacterial networks on the skin. Mechanisms of colonization resistance toward fungi in the skin microbiome of animals have advanced our understanding in conservation strategies, yet in the human skin, the fungal microbiome (mycobiome) remains vastly unexplored. Here, we review recent studies on the role of fungi in the skin microbiome, emphasizing how fungal-bacterial interactions at the skin surface play an important ecological function in vertebrate hosts.},
}
@article {pmid36371733,
year = {2022},
author = {Rog, J and Skonieczna-Żydecka, K and Juchnowicz, D and Padała, O and Łoniewski, I and Budzyńska, B and Karakula-Juchnowicz, H},
title = {Gut microbiota and intestinal barrier-related markers in patients with anorexia nervosa: Systematic review.},
journal = {Psychiatria polska},
volume = {},
number = {},
pages = {1-20},
doi = {10.12740/PP/OnlineFirst/140069},
pmid = {36371733},
issn = {2391-5854},
abstract = {The aim of this systematic review was to determine: 1. alternations of gut microbiota community; 2. intestinal barrier-related markers; 3. relationship between the intestinal ecosystem and health-related factors in AN individuals. We conducted a systematic literature search (PubMed/Embase/ClinicalTrials registry) until 30 September 2020 for studies reporting gut microbiome and intestinal barrier-related markers in patients with AN. Six studies on intestinal microbiota were eligible for this review, including three papers also describing intestinal barrier markers. Among five studies analyzing microbiota diversity, four of them found differences between AN patients and healthy controls (HC). The studies confirm alterations of the markers, which can affect intestinal barrier integrity of patients with ED. The systematic review confirms changes in the gut ecosystem of patients with eating disorder, without a clear consensus of microbiota patterns in AN. Damage of intestinal barrier integrity is poorly documented in AN patients and needs more attention in further studies.},
}
@article {pmid36371714,
year = {2022},
author = {Rushworth, CA and Wagner, MR and Mitchell-Olds, T and Anderson, JT},
title = {The Boechera model system for evolutionary ecology.},
journal = {American journal of botany},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajb2.16090},
pmid = {36371714},
issn = {1537-2197},
abstract = {Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.},
}
@article {pmid36371652,
year = {2022},
author = {Lang-Yona, N and Alster, A and Cummings, D and Freiman, Z and Kaplan-Levy, R and Lupu, A and Malinsky-Rushansky, N and Ninio, S and Sukenik, A and Viner-Mozzini, Y and Zohary, T},
title = {Gloeotrichia pisum in Lake Kinneret: A successful epiphytic cyanobacterium.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.13301},
pmid = {36371652},
issn = {1529-8817},
abstract = {With climate change and re-oligotrophication of lakes due to restoration efforts, the relative importance of benthic cyanobacteria is increasing, but they are much less studied than their planktonic counterparts. Following a major water level rise event that inundated massive reed stands in Lake Kinneret, Israel, we discovered the appearance in vast abundance of Gloeotrichia pisum (cyanobacteria). This provided an opportunity to investigate the biology and ecology of a benthic epiphytic colonial cyanobacterium, proliferating under altered environmental conditions, with possible toxin production potential and as a model for an invasive epiphyte. The species was identified by its typical morphology, and by sequencing its 16S rRNA gene and the intragenic space. We report on the abundance and spatial distribution of the detected colonies, their morphological characteristics and pigment composition. High phycoerythrin content provides the brownish color and supports growth at low light levels. Genomic community composition analysis revealed that G. pisum colonies host a diverse microbial community of microalgae, cyanobacteria, bacteria, and archaea with a conserved and characteristic taxonomic composition. The Synechococcales order showed high relative abundance in the colony, as well as other prokaryotes producing secondary metabolites, such as the rhodopsin producer Pseudorhodobacter. The microbial consortium in the colonies performed nitrogen fixation. The diazotroph's phylogenetic relations were demonstrated. Tests for presence of cyanotoxins (microcystin, cylindrospermopsin) proved negative. This study is the first documentation of the genus in Israel, providing insight on the invasive nature of G. pisum, and on the ecological implications of its appearance in a lake ecosystem.},
}
@article {pmid36371394,
year = {2022},
author = {Goubran, H and Ragab, G and Seghatchian, J and Burnouf, T},
title = {Blood transfusion in autoimmune rheumatic diseases.},
journal = {Transfusion and apheresis science : official journal of the World Apheresis Association : official journal of the European Society for Haemapheresis},
volume = {},
number = {},
pages = {103596},
doi = {10.1016/j.transci.2022.103596},
pmid = {36371394},
issn = {1473-0502},
abstract = {Autoimmune rheumatic disorders (ARD) represent a wide spectrum of disorders that affect in priority the joints, bones, muscles, and connective tissues. Examples of ARD include rheumatoid arthritis, systemic lupus erythematosus, Sjögren syndrome, polymyositis, systemic sclerosis, antiphospholipid syndrome and mixed connective tissue disease. Patients with ARD often require transfusion of red cell concentrates (RCC) or other blood-derived components. The presence of an autoimmune background, often complicated by the use of immunosuppressive medications, renders these patients quite vulnerable. Exposing them to RCC, when indicated, can trigger transfusion-related immunomodulation that can be aggravated by the role played by the donor microbiome, and the complement activation and the immune dysregulation induced by iron, leading to an amplification of the immune problems. Furthermore, patients are challenged by the transfused extracellular vesicles which could have a potentially negative role, particularly in patients with antiphospholipid syndrome. Despite the very vigorous screening, transfusion transmissible infections can still represent a risk to these patients, particularly in cytomegalovirus seronegative patients or when dormant pathogens are activated in the immunosuppressed transfusion recipient. The ARD population is also more at risk for transfusion-related reactions. One, therefore, has to consider a restrictive transfusion strategy if possible and, if needed, resort to the numerous blood bank procedures to reduce the immunogenicity of blood products or use safer, more targeted, industrial plasma-derived products subjected to purification and pathogen reduction technologies.},
}
@article {pmid36371065,
year = {2022},
author = {Fodor, CC and Fouhse, J and Drouin, D and Ma, T and Willing, BP and Guan, LL and Cobo, ER},
title = {Colonic innate immune defenses and microbiota alterations in acute swine dysentery.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {105873},
doi = {10.1016/j.micpath.2022.105873},
pmid = {36371065},
issn = {1096-1208},
abstract = {Brachyspira hyodysenteriae, an etiologic agent of swine dysentery (SD), is known for causing colitis. Although some aspects of colonic defenses during infection have been described previously, a more comprehensive picture of the host and microbiota interaction in clinically affected animals is required. This study aimed to characterize multiple aspects of colonic innate defenses and microbiome factors in B. hyodysenteriae-infected pigs that accompany clinical presentation of hemorrhagic diarrhea. We examined colonic mucus barrier modifications, leukocyte infiltration, cathelicidin expression, as well as microbiome composition. We showed that B. hyodysenteriae infection caused microscopic hemorrhagic colitis with abundant neutrophil infiltration in the colonic lamina propria and lumen, with minor macrophage infiltration. Mucus hypersecretion with abundant sialylated mucus in the colon, as well as mucosal colonization by [Acetivibrio] ethanolgignens, Lachnospiraceae, and Campylobacter were pathognomonic of B. hyodysenteriae infection. These findings demonstrate that B. hyodysenteriae produces clinical disease through multiple effects on host defenses, involving alterations of mucosal innate immunity and microbiota. Given that B. hyodysenteriae is increasingly resistant to antimicrobials, this understanding of SD pathogenesis may lead to future development of non-antibiotic and anti-inflammatory alternative therapeutics.},
}
@article {pmid36371056,
year = {2022},
author = {Wang, R and Halimulati, M and Huang, X and Ma, Y and Li, L and Zhang, Z},
title = {Sulforaphane-driven reprogramming of gut microbiome and metabolome ameliorates the progression of hyperuricemia.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2022.11.003},
pmid = {36371056},
issn = {2090-1224},
abstract = {INTRODUCTION: Currently, revealing how to prevent and control hyperuricemia has become an essential public health issue. Sulforaphane hasawiderangeofapplications in the management of hyperuricemia.<br><br>OBJECTIVE: The study objective was to verify the uric acid-lowering effects and the regulation of the gut-kidney axis mediated by sulforaphane and identify host-microbial co-metabolites in hyperuricemia.<br><br>METHODS: A hyperuricemia model was established by administering feedstuffs with 4% potassium oxonate and 20% yeast. Forty male Sprague-Dawley rats were randomly divided into the normal control, hyperuricemia, allopurinol, and sulforaphane groups. Animals were treated by oral gavage for six consecutive weeks, and then phenotypic parameters, metabolomic profiling, and metagenomicsequencing were performed.<br><br>RESULTS: Sulforaphane could lower uric acid by decreasing urate synthesis and increasing renal urate excretion in hyperuricemic rats (P＜0.05). We identified succinic acid and oxoglutaric acid as critical host-gut microbiome co-metabolites. Moreover, sulforaphane improved the diversity of microbial ecosystems and functions, as well as metabolic control of the kidney. Notably, sulforaphane exerted its renoprotective effect through epigenetic modification of Nrf2 and interaction between gut microbiota and epigenetic modification in hyperuricemic rats.<br><br>CONCLUSION: We revealed that sulforaphane could ameliorate the progression of hyperuricemia by reprogramming the gut microbiome and metabolome. Our findings may provide a good means for efficiently preventing and treating hyperuricemia.},
}
@article {pmid36370970,
year = {2022},
author = {Zhou, N and Wang, Z and Yang, L and Zhou, W and Qin, Z and Zhang, H},
title = {Size-dependent toxicological effects of polystyrene microplastics in the shrimp Litopenaeus vannamei using a histomorphology, microbiome, and metabolic approach authorship.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {120635},
doi = {10.1016/j.envpol.2022.120635},
pmid = {36370970},
issn = {1873-6424},
abstract = {Due to the wide application of plastic products in human life, microplastic pollution in water has recently attracted more attention. Many studies have revealed the size-dependent toxicity of microplastics. Here, we investigated the toxicological effects of polystyrene microplastics (PS-MPs) on the white leg shrimp, Litopenaeus vannamei, a profitable aquaculture species, using a comprehensive histomorphological, microbiome, and metabolomic approach to verify whether smaller particles are more toxic than larger particles. L. vannamei were experimentally exposed to water containing PS-MPs of four sizes (0.1, 1.0, 5.0, and 20.0 μm) for 24 h at 10 mg/L (acute experiment) and 12 d at 1 mg/L (subchronic experiment). After 24 h of acute exposure, PS-MP accumulation in shrimp indicated that the ingestion and egestion of PS-MPs had a size-dependent effect, and smaller particles were more bioavailable. The tissue morphological results of subchronic experiments showed that, for the guts and gills, the smaller sizes of the PS-MPs exhibited greater damage. In addition, 16 S rRNA gene amplicon sequencing showed that the alpha diversity was higher under larger PS-MP exposure. Correlated with changes in intestinal bacteria, we found a greater enrichment of metabolic pathways in hemolymph proteins and metabolites in larger PS-MP groups, such as "arginine and proline metabolism", "protein digestion and absorption", "lysine degradation". Interestingly, the activity or content of biomarkers of oxidative stress showed a peak at 1 μm and 5 μm. Under specific sizes of PS-MPs, the abundance of the pathogen Vibrio and probiotic bacteria Rhodobacter (5-μm) and Bacillus and Halomonas (1-μm) were simultaneously enriched. Our results indicated that PS-MP exposure can cause size-dependent damage to shrimp, yet specific particle size can be influential differently in regard to some research indicators. Therefore, it can enhance our comprehensive understanding of the impacts of microplastics on shrimp health and suggests that specific particle size should be considered when assessing the size-dependent toxicity of microplastics.},
}
@article {pmid36370790,
year = {2022},
author = {Das, TK and Kabir, A and Zhao, W and Stenstrom, MK and Dittrich, TM and Mohanty, SK},
title = {A review of compaction effect on subsurface processes in soil: Implications on stormwater treatment in roadside compacted soil.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {160121},
doi = {10.1016/j.scitotenv.2022.160121},
pmid = {36370790},
issn = {1879-1026},
abstract = {Sustainable cities require spacious infrastructures such as roadways to serve multiple functions, including transportation and water treatment. This can be achieved by installing stormwater control measures (SCM) such as biofilters and swales on the roadside compacted soil, but compacted soil limits infiltration and other functions of SCM. Understanding the effect of compaction on the subsurface process could help design SCM that could alleviate the negative impacts of compaction. Therefore, reported data on compaction effects on subsurface processes are synthesized relevant for SCM, including infiltration rate, plant health, root microbiome, and biochemical processes. The results show that compaction could reduce runoff infiltration rate, but adding sand to roadside soil could alleviate the negative impact of compaction. Compaction could decrease the oxygen diffusion rate in the root zone, thereby affecting plant root activities, vegetation establishment, and microbial functions in SCM. The impacts of compaction on carbon mineralization rate and root biomass varied widely based on soil type, aeration status, plant species, and inherent soil compaction level. As these processes are critical in maintaining the long-term functions of SCM, the analysis would help develop strategies to alleviate the negative impacts of compaction and turn road infrastructure into a water solution in sustainable cities.},
}
@article {pmid36370671,
year = {2022},
author = {Darrigues, J and Almeida, V and Conti, E and Ribot, JC},
title = {The multisensory regulation of unconventional T cell homeostasis.},
journal = {Seminars in immunology},
volume = {61-64},
number = {},
pages = {101657},
doi = {10.1016/j.smim.2022.101657},
pmid = {36370671},
issn = {1096-3618},
abstract = {Unconventional T cells typically group γδ T cells, invariant Natural Killer T cells (NKT) and Mucosal Associated Invariant T (MAIT) cells. With their pre-activated status and biased tropism for non-lymphoid organs, they provide a rapid (innate-like) and efficient first line of defense against pathogens at strategical barrier sites, while they can also trigger chronic inflammation, and unexpectedly contribute to steady state physiology. Thus, a tight control of their homeostasis is critical to maintain tissue integrity. In this review, we discuss the recent advances of our understanding of the factors, from neuroimmune to inflammatory regulators, shaping the size and functional properties of unconventional T cell subsets in non-lymphoid organs. We present a general overview of the mechanisms common to these populations, while also acknowledging specific aspects of their diversity. We mainly focus on their maintenance at steady state and upon inflammation, highlighting some key unresolved issues and raising upcoming technical, fundamental and translational challenges.},
}
@article {pmid36370636,
year = {2022},
author = {Sica, VP and Friberg, MA and Teufel, AG and Streicher-Scott, JL and Hu, P and Sauer, UG and Krivos, KL and Price, JM and Baker, TR and Abbinante-Nissen, JM and Woeller, KE},
title = {Safety assessment scheme for menstrual cups and application for the evaluation of a menstrual cup comprised of medical grade silicone.},
journal = {EBioMedicine},
volume = {86},
number = {},
pages = {104339},
doi = {10.1016/j.ebiom.2022.104339},
pmid = {36370636},
issn = {2352-3964},
abstract = {BACKGROUND: Ensuring menstrual cup safety is paramount, yet a menstrual cup safety assessment scheme is lacking. This paper presents a quadripartite scheme, showing how it can be applied.<br><br>METHODS: The Tampax Menstrual Cup was evaluated in the safety assessment scheme: (1) Biocompatibility and chemical safety of cup constituents. Extractables were obtained under different use condition; exposure-based risk assessments (EBRA) were conducted for extractables exceeding thresholds of toxicological concern. (2) Physical impact to vaginal mucosa. After physical evaluations, the Tampax Cup and another cup were assessed in a randomised double-blinded, two-product, two-period cross-over clinical trial (65 women, mean age 34.2 years). (3) Impact to vaginal microbiota (in vitro mixed microflora assay and evaluation of vaginal swabs). (4) In vitro growth of Staphylococcus aureus and toxic shock syndrome toxin-1 (TSST-1) production.<br><br>FINDINGS: Biocompatibility assessments and EBRA of cup constituents showed no safety concerns. In the randomised clinical trial, all potentially product-related adverse effects were mild, vaginal exams were unremarkable, no clinically relevant pH changes occurred, post-void residual urine volume with and without cup were similar, and self-reported measures of comfort along with reports of burning, itching and stinging between cups were comparable. Cup use had no effect on microbial growth in vitro or in the 62 subjects who completed the trial or on in vitro TSST-1 production.<br><br>INTERPRETATION: The quadripartite safety assessment scheme allows evaluation of menstrual cup safety. The Tampax Cup is safe and well-tolerated upon intended use. As with all feminine hygiene products, post-market safety surveillance confirmed this conclusion.<br><br>FUNDING: By Procter &amp; Gamble.},
}
@article {pmid36370453,
year = {2022},
author = {Alfradique Monteiro, D and Barbosa, CSF and Martins, LF and Tavora Coelho da Costa Rachid, C},
title = {The bacteriome of the halophyte Atriplex nummularia (old man saltbush) in salt-affected soils - an ecological model.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiac135},
pmid = {36370453},
issn = {1574-6941},
abstract = {Halophytes, plants capable of growing under saline conditions, are an important source of bacteria with biotechnological potential for plant growth under extreme conditions. In this study, we evaluated the halophyte Atriplex nummularia bacteriome assemblage from three different salinized sites in northeastern Brazil with different edaphoclimatic characteristics, understanding the participation of the plant in the assembly of its microbiome. We sampled 30 specimens, from which the leaves, roots, and rhizospheric soil were subjected to 16S rRNA gene sequencing, bringing forth patterns of alpha and beta diversity, taxonomical composition, co-occurrence network, and the core microbiome of each compartment. Overall, this species harbors a very restricted set of endophytic microbes, and communities showed an increasing gradient of complexity (soil > root > leaf), reflecting a change in the main selective pressure being active over the microbial community. Although the leaf bacteriome was influenced basically by host factors, the soil community was modulated by the environment, and the root bacteriome was structured by both factors. These results help us understand how plant-microbe interactions occur in saline environments. As these plants shelter microbes that potentially alleviate abiotic stresses, we discuss how culture-independent methods could contribute to the prospection of plant growth promoting bacteria in plants.},
}
@article {pmid36370451,
year = {2022},
author = {D'Aloisio, LD and Shetty, V and Ballal, M and Gibson, DL},
title = {Following the Indian Immigrant: adoption of westernization results in a western gut microbiome and an increased risk of inflammatory bowel diseases.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiac133},
pmid = {36370451},
issn = {1574-6941},
abstract = {Indians who migrate to westernized countries such as Canada, the United States (US), and the United Kingdom (UK) are at an increased risk of developing inflammatory bowel disease (IBD). While the underlying etiology of IBD remains unclear, a gut microbiome that is no longer symbiotic with its host is a major player. Increasing IBD incidence in Indian immigrants may be due to the adoption of western practices that result in loss of tolerance of a symbiotic community in the gut and its underlying immune responses. However, little is known about the microbial changes in the Indian gut, including shifts in the microbiome when they migrate to westernized countries. In this Current Opinion, we discuss what is known about the Indian gut microbiome and how living in a westernized environment may be impeding what was once a symbiotic relationship with their gut microbiome and intestinal mucosae, which may be the driving factor in their increased risk of IBD.},
}
@article {pmid36370246,
year = {2022},
author = {Dai, W and Ye, J and Xue, Q and Liu, S and Xu, H and Liu, M and Lin, Z},
title = {Changes in Bacterial Communities of Kumamoto Oyster Larvae During Their Early Development and Following Vibrio Infection Resulting in a Mass Mortality Event.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {},
number = {},
pages = {},
pmid = {36370246},
issn = {1436-2236},
support = {32202989//National Natural Science Foundation of China/ ; },
abstract = {Vibrio and Ostreid herpesvirus 1 are responsible for mass mortalities of oyster larvae in hatcheries. Relevant works have focused on their relationships with the disease when larval mortality occurs. On the contrary, little is known about how the resident microbiota in oyster larvae responds to Vibrio-infected disease causing mortality as the disease progressed, whereas this knowledge is fundamental to unveil the etiology of the disease. Here, we analyzed the temporal succession of the microbiome of Kumamoto oyster (Crassostrea sikamea) larvae during their early development, accompanied by a Vibrio-caused mortality event that occurred at the post D-stage of larval development in a shellfish hatchery in Ningbo, China, on June 2020. The main causative agent of larval mortality was attributable to Vibrio infection, which was confirmed by linearly increased Vibrio abundance over disease progression. Larval bacterial communities dramatically changed over host development and disease progression, as highlighted by reduced α-diversity and less diverse core taxa when the disease occurred. Null model and phylogenetic-based mean nearest taxon distance analyses showed that the relative importance of deterministic processes governing larval bacterial assembly initially increased over host development, whereas this dominance was depleted over disease progression. Furthermore, we screened the disease-discriminatory taxa with a significant change in their relative abundances, which could be indicative of disease progression. In addition, network analysis revealed that disease occurrence remodeled the co-occurrence patterns and niche characteristics of larval microbiota. Our findings demonstrate that the dysbiosis of resident bacterial communities and the shift of microecological mechanisms in the larval microbiome may contribute to mortality during oyster early development.},
}
@article {pmid36369926,
year = {2022},
author = {Boytar, AN and Nitert, MD and Morrision, M and Skinner, TL and Jenkins, DG},
title = {Exercise-induced changes to the human gut microbiota and implications for colorectal cancer: A narrative review.},
journal = {The Journal of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/JP283702},
pmid = {36369926},
issn = {1469-7793},
abstract = {Physical activity is associated with reduced risks of colorectal cancer (CRC) incidence, recurrence, and mortality. While these findings are consistent, the mechanism/s underlying this association remain unclear. Growing evidence supports the many ways in which differing characteristics of the gut microbiota can be tumourigenic or protective against CRC. CRC is characterised by significant dysbiosis including reduced short chain fatty acid-producing bacteria. Recent findings suggest that exercise can modify the gut microbiota, and these changes are inverse to the changes seen with CRC; however, this exercise-microbiota interaction is currently understudied in CRC. This review summarises parallel areas of research that are rapidly developing: The exercise-gut microbiota research and cancer-gut microbiota research and highlights the salient similarities. Preliminary evidence suggests that these areas are linked, with exercise mediating changes that promote the antitumorigenic characteristics of the gut microbiota. Future mechanistic and population-specific studies are warranted to confirm the physiological mechanism/s by which exercise changes the gut microbiota, and the influence of the exercise-gut interaction on cancer specific outcomes in CRC. Abstract figure legend The exercise-gut microbiota interaction appears to produce changes that may protect against colorectal cancer, explaining, at least in part, the inverse relationship between exercise and colorectal cancer. This article is protected by copyright. All rights reserved.},
}
@article {pmid36369876,
year = {2022},
author = {Zhang, C and Chen, F and Shen, Y and Chen, Y and Ma, J},
title = {Sleep apnea is associated with the increase of certain genera of Ruminococcaceae and Lachnospiraceae in the gut microbiome of hypertensive patients.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2022.2147509},
pmid = {36369876},
issn = {1747-6356},
abstract = {BACKGROUND: Obstructive sleep apnea (OSA) and hypertension are interrelated diseases linked to gut dysbiosis. This study aimed to investigate the effect of OSA on the gut microbiome in the context of hypertension and vice versa.<br><br>RESEARCH DESIGN AND METHODS: Of 211 consecutively screened patients, 52 completed polysomnography study, medical history questionnaires, and fecal sample collection. 16S rRNA gene sequencing was performed on fecal samples, and diversity, richness, and microbial taxa were analyzed using bioinformatics.<br><br>RESULTS: Alpha diversity showed slightly decreased diversity in OSA and hypertension groups without significant difference, and the hypoxia burden index (HBI) showed a weak positive correlation with Chao1 index (r=0.342, p<0.05) in OSA patients. Firmicutes-to-Bacteroidetes ratio was higher in patients with than without OSA. In hypertensive patients, those with OSA had higher Ruminococcus_1, Lachnoclostridium, Lachnospira, [Ruminococcus]_torques_group, and unidentified Lachnospiraceae levels than those without OSA. Conversely, in OSA patients, hypertensive patients had lower Faecalibacterium and Lachnospiraceae_NK4A136_group levels.<br><br>CONCLUSION: The present study suggests a possible compensatory mechanism for gut microbiome changes in sleep apnea pathophysiology. The positive correlation between HBI and alpha diversity and increase in certain genera of Ruminococcaceae and Lachnospiraceae in OSA patients may represent an adaptive response to hypoxia.},
}
@article {pmid36369654,
year = {2022},
author = {Wareham-Mathiassen, S and Pinto Glenting, V and Bay, L and Allesen-Holm, M and Bengtsson, H and Bjarnsholt, T},
title = {Characterization of pig skin microbiome and appraisal as an in vivo subcutaneous injection model.},
journal = {Laboratory animals},
volume = {},
number = {},
pages = {236772221136173},
doi = {10.1177/00236772221136173},
pmid = {36369654},
issn = {1758-1117},
abstract = {Pig skin is commonly used in the medical industry as an injection model due to its compelling physiological affinity to human skin. However, the pig neck skin microflora remains largely uncharacterized, which may have undesirable implications for the translatability of results to humans. This study aimed to characterize pig neck skin microbiome with direct comparison with human skin microflora at emblematic injection sites to appraise its suitability as an injection model. Ten minipigs were sampled with tape strips and swabs and analysed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and 16S/ITS high throughput sequencing and confocal laser scanning microscopy. Results were directly compared with previous investigations of human injection sites. Pig skin was dominated by phyla 94.8% Firmicutes, 3% Proteobacteria, and 2.2% Actinobacteria. Staphylococcus spp. prevailed (44.4%) at the genus level with S. capitis and S. chromogenes present in all samples. Pig skin revealed populations in the 10[4] colony-forming units (CFU)/cm[2] range with 3% identified as Gram-negative and increased alpha diversity (compared with 10[2] CFU/cm[2] and 10% in humans). While notable taxonomical differences on species levels were seen, pig skin encompassed 97.1% of genera found in human samples. The increased population and variation found support the pig neck as an imperfect but fidelitous subcutaneous injection model that can adequately challenge devices from a microbial standpoint.},
}
@article {pmid36369611,
year = {2022},
author = {Weng, JQ and Li, JB and Yuan, MF and Yao, TT and Zhang, JF and Zeng, YY and Zhao, J and Li, Y and Xu, K and Shen, XX},
title = {Effects of Buyang Huanwu Decoction on Intestinal Barrier, Intestinal Flora, and Trimethylamine Oxide in Rats with Heart Failure.},
journal = {Chinese journal of integrative medicine},
volume = {},
number = {},
pages = {},
pmid = {36369611},
issn = {1672-0415},
abstract = {OBJECTIVE: To explore the mechanisms of Buyang Huanwu Decoction (BYHWD) modulating the gut microbiome and trimethylamine oxide (TAMO) to exert cardioprotective effects.<br><br>METHODS: Ligation of the left anterior descending coronary artery was performed in rats to induce heart failure (HF). Except for the sham-operation group (n=10), 36 operation-induced models were randomized into 3 groups using a random number table (n=12 in each group): the model group, the BYHWD group (15.02 g/kg BYHWD), and the positive group (4.99 g/kg metoprolol succinate). After 4-week treatment (once daily by gavage), echocardiography was applied to evaluate the cardiac function and the Tei index (the ratio of ventricular isovolumic contraction time (IVCT) and isovolumic diastolic time (IVRT) to ejection time (ET)) was calculated; hematoxylin-eosin (HE) staining was observed to characterize the pathology of the myocardium and small intestinal villi. D-lactic acid was detected by an enzyme-linked immunosorbent assay (ELISA). Expressions of occludin, claudin-1, and zonula occludens (ZO-1) were detected by Western blot. 16S ribosomal ribonucleic acid (16S rRNA) sequencing was used to explore the changes in the intestinal flora. TMAO was detected via liquid chromatography-tandem mass spectrometry (LC-MS/MS).<br><br>RESULTS: In the echocardiography, the Tei index was considerably lower in the positive and BYHWD groups compared with the model group (P<0.05). Besides, BYHWD improved the pathology of myocardium and small intestine of HF rats and lowered the D-lactic acid content in the serum, when compared with the model group (P<0.05). BYHWD also improved the expression of occludin and claudin-1 (P<0.05); in the gut microbiota analysis, BYHWD slowed down modifications in the structure distribution of gut microbiota and regulated the diversity of intestinal flora in HF rats. The content of TMAO in the serum was significantly lowered by BYWHT compared with the model group (P<0.05).<br><br>CONCLUSION: BYHWD may delay progression of HF by enhancing the intestinal barrier structure, and regulating intestinal flora and TAMO.},
}
@article {pmid36369518,
year = {2022},
author = {Mankiewicz-Boczek, J and Font-Nájera, A},
title = {Temporal and functional interrelationships between bacterioplankton communities and the development of a toxigenic Microcystis bloom in a lowland European reservoir.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {19332},
pmid = {36369518},
issn = {2045-2322},
support = {2019/33/B/NZ8/02093//Narodowym Centrum Nauki/ ; },
abstract = {The cyanobacteria-associated microbiome is constantly reshaped by bloom development. However, the synergistic-antagonistic nature of the relationships between Microcystis and its microbiome still remains unclear. Therefore, temporal changes of bacterioplankton communities and their functional potential through different developing stages of a Microcystis toxigenic bloom were investigated, considering bacterioplankton assemblages as particle-attached (PAB) and free-living (FLB) bacteria. 16S rRNA sequencing revealed that PAB were represented by Proteobacteria and Cyanobacteria, while FLB by Proteobacteria and Actinobacteria. Network and ordination analyses indicated that PAB inter-relationships were more complex-numerous connections between taxa with stronger correlations, than FLB-rather influenced by physico-chemical parameters. PAB in pre-summer was diverse with Proteobacteria containing potential taxa involved in nitrogen-transforming processes. In mid-summer, PAB presented a mix-bloom dominated by Snowella, Aphanizomenon, and Microcystis, which were succeeded by toxigenic Microcystis in post-summer. Both periods were associated to potential taxa with parasitic/predatory lifestyles against cyanobacteria. In post-summer, Sutterellaceae were recognized as poor water quality indicators, and their strong association with Microcystis could have represented an increased threat for that period. Microcystis was a major factor significantly reducing PAB diversity and evenness, suggesting that it negatively influenced bacterioplankton assemblages, probably also altering the overall community functional potential.},
}
@article {pmid36369477,
year = {2022},
author = {Ramandi, A and Nourashrafeddin, SM and Marashi, SH and Seifi, A},
title = {Microbiome contributes to phenotypic plasticity in saffron crocus.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {39},
number = {1},
pages = {9},
pmid = {36369477},
issn = {1573-0972},
support = {3/54400//Ferdowsi University of Mashhad/ ; },
abstract = {Saffron crocus is a sterile plant species that propagates vegetatively, and consequently, narrow genetic variation is detected in this species. Besides the narrow genetic variation, there is significant phenotypic variation in different traits in this plant. Here we tested this hypothesis that plant microbiome is a major contributor to the phenotypic variation. We focused our analysis on culturable bacteria that were dominant in saffron fields with high stigma yield compared to the fields with low stigma yield. Following this strategy, four rhizospheric (Cupriavidus metallidurans, Bacillus sp., Solibacillus sp., and Planococcus sp.) and two endophytic bacteria (Serratia oryzae and S. odorifera) were identified. The effects of the bacteria on the growth and development of the model plant Arabidopsis were assessed both in agar plate and pot assays. Results showed that these bacteria influence the vegetative growth and flowering time of Arabidopsis. In the next step, corms of saffron were inoculated with these bacteria and the growth and development of the saffron plants were monitored for five months. Remarkably, inoculation of the bacteria had significant influence on vegetative growth, flowering time, and stigma yield of saffron crocus. Furthermore, one of the bacteria, C. metallidurans, is reported here for the first time as a naturally occurring plant-associated bacteria. Altogether our results suggest that plant microbiome is an important factor in phenotypic variation in saffron crocus.},
}
@article {pmid36369356,
year = {2022},
author = {Kumaishi, K and Usui, E and Suzuki, K and Kobori, S and Sato, T and Toda, Y and Takanashi, H and Shinozaki, S and Noda, M and Takakura, A and Matsumoto, K and Yamasaki, Y and Tsujimoto, H and Iwata, H and Ichihashi, Y},
title = {High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {19289},
pmid = {36369356},
issn = {2045-2322},
support = {JPMJCR16O2//CREST/ ; JPMJMI20C7//Mirai Program/ ; },
abstract = {Microbiota are a major component of agroecosystems. Root microbiota, which inhabit the inside and surface of plant roots, play a significant role in plant growth and health. As next-generation sequencing technology allows the capture of microbial profiles without culturing the microbes, profiling of plant microbiota has become a staple tool in plant science and agriculture. Here, we have increased sample handling efficiency in a two-step PCR amplification protocol for 16S rRNA gene sequencing of plant root microbiota, improving DNA extraction using AMPure XP magnetic beads and PCR purification using exonuclease. These modifications reduce sample handling and capture microbial diversity comparable to that obtained by the manual method. We found a buffer with AMPure XP magnetic beads enabled efficient extraction of microbial DNA directly from plant roots. We also demonstrated that purification using exonuclease before the second PCR step enabled the capture of higher degrees of microbial diversity, thus allowing for the detection of minor bacteria compared with the purification using magnetic beads in this step. In addition, our method generated comparable microbiome profile data in plant roots and soils to that of using common commercially available DNA extraction kits, such as DNeasy PowerSoil Pro Kit and FastDNA SPIN Kit for Soil. Our method offers a simple and high-throughput option for maintaining the quality of plant root microbial community profiling.},
}
@article {pmid36369211,
year = {2022},
author = {Saeedi, BJ and Hunter-Chang, S and Luo, L and Li, K and Liu, KH and Robinson, BS},
title = {Oxidative stress mediates end-organ damage in a novel model of acetaminophen-toxicity in Drosophila.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {19309},
pmid = {36369211},
issn = {2045-2322},
support = {DK117570/DK/NIDDK NIH HHS/United States ; DK108735-01/DK/NIDDK NIH HHS/United States ; },
abstract = {Acetaminophen is the most common cause of acute drug-induced liver injury in the United States. However, research into the mechanisms of acetaminophen toxicity and the development of novel therapeutics is hampered by the lack of robust, reproducible, and cost-effective model systems. Herein, we characterize a novel Drosophila-based model of acetaminophen toxicity. We demonstrate that acetaminophen treatment of Drosophila results in similar pathophysiologic alterations as those observed in mammalian systems, including a robust production of reactive oxygen species, depletion of glutathione, and dose-dependent mortality. Moreover, these effects are concentrated in the Drosophila fat body, an organ analogous to the mammalian liver. Utilizing this system, we interrogated the influence of environmental factors on acetaminophen toxicity which has proven difficult in vertebrate models due to cost and inter-individual variability. We find that both increasing age and microbial depletion sensitize Drosophila to acetaminophen toxicity. These environmental influences both alter oxidative stress response pathways in metazoans. Indeed, genetic and pharmacologic manipulations of the antioxidant response modify acetaminophen toxicity in our model. Taken together, these data demonstrate the feasibility of Drosophila for the study of acetaminophen toxicity, bringing with it an ease of genetic and microbiome manipulation, high-throughput screening, and availability of transgenic animals.},
}
@article {pmid36369178,
year = {2022},
author = {Liu, L and Khan, A and Sanchez-Rodriguez, E and Zanoni, F and Li, Y and Steers, N and Balderes, O and Zhang, J and Krithivasan, P and LeDesma, RA and Fischman, C and Hebbring, SJ and Harley, JB and Moncrieffe, H and Kottyan, LC and Namjou-Khales, B and Walunas, TL and Knevel, R and Raychaudhuri, S and Karlson, EW and Denny, JC and Stanaway, IB and Crosslin, D and Rauen, T and Floege, J and Eitner, F and Moldoveanu, Z and Reily, C and Knoppova, B and Hall, S and Sheff, JT and Julian, BA and Wyatt, RJ and Suzuki, H and Xie, J and Chen, N and Zhou, X and Zhang, H and Hammarström, L and Viktorin, A and Magnusson, PKE and Shang, N and Hripcsak, G and Weng, C and Rundek, T and Elkind, MSV and Oelsner, EC and Barr, RG and Ionita-Laza, I and Novak, J and Gharavi, AG and Kiryluk, K},
title = {Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {6859},
pmid = {36369178},
issn = {2041-1723},
support = {R01-DK105124, RC2-DK116690, and R01-DK082753//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; },
abstract = {Immunoglobulin A (IgA) mediates mucosal responses to food antigens and the intestinal microbiome and is involved in susceptibility to mucosal pathogens, celiac disease, inflammatory bowel disease, and IgA nephropathy. We performed a genome-wide association study of serum IgA levels in 41,263 individuals of diverse ancestries and identified 20 genome-wide significant loci, including 9 known and 11 novel loci. Co-localization analyses with expression QTLs prioritized candidate genes for 14 of 20 significant loci. Most loci encoded genes that produced immune defects and IgA abnormalities when genetically manipulated in mice. We also observed positive genetic correlations of serum IgA levels with IgA nephropathy, type 2 diabetes, and body mass index, and negative correlations with celiac disease, inflammatory bowel disease, and several infections. Mendelian randomization supported elevated serum IgA as a causal factor in IgA nephropathy. African ancestry was consistently associated with higher serum IgA levels and greater frequency of IgA-increasing alleles compared to other ancestries. Our findings provide novel insights into the genetic regulation of IgA levels and its potential role in human disease.},
}
@article {pmid36368924,
year = {2022},
author = {Du, C and Zhou, X and Zhang, K and Huang, S and Wang, X and Zhou, S and Chen, Y},
title = {Inactivation of the MSTN gene expression changes the composition and function of the gut microbiome in sheep.},
journal = {BMC microbiology},
volume = {22},
number = {1},
pages = {273},
pmid = {36368924},
issn = {1471-2180},
abstract = {BACKGROUND: Myostatin (MSTN) negatively regulates the muscle growth in animals and MSTN deficient sheep have been widely reported previously. The goal of this study was to explore how MSTN inactivation influences their gut microbiota composition and potential functions.<br><br>RESULTS: We compared the slaughter parameters and meat quality of 3 MSTN-edited male sheep and 3 wild-type male sheep, and analyzed the gut microbiome of the MSTN-edited sheep (8 female and 8 male sheep) and wild-type sheep (8 female and 8 male sheep) through metagenomic sequencing. The results showed that the body weight, carcass weight and eye muscle area of MSTN-edited sheep were significantly higher, but there were no significant differences in the meat quality indexes. At the microbial level, the alpha diversity was significantly higher in the MSTN-edited sheep (P < 0.05), and the microbial composition was significantly different by PCoA analysis in the MSTN-edited and wild-type sheep. The abundance of Firmicutes significantly increased and Bacteroidota significantly decreased in the MSTN-edited sheep. At genus level, the abundance of Flavonifractor, Subdoligranulum, Ruthenibacterium, Agathobaculum, Anaerotignum, Oribacterium and Lactobacillus were significantly increased in the MSTN-edited sheep (P < 0.05). Further analysis of functional differences was found that the carotenoid biosynthesis was significantly increased and the peroxisome, apoptosis, ferroptosis, N-glycan biosynthesis, thermogenesis, and adipocytokines pathways were decreased in the MSTN-edited sheep (P < 0.05). Moreover, carbohydrate-active enzymes (CAZymes) results certified the abundance of the GH13_39, GH4, GH137, GH71 and PL17 were upregulated, and the GT41 and CBM20 were downregulated in the MSTN-edited sheep (P < 0.05).<br><br>CONCLUSIONS: Our study suggested that MSTN inactivation remarkably influenced the composition and potential function of hindgut microbial communities of the sheep, and significantly promoted growth performance without affecting meat quality.},
}
@article {pmid36368923,
year = {2022},
author = {Rosenboom, I and Scheithauer, T and Friedrich, FC and Pörtner, S and Hollstein, L and Pust, MM and Sifakis, K and Wehrbein, T and Rosenhahn, B and Wiehlmann, L and Chhatwal, P and Tümmler, B and Davenport, CF},
title = {Wochenende - modular and flexible alignment-based shotgun metagenome analysis.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {748},
pmid = {36368923},
issn = {1471-2164},
abstract = {BACKGROUND: Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy, particularly with regard to visualization of read mapping location, normalization options, growth dynamics and functional gene repertoires. Current read classification tools use non-standard output formats, or do not fully show information on mapping location. As reference datasets are not perfect, portrayal of mapping information is critical for judging results effectively.<br><br>RESULTS: Our alignment-based pipeline, Wochenende, incorporates flexible quality control, trimming, mapping, various filters and normalization. Results are completely transparent and filters can be adjusted by the user. We observe stringent filtering of mismatches and use of mapping quality sharply reduces the number of false positives. Further modules allow genomic visualization and the calculation of growth rates, as well as integration and subsequent plotting of pipeline results as heatmaps or heat trees. Our novel normalization approach additionally allows calculation of absolute abundance profiles by comparison with reads assigned to the human host genome.<br><br>CONCLUSION: Wochenende has the ability to find and filter alignments to all kingdoms of life using both short and long reads, and requires only good quality reference genomes. Wochenende automatically combines multiple available modules ranging from quality control and normalization to taxonomic visualization. Wochenende is available at https://github.com/MHH-RCUG/nf_wochenende .},
}
@article {pmid36368787,
year = {2022},
author = {Hoefer, CC and Hollon, LK and Campbell, JA},
title = {The Role of the Human Gutome on Chronic Disease: A Review of the Microbiome and Nutrigenomics.},
journal = {Clinics in laboratory medicine},
volume = {42},
number = {4},
pages = {627-643},
doi = {10.1016/j.cll.2022.09.015},
pmid = {36368787},
issn = {1557-9832},
}
@article {pmid36368750,
year = {2022},
author = {Kong, FYS and Unemo, M and Lim, SH and Latch, N and Williamson, DA and Roberts, JA and Wallis, SC and Parker, SL and Landersdorfer, CB and Yap, T and Fairley, CK and Chow, EPF and Lewis, DA and Hammoud, MA and Hocking, JS},
title = {Optimisation of treatments for oral Neisseria gonorrhoeae infection: Pharmacokinetics Study (STI-PK project) - study protocol for non-randomised clinical trial.},
journal = {BMJ open},
volume = {12},
number = {11},
pages = {e064782},
doi = {10.1136/bmjopen-2022-064782},
pmid = {36368750},
issn = {2044-6055},
abstract = {INTRODUCTION: Neisseria gonorrhoeae infections are common and incidence increasing. Oropharyngeal infections are associated with greater treatment failure compared with other sites and drive transmission to anogenital sites through saliva. Gonococcal resistance is increasing and new treatments are scarce, therefore, clinicians must optimise currently available and emerging treatments in order to have efficacious therapeutic options. This requires pharmacokinetic data from the oral cavity/oropharynx, however, availability of such information is currently limited.<br><br>METHODS AND ANALYSIS: Healthy male volunteers (participants) recruited into the study will receive single doses of either ceftriaxone 1 g, cefixime 400 mg or ceftriaxone 500 mg plus 2 g azithromycin. Participants will provide samples at 6-8 time points (treatment regimen dependent) from four oral sites, two oral fluids, one anorectal swab and blood. Participants will complete online questionnaires about their medical history, sexual practices and any side effects experienced up to days 5-7. Saliva/oral mucosal pH and oral microbiome analysis will be undertaken. Bioanalysis will be conducted by liquid chromatography-mass spectrometry. Drug concentrations over time will be used to develop mathematical models for optimisation of drug dosing regimens and to estimate pharmacodynamic targets of efficacy.<br><br>ETHICS AND DISSEMINATION: This study was approved by Royal Melbourne Hospital Human Research Ethics Committee (60370/MH-2021). The study results will be submitted for publication in peer-reviewed journals and reported at conferences. Summary results will be sent to participants requesting them. All data relevant to the study will be included in the article or uploaded as supplementary information.<br><br>TRIAL REGISTRATION NUMBER: ACTRN12621000339853.},
}
@article {pmid36368026,
year = {2022},
author = {Shakyawar, SK and Mishra, NK and Vellichirammal, NN and Cary, L and Helikar, T and Powers, R and Oberley-Deegan, RE and Berkowitz, DB and Bayles, KW and Singh, VK and Guda, C},
title = {A Review of Radiation-Induced Alterations of Multi-Omic Profiles, Radiation Injury Biomarkers, and Countermeasures.},
journal = {Radiation research},
volume = {},
number = {},
pages = {},
doi = {10.1667/RADE-21-00187.1},
pmid = {36368026},
issn = {1938-5404},
abstract = {Increasing utilization of nuclear power enhances the risks associated with industrial accidents, occupational hazards, and the threat of nuclear terrorism. Exposure to ionizing radiation interferes with genomic stability and gene expression resulting in the disruption of normal metabolic processes in cells and organs by inducing complex biological responses. Exposure to high-dose radiation causes acute radiation syndrome, which leads to hematopoietic, gastrointestinal, cerebrovascular, and many other organ-specific injuries. Altered genomic variations, gene expression, metabolite concentrations, and microbiota profiles in blood plasma or tissue samples reflect the whole-body radiation injuries. Hence, multi-omic profiles obtained from high-resolution omics platforms offer a holistic approach for identifying reliable biomarkers to predict the radiation injury of organs and tissues resulting from radiation exposures. In this review, we performed a literature search to systematically catalog the radiation-induced alterations from multi-omic studies and radiation countermeasures. We covered radiation-induced changes in the genomic, transcriptomic, proteomic, metabolomic, lipidomic, and microbiome profiles. Furthermore, we have covered promising multi-omic biomarkers, FDA-approved countermeasure drugs, and other radiation countermeasures that include radioprotectors and radiomitigators. This review presents an overview of radiation-induced alterations of multi-omics profiles and biomarkers, and associated radiation countermeasures.},
}
@article {pmid36367776,
year = {2023},
author = {Zhou, Y and Medik, YB and Patel, B and Zamler, DB and Chen, S and Chapman, T and Schneider, S and Park, EM and Babcock, RL and Chrisikos, TT and Kahn, LM and Dyevoich, AM and Pineda, JE and Wong, MC and Mishra, AK and Cass, SH and Cogdill, AP and Johnson, DH and Johnson, SB and Wani, K and Ledesma, DA and Hudgens, CW and Wang, J and Wadud Khan, MA and Peterson, CB and Joon, AY and Peng, W and Li, HS and Arora, R and Tang, X and Raso, MG and Zhang, X and Foo, WC and Tetzlaff, MT and Diehl, GE and Clise-Dwyer, K and Whitley, EM and Gubin, MM and Allison, JP and Hwu, P and Ajami, NJ and Diab, A and Wargo, JA and Watowich, SS},
title = {Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration.},
journal = {The Journal of experimental medicine},
volume = {220},
number = {2},
pages = {},
doi = {10.1084/jem.20221333},
pmid = {36367776},
issn = {1540-9538},
support = {R01AI109294/NH/NIH HHS/United States ; //Wilks Family Fund/ ; RP170067//Cancer Prevention and Research Institute of Texas/ ; //Parker Institute for Cancer Immunotherapy/ ; //University of Texas MD Anderson/ ; HL158796/HL/NHLBI NIH HHS/United States ; P30CA016672/CA/NCI NIH HHS/United States ; },
abstract = {Immune checkpoint blockade (ICB) has revolutionized cancer treatment, yet quality of life and continuation of therapy can be constrained by immune-related adverse events (irAEs). Limited understanding of irAE mechanisms hampers development of approaches to mitigate their damage. To address this, we examined whether mice gained sensitivity to anti-CTLA-4 (αCTLA-4)-mediated toxicity upon disruption of gut homeostatic immunity. We found αCTLA-4 drove increased inflammation and colonic tissue damage in mice with genetic predisposition to intestinal inflammation, acute gastrointestinal infection, transplantation with a dysbiotic fecal microbiome, or dextran sodium sulfate administration. We identified an immune signature of αCTLA-4-mediated irAEs, including colonic neutrophil accumulation and systemic interleukin-6 (IL-6) release. IL-6 blockade combined with antibiotic treatment reduced intestinal damage and improved αCTLA-4 therapeutic efficacy in inflammation-prone mice. Intestinal immune signatures were validated in biopsies from patients with ICB colitis. Our work provides new preclinical models of αCTLA-4 intestinal irAEs, mechanistic insights into irAE development, and potential approaches to enhance ICB efficacy while mitigating irAEs.},
}
@article {pmid36367655,
year = {2022},
author = {Ščevková, J and Vašková, Z and Dušička, J and Žilka, M and Zvaríková, M},
title = {Co-occurrence of airborne biological and anthropogenic pollutants in the central European urban ecosystem.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {36367655},
issn = {1614-7499},
support = {1/0180/22//Kultúrna a Edukacná Grantová Agentúra MŠVVaŠ SR/ ; },
abstract = {The interactions between organic and inorganic air pollutants, enhanced by the impact of weather parameters, may worsen the respiratory allergy symptoms in allergy sufferers. Pollen grains and fungal spores belong to some of the most crucial aeroallergens. Other allergenic bioparticles in the atmospheric microbiome can include microalgae, fern spores and mites. In this study, we evaluated if and to what extent air pollutants and weather parameters drive the daily variation in airborne concentrations of broad spectrum of bioparticles (pollen grains, fungal spores, microalgae, fern spores and invertebrates) in the air of Bratislava over 3 years, 2019-2021. Air samples were collected using a Hirst-type volumetric sampler. Based on the results of Spearman's correlation analysis, air temperature seems to be the most influential meteorological factor, positively associated with the concentration of all types of bioparticles at assemblage level, even though the association with microalgae was negative. Wind speed, known to have a diluting effect on most airborne particles, appears to be the most influential for microalgae, as their concentration in the air increases along with rising wind speed. Considering air pollutants, correlation analysis revealed that as the daily concentrations of ozone, PM10, CO and/or NO2 increased, so did the levels of most types of analysed bioaerosols at the assemblage level. Regarding that bioparticles may act as carriers for inorganic particles and amplify their allergenic impact, a concomitant increment in the airborne concentration of both organic and inorganic pollutants poses a threat to allergy sufferers in the study area. The concentration of microalgae, on the other hand, decreases with rising levels of CO, NO2 and PM10; thereby, their synergistic effect on allergy sufferers is negligible. Based on our findings, we suggest that the response of pollen and fungal spore concentration to environmental conditions should be investigated at the taxon, not the assemblage level, as each pollen/spore taxon has a different pattern in response to meteorological parameters and air pollutants.},
}
@article {pmid36367636,
year = {2022},
author = {Mehta, SD},
title = {The Effects of Medical Male Circumcision on Female Partners' Sexual and Reproductive Health.},
journal = {Current HIV/AIDS reports},
volume = {},
number = {},
pages = {},
pmid = {36367636},
issn = {1548-3576},
abstract = {PURPOSE OF REVIEW: Voluntary medical male circumcision (VMMC) reduces the risk of HIV acquisition by 60% among heterosexual men, provides protection against certain sexually transmitted infections (STI), and leads to penile microbiome composition changes associated with reduced risk of HIV infection. Intuitively, the benefits of VMMC for female sex partners in relation to STI are likely and have been evaluated. The purpose of this review is to examine emerging findings of broader sexual and reproductive health (SRH) benefits of VMMC for female sex partners.<br><br>RECENT FINDINGS: Systematic reviews find strong evidence for beneficial effects of VMMC on female sex partners risk of HPV, cervical dysplasia, cervical cancer, and with likely protection against trichomoniasis and certain genital ulcerative infections. Few studies assess the direct impact of VMMC on the vaginal microbiome (VMB), though several studies demonstrate reductions in BV, which is mediated by the VMB. Studies are lacking regarding male circumcision status and outcomes associated with non-optimal VMB, such as female infertility and adverse pregnancy outcomes. VMMC has positive effects on women's perceptions of sexual function and satisfaction, and perceptions of disease risk and hygiene, without evidence of risk compensation. VMMC has consistent association with a broad range of women's SRH outcomes, highlighting the biological and non-biological interdependencies within sexual relationships, and need for couples-level approaches to optimize SRH for men and women. The paucity of information on VMMC and influence on VMB is a barrier to optimizing VMB-associated SRH outcomes in female partners.},
}
@article {pmid36367009,
year = {2022},
author = {Santamaria, E and Åkerström, U and Berger-Picard, N and Lataste, S and Gillbro, JM},
title = {A randomized comparative double-blind study assessing the difference between topically applied microbiome supporting skincare versus conventional skincare on the facial microbiome in correlation to biophysical skin parameters.},
journal = {International journal of cosmetic science},
volume = {},
number = {},
pages = {},
doi = {10.1111/ics.12826},
pmid = {36367009},
issn = {1468-2494},
abstract = {BACKGROUND: There are trillions of live bacteria, of around 1000 different species, living in human skin which are considered essential for the balance and barrier function of the skin. The gut microbiome has been a subject of extensive research and evidence shows that the gut flora is affected by preservatives and processed foods. In conventional skincare, preservatives are used, and this raises the question of how it affects the skin flora and its balance.<br><br>METHODS: A randomized double-blind study on 14 healthy volunteers ages 23-45 years old were advised to use microbiome supporting (MS) products on one cheek and benchmark (BM) products on the other cheek daily for three weeks. To investigate how the skin was affected, the skin microbiome was analyzed using 16S rRNA sequencing and biophysical parameters were assessed using an Antera 3D camera. Measurements were performed before and after the three weeks of using the products.<br><br>RESULTS: The use of MS-products for 3 weeks significantly increased the total number of reads mapped to unique bacterial species (p < 0.05) and the number of different unique species (p < 0.05). In addition, the use of MS-products significantly reduced redness (p < 0.05) and improved skin texture (p < 0.01). The use of BM-products showed no significant difference in any of the parameters except improved skin texture (p < 0.05). Additionally, the MS-side showed a significantly improved diversity (p < 0.05) compared to the BM-side. The four major phyla found were, similarly to previous findings by others, Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. Some of the most prevalent species were Cutibacterium acnes, Staphylococcus epidermidis and Pseudonomas aeruginosa.<br><br>CONCLUSION: The findings of this study showed significant improvements in the microbiome and biophysical parameters within 3 weeks of using MS-skincare alone, while BM-skincare only gave significantly improved skin roughness. Although MS-skincare gave significant improvements in several parameters compared to baseline, they were not yet significant when compared to using BM-skincare. Importantly, this is the first study to investigate how preservatives affect the facial microbiome in vivo and has raised a need for further investigation. These results together with further studies can lead to innovations within the cosmetic industry that promote healthier skin.},
}
@article {pmid36366823,
year = {2022},
author = {Higashiyama, M and Hokaria, R},
title = {New and Emerging Treatments for Inflammatory Bowel Disease.},
journal = {Digestion},
volume = {},
number = {},
pages = {1-8},
doi = {10.1159/000527422},
pmid = {36366823},
issn = {1421-9867},
abstract = {BACKGROUND: The specific etiopathogenesis of inflammatory bowel disease (IBD) is still unknown. Although the conventional anti-inflammatory or immunomodulatory drugs relatively nonspecific to pathogenesis have been quite useful in many cases, elucidating the pathogenesis has gradually facilitated developments of disease-specific therapies for refractory cases in the last 2 decades.<br><br>SUMMARY: With a greater understanding of the multiple overactive signaling pathways of the gut mucosal immune response and enhanced leukocyte trafficking, several biological agents or small molecule drugs following the first novel biologic, anti-tumor necrosis factor α (anti-TNFα), have been developed against several modes of action including adhesion molecules, sphingosine-1-phospate receptors, cytokines (IL-12/23, TL1A, and IL-36), Janus kinase (JAK), and phosphodiesterase. Although preceding biological agents have dramatically changed the IBD treatment strategy, many patients still require alternative therapies due to failure or side effects. Newer treatments are now expected to be provided for better efficacy with an improved adverse event profile. In addition, translational studies have highlighted the new therapeutic concepts' potential, including modulation of host-microbiome interactions, stem therapy for perianal fistula, regulation of fibrosis, regulation of the gut-brain axis, and control of previously less targeted immune cells (B cells and innate lymphoid cells). This paper comprehensively reviewed not only the latest already or shortly available therapies but also emerging promising treatments that will be hopefully established in the future for IBD.<br><br>KEY MESSAGES: Many kinds of new treatments are available, and promising treatments with new perspectives are expected to emerge for refractory IBD in the future.},
}
@article {pmid36366495,
year = {2022},
author = {Wang, Z and Jenabian, MA and Alexandrova, Y and Pagliuzza, A and Olivenstein, R and Samarani, S and Chomont, N and Kembel, SW and Costiniuk, CT},
title = {Interplay between the Lung Microbiome, Pulmonary Immunity and Viral Reservoirs in People Living with HIV under Antiretroviral Therapy.},
journal = {Viruses},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/v14112395},
pmid = {36366495},
issn = {1999-4915},
support = {153082/CAPMC/CIHR/Canada ; Team Grant HB2 - 164064//Canadian HIV Cure Enterprise/ ; N/A//Fonds de Recherche du Québec - Santé/ ; },
mesh = {Humans ; *HIV Infections ; CD4-Positive T-Lymphocytes ; Lung ; Bronchoalveolar Lavage Fluid ; *Microbiota ; },
abstract = {Pulmonary dysbiosis may predispose people living with HIV (PLWH) to chronic lung disease. Herein, we assessed whether intrapulmonary HIV reservoir size and immune disruption are associated with reduced bacterial lung diversity in PLWH. Bacterial DNA was extracted and PCR-amplified from cell-free bronchoalveolar lavage (BAL) fluid from 28 PLWH and 9 HIV-negative controls. Amplicon sequence variant (ASV) relative abundances and taxonomic identities were analyzed using joint species distribution modeling. HIV-DNA was quantified from blood and pulmonary CD4+ T-cells using ultra-sensitive qPCR. Immunophenotyping of BAL T-cells was performed using flow cytometry. Lung microbiome diversity was lower in smokers than non-smokers and microbiome composition was more variable in PLWH than HIV-negative individuals. Frequencies of effector memory BAL CD4+ and CD8+ T-cells positively correlated with abundance of several bacterial families while frequencies of BAL activated CD4+ T-cells negatively correlated with abundance of most lung bacterial families. Higher HIV-DNA levels in blood, but not in BAL, as well as frequencies of senescent CD4+ T-cells were associated with reduced bacterial diversity. These findings suggest that HIV infection may weaken the relationship between the lung microbiome and smoking status. Viral reservoir and immune activation levels may impact the lung microbiome, predisposing PLWH to pulmonary comorbidities.},
}
@article {pmid36365369,
year = {2022},
author = {Bunyoo, C and Roongsattham, P and Khumwan, S and Phonmakham, J and Wonnapinij, P and Thamchaipenet, A},
title = {Dynamic Alteration of Microbial Communities of Duckweeds from Nature to Nutrient-Deficient Condition.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {21},
pages = {},
doi = {10.3390/plants11212915},
pmid = {36365369},
issn = {2223-7747},
support = {2002//Kasetsart University Reinventing University Program/ ; FF(KU)4.64//Kasetsart University Research and Development Institute (KURDI)/ ; 2021-2026//The Science and Technology Research Partnership for Sustainable Development (SATREPS), JICA, Japan/ ; },
abstract = {Duckweeds live with complex assemblages of microbes as holobionts that play an important role in duckweed growth and phytoremediation ability. In this study, the structure and diversity of duckweed-associated bacteria (DAB) among four duckweed subtypes under natural and nutrient-deficient conditions were investigated using V3-V4 16S rRNA amplicon sequencing. High throughput sequencing analysis indicated that phylum Proteobacteria was predominant in across duckweed samples. A total of 24 microbial genera were identified as a core microbiome that presented in high abundance with consistent proportions across all duckweed subtypes. The most abundant microbes belonged to the genus Rhodobacter, followed by other common DAB, including Acinetobacter, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and Pseudomonas. After nutrient-deficient stress, diversity of microbial communities was significantly deceased. However, the relative abundance of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Pelomonas, Roseateles and Novosphingobium were significantly enhanced in stressed duckweeds. Functional prediction of the metagenome data displayed the relative abundance of essential pathways involved in DAB colonization, such as bacterial motility and biofilm formation, as well as biodegradable ability, such as benzoate degradation and nitrogen metabolism, were significantly enriched under stress condition. The findings improve the understanding of the complexity of duckweed microbiomes and facilitate the establishment of a stable microbiome used for co-cultivation with duckweeds for enhancement of biomass and phytoremediation under environmental stress.},
}
@article {pmid36365346,
year = {2022},
author = {Aleynova, OA and Nityagovsky, NN and Suprun, AR and Ananev, AA and Dubrovina, AS and Kiselev, KV},
title = {The Diversity of Fungal Endophytes from Wild Grape Vitis amurensis Rupr.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {21},
pages = {},
doi = {10.3390/plants11212897},
pmid = {36365346},
issn = {2223-7747},
support = {22-74-10001//Russian Science Foundation/ ; },
abstract = {Grapevine endophytic fungi have great potential for application in agriculture and represent an important source of various compounds with valuable biological activities. Wild grapevine is known to host a great number of rare and unidentified endophytes and may represent a rich repository of potential vineyard biocontrol agents. This investigation aimed to study the fungal endophytic community of wild grape Vitis amurensis Rupr. using a cultivation-dependent (fungi sowing) and a cultivation-independent (next-generation sequencing, NGS) approach. A comprehensive analysis of the endophytic fungal community in different organs of V. amurensis and under different environmental conditions has been performed. According to the NGS analysis, 12 taxa of class level were presented in different grapevine organs (stem, leaf, berry, seed). Among the 12 taxa, sequences of two fungal classes were the most represented: Dothideomycetes-60% and Tremellomycetes-33%. The top five taxa included Vishniacozyma, Aureobasidiaceae, Cladosporium, Septoria and Papiliotrema. The highest number of fungal isolates and sequences were detected in the grape leaves. The present data also revealed that lower temperatures and increased precipitation favored the number and diversity of endophytic fungi in the wild Amur grape. The number of fungi recovered from grape tissues in autumn was two times higher than in summer. Thus, this study is the first to describe and analyze the biodiversity of the endophytic fungal community in wild grapevine V. amurensis.},
}
@article {pmid36365287,
year = {2022},
author = {Jo, Y and Jung, DR and Park, TH and Lee, D and Park, MK and Lim, K and Shin, JH},
title = {Changes in Microbial Community Structure in Response to Gummosis in Peach Tree Bark.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {21},
pages = {},
doi = {10.3390/plants11212834},
pmid = {36365287},
issn = {2223-7747},
support = {321097-3//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries/ ; PJ017033//Rural Development Administration/ ; },
abstract = {Peach gummosis disease has been identified as a serious challenge in Korean agriculture and has developed to become a major cause of agricultural productivity losses. However, treatments for gummosis have not been systemically established and studies of the microbiome closely related to this plant disease are lacking. Therefore, we analyzed the bacterial and fungal communities in the bark and rhizosphere soil of healthy peach trees and those with gummosis. Through high-throughput sequencing, we obtained unprecedented insights into the bacterial and fungal dynamics of each group, including their diversity and taxonomic classification, as well as network analyses. We found that the presence of gummosis drives a significantly higher alpha diversity in the bark bacterial community. Peach gummosis bark mycobiomes included greater numbers of opportunistic pathogens such as Ascochyta, Botryosphaeria, Saccharomyces, Nectriaceae_NA, Trametes, and Valsaceae_NA. However, the microbiome also included bacteria beneficial to plant growth and the production of polysaccharides-namely, 1174-901-12, Catenibacterium, Cutibacterium, Friedmanniella, Methylobacterium-Methylorubrum, Pseudomonas, Rhodobacter, and Sphingomonas. Furthermore, we confirmed that gummosis induced a more complex structure in the bark microbiome network. We conclude that the findings of this study provide a valuable aid in profiling the overall peach tree microbial ecosystem, which can be utilized to develop precise biomarkers for the early diagnosis of gummosis.},
}
@article {pmid36365278,
year = {2022},
author = {Wang, Y and Zhang, M and Li, S and Li, P and Lang, Z},
title = {Effects of Insect-Resistant Maize HGK60 on Community Diversity of Bacteria and Fungi in Rhizosphere Soil.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {21},
pages = {},
doi = {10.3390/plants11212824},
pmid = {36365278},
issn = {2223-7747},
support = {No. 2016ZX08003-001//Genetically Modified Organisms Breeding Major Projects of China/ ; ZDRW202004//Agricultural Science and Technology Innovation Program of CAAS/ ; },
abstract = {The influence of biotech crops on microbial communities in rhizosphere soil is an important issue in biosafety assessments. The transgenic maize HGK60 harboring the Bt cry1Ah gene enhanced the resistance to lepidopteran pests, while the ecological risk of HGK60 maize on rhizosphere microorganisms is unclear. In this study, we comprehensively analyzed the diversity and composition of bacterial and fungal communities in the rhizosphere soil around Bt maize HGK60 and the near-isogenic non-Bt maize ZD958 at four growth stages via a high-throughput sequencing technique. The results showed that HGK60 maize unleashed temporary effects on the bacterial and fungal diversity and richness during the study plant's development, which would be restored after one cycle of plant cultivation due to the application of the same agricultural management. The differences of bacterial and fungal communities were marked by seasonality, while the different growth stage was the important factor as opposed to the cultivar contributing to the shifts in the bacterial and fungal communities' structure. This study will provide useful information regarding the impact of Bt transgenic maize on the soil microbiome and a theoretical basis for the development of a safety assessment approach for Bt maize in China.},
}
@article {pmid36365048,
year = {2022},
author = {Wang, Z and Pu, W and Liu, Q and Zhu, M and Chen, Q and Xu, Y and Zhou, C},
title = {Association of Gut Microbiota Composition in Pregnant Women Colonized with Group B Streptococcus with Maternal Blood Routine and Neonatal Blood-Gas Analysis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/pathogens11111297},
pmid = {36365048},
issn = {2076-0817},
support = {82074504 and 81774021//National Natural Science Foundation of China/ ; YKK16242//Nanjing Health Science and Technology Development Project/ ; NMUB2018191//Nanjing Medical University Science and Technology Development Project/ ; },
abstract = {Group B Streptococcus (GBS) colonizes the vaginal and rectal mucosa in a substantial proportion of healthy women, and GBS is a risk factor for GBS-associated adverse birth outcomes, such as bacterial infection, in neonates. Whether changes in the gut microbiota of GBS-infected pregnant women are associated with maternal complete blood cell count (CBC) and neonatal blood-gas analysis is unknown. To explore the relationship between the intestinal microecological composition of pregnant women and maternal blood routine and neonatal blood-gas analysis, we collected intestinal microecology samples of 26 pregnant women in clinic. They were divided into a positive group(GBS positive,GBS +) and a negative group (GBS negative, GBS-), with 12 in the positive group and 14 in the negative group. 16S rRNA gene sequencing was used to examine the gut microbiota profile from a fecal sample of pregnant women. CBC was carried out in enrolled pregnant women and umbilical arterial blood-gas analysis (UABGA)was conducted for analysis of intestinal microbiota composition, maternal blood routine and neonatal blood gas. Our results showed significant differences in the total number of organisms and microbial diversity of intestinal microbiota between healthy pregnant women and GBS-positive pregnant women. Particularly, abundances of Lentisphaerae,&amp;nbsp;Chlorobi, Parcubacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria, Fusobacteria and Fibrobacteres were only detected in participants with GBS colonization. Blood-gas analysis revealed that neonates born to mothers with GBS colonization had significantly higher fractions of carboxyhemoglobin (FCOHb) and lower methemoglobin (FMetHb), and abundances of OTU80, OTU122, OTU518 and OTU375 were associated with blood-gas indicators, such as carboxyhemoglobin, methemoglobin, PCO2, PH and ABE. Interestingly, there were significant correlations between OTU levels and inflammatory indexes in pregnant women with GBS infection. Together, this study revealed for the first time that altered gut microbiota compositions are related to the inflammatory state in GBS-positive pregnant women and neonatal blood-gas indicators. GBS colonization may lead to significant changes in the gut microbiome, which might be involved in the pathogenesis of the maternal inflammatory state and neonatal blood gas abnormalities.},
}
@article {pmid36365032,
year = {2022},
author = {O'Donnell, M and Teasdale, SB and Chua, XY and Hardman, J and Wu, N and Curtis, J and Samaras, K and Bolton, P and Morris, MJ and Shannon Weickert, C and Purves-Tyson, T and El-Assaad, F and Jiang, XT and Hold, GL and El-Omar, E},
title = {The Role of the Microbiome in the Metabolic Health of People with Schizophrenia and Related Psychoses: Cross-Sectional and Pre-Post Lifestyle Intervention Analyses.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/pathogens11111279},
pmid = {36365032},
issn = {2076-0817},
support = {#PS49770//UNSW Medicine Neuroscience, Mental Health and Addiction Theme and Sydney Partnership for Health Education, Research and Enterprise (SPHERE) Clinical Academic Group/ ; },
abstract = {The microbiome has been implicated in the development of metabolic conditions which occur at high rates in people with schizophrenia and related psychoses. This exploratory proof-of-concept study aimed to: (i) characterize the gut microbiota in antipsychotic naïve or quasi-naïve people with first-episode psychosis, and people with established schizophrenia receiving clozapine therapy; (ii) test for microbiome changes following a lifestyle intervention which included diet and exercise education and physical activity. Participants were recruited from the Eastern Suburbs Mental Health Service, Sydney, Australia. Anthropometric, lifestyle and gut microbiota data were collected at baseline and following a 12-week lifestyle intervention. Stool samples underwent 16S rRNA sequencing to analyse microbiota diversity and composition. Seventeen people with established schizophrenia and five people with first-episode psychosis were recruited and matched with 22 age-sex, BMI and ethnicity matched controls from a concurrent study for baseline comparisons. There was no difference in α-diversity between groups at baseline, but microbial composition differed by 21 taxa between the established schizophrenia group and controls. In people with established illness pre-post comparison of α-diversity showed significant increases after the 12-week lifestyle intervention. This pilot study adds to the current literature that detail compositional differences in the gut microbiota of people with schizophrenia compared to those without mental illness and suggests that lifestyle interventions may increase gut microbial diversity in patients with established illness. These results show that microbiome studies are feasible in patients with established schizophrenia and larger studies are warranted to validate microbial signatures and understand the relevance of lifestyle change in the development of metabolic conditions in this population.},
}
@article {pmid36364994,
year = {2022},
author = {Nakama, C and Thompson, B and Szybala, C and McBeth, A and Dobner, P and Zwickey, H},
title = {The Continuum of Microbial Ecosystems along the Female Reproductive Tract: Implications for Health and Fertility.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/pathogens11111244},
pmid = {36364994},
issn = {2076-0817},
support = {N/A//Thaena, Inc./ ; },
abstract = {The microbial ecosystem of the female urogenital tract is composed of many niche microenvironments across multiple organ systems in the urinary and reproductive tract. It is complex and contains a variety of bacteria, archaea, viruses, yeast, and protozoa-Many of which are still unidentified or whose functionality is unknown. Unlike the gut microbiome, whose composition is relatively stable in the absence of external perturbations, the urogenital microbiome is constantly shifting in response to biological cycles such as hormonal fluctuations during menstruation. Microbial composition differs between women but the dominance of some microbial families, such as Lactobacillaceae and other lactic acid-producing bacteria, are shared. Research suggests that it is difficult to define a universal healthy urogenital microbiome and consequently map a path to recovery from disease due to dysbiosis. Due to its temporal shifts, the female urogenital microbiome offers a unique opportunity to examine the biological mechanisms that work to restore a microbiome to its baseline. Common functional disorders in women's health are often difficult to diagnose and treat, are prone to recurrence, and can lead to subfertility or infertility. Knowledge of the interconnected microorganism communities along the continuum of the female reproductive tract could revolutionize the quality of women's healthcare.},
}
@article {pmid36364969,
year = {2022},
author = {Solano-Aguilar, GI and Lakshman, S and Shao, J and Chen, C and Beshah, E and Dawson, HD and Vinyard, B and Schroeder, SG and Jang, S and Molokin, A and Urban, JF},
title = {Correction: Solano-Aguilar et al. Fruit and Vegetable Supplemented Diet Modulates the Pig Transcriptome and Microbiome after a Two-Week Feeding Intervention. Nutrients 2021, 13, 4350.},
journal = {Nutrients},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/nu14214513},
pmid = {36364969},
issn = {2072-6643},
abstract = {There was an error in the original publication [...].},
}
@article {pmid36364961,
year = {2022},
author = {Mavrogeni, ME and Asadpoor, M and Henricks, PAJ and Keshavarzian, A and Folkerts, G and Braber, S},
title = {Direct Action of Non-Digestible Oligosaccharides against a Leaky Gut.},
journal = {Nutrients},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/nu14214699},
pmid = {36364961},
issn = {2072-6643},
mesh = {Humans ; Tight Junctions/metabolism ; Oligosaccharides/pharmacology/metabolism ; Epithelial Cells ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/metabolism ; Intestinal Mucosa/metabolism ; Permeability ; },
abstract = {The epithelial monolayer is the primary determinant of mucosal barrier function, and tight junction (TJ) complexes seal the paracellular space between the adjacent epithelial cells and represent the main "gate-keepers" of the paracellular route. Impaired TJ functionality results in increased permeation of the "pro-inflammatory" luminal contents to the circulation that induces local and systemic inflammatory and immune responses, ultimately triggering and/or perpetuating (chronic) systemic inflammatory disorders. Increased gut leakiness is associated with intestinal and systemic disease states such as inflammatory bowel disease and neurodegenerative diseases such as Parkinson's disease. Modulation of TJ dynamics is an appealing strategy aiming at inflammatory conditions associated with compromised intestinal epithelial function. Recently there has been a growing interest in nutraceuticals, particularly in non-digestible oligosaccharides (NDOs). NDOs confer innumerable health benefits via microbiome-shaping and gut microbiota-related immune responses, including enhancement of epithelial barrier integrity. Emerging evidence supports that NDOs also exert health-beneficial effects on microbiota independently via direct interactions with intestinal epithelial and immune cells. Among these valuable features, NDOs promote barrier function by directly regulating TJs via AMPK-, PKC-, MAPK-, and TLR-associated pathways. This review provides a comprehensive overview of the epithelial barrier-protective effects of different NDOs with a special focus on their microbiota-independent modulation of TJs.},
}
@article {pmid36364953,
year = {2022},
author = {Cerdó, T and García-Santos, JA and Rodríguez-Pöhnlein, A and García-Ricobaraza, M and Nieto-Ruíz, A and G Bermúdez, M and Campoy, C},
title = {Impact of Total Parenteral Nutrition on Gut Microbiota in Pediatric Population Suffering Intestinal Disorders.},
journal = {Nutrients},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/nu14214691},
pmid = {36364953},
issn = {2072-6643},
mesh = {Infant ; Humans ; Child ; Infant, Newborn ; *Gastrointestinal Microbiome ; Parenteral Nutrition, Total/adverse effects ; *Short Bowel Syndrome/complications/therapy ; Parenteral Nutrition/adverse effects ; Dysbiosis/complications ; *Enterocolitis, Necrotizing/etiology ; },
abstract = {Parenteral nutrition (PN) is a life-saving therapy providing nutritional support in patients with digestive tract complications, particularly in preterm neonates due to their gut immaturity during the first postnatal weeks. Despite this, PN can also result in several gastrointestinal complications that are the cause or consequence of gut mucosal atrophy and gut microbiota dysbiosis, which may further aggravate gastrointestinal disorders. Consequently, the use of PN presents many unique challenges, notably in terms of the potential role of the gut microbiota on the functional and clinical outcomes associated with the long-term use of PN. In this review, we synthesize the current evidence on the effects of PN on gut microbiome in infants and children suffering from diverse gastrointestinal diseases, including necrotizing enterocolitis (NEC), short bowel syndrome (SBS) and subsequent intestinal failure, liver disease and inflammatory bowel disease (IBD). Moreover, we discuss the potential use of pre-, pro- and/or synbiotics as promising therapeutic strategies to reduce the risk of severe gastrointestinal disorders and mortality. The findings discussed here highlight the need for more well-designed studies, and harmonize the methods and its interpretation, which are critical to better understand the role of the gut microbiota in PN-related diseases and the development of efficient and personalized approaches based on pro- and/or prebiotics.},
}
@article {pmid36364950,
year = {2022},
author = {Neuffer, J and González-Domínguez, R and Lefèvre-Arbogast, S and Low, DY and Driollet, B and Helmer, C and Du Preez, A and de Lucia, C and Ruigrok, SR and Altendorfer, B and Aigner, L and Lucassen, PJ and Korosi, A and Thuret, S and Manach, C and Pallàs, M and Urpi-Sardà, M and Sánchez-Pla, A and Andres-Lacueva, C and Samieri, C},
title = {Exploration of the Gut-Brain Axis through Metabolomics Identifies Serum Propionic Acid Associated with Higher Cognitive Decline in Older Persons.},
journal = {Nutrients},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/nu14214688},
pmid = {36364950},
issn = {2072-6643},
mesh = {Humans ; Aged ; Aged, 80 and over ; Case-Control Studies ; *Brain-Gut Axis ; *Cognitive Dysfunction/metabolism ; Metabolomics ; },
abstract = {The gut microbiome is involved in nutrient metabolism and produces metabolites that, via the gut-brain axis, signal to the brain and influence cognition. Human studies have so far had limited success in identifying early metabolic alterations linked to cognitive aging, likely due to limitations in metabolite coverage or follow-ups. Older persons from the Three-City population-based cohort who had not been diagnosed with dementia at the time of blood sampling were included, and repeated measures of cognition over 12 subsequent years were collected. Using a targeted metabolomics platform, we identified 72 circulating gut-derived metabolites in a case-control study on cognitive decline, nested within the cohort (discovery n = 418; validation n = 420). Higher serum levels of propionic acid, a short-chain fatty acid, were associated with increased odds of cognitive decline (OR for 1 SD = 1.40 (95% CI 1.11, 1.75) for discovery and 1.26 (1.02, 1.55) for validation). Additional analyses suggested mediation by hypercholesterolemia and diabetes. Propionic acid strongly correlated with blood glucose (r = 0.79) and with intakes of meat and cheese (r > 0.15), but not fiber (r = 0.04), suggesting a minor role of prebiotic foods per se, but a possible link to processed foods, in which propionic acid is a common preservative. The adverse impact of propionic acid on metabolism and cognition deserves further investigation.},
}
@article {pmid36364942,
year = {2022},
author = {Agrizzi Verediano, T and Agarwal, N and Stampini Duarte Martino, H and Kolba, N and Grancieri, M and Dias Paes, MC and Tako, E},
title = {Effect of Black Corn Anthocyanin-Rich Extract (Zea mays L.) on Cecal Microbial Populations In Vivo (Gallus gallus).},
journal = {Nutrients},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/nu14214679},
pmid = {36364942},
issn = {2072-6643},
mesh = {Animals ; *Chickens/metabolism ; *Zea mays/metabolism ; Anthocyanins/pharmacology/metabolism ; Escherichia coli/metabolism ; Cecum/metabolism ; Bifidobacterium/metabolism ; Clostridium ; Plant Extracts/pharmacology ; },
abstract = {Black corn has been attracting attention to investigate its biological properties due to its anthocyanin composition, mainly cyanidin-3-glucoside. Our study evaluated the effects of black corn extract (BCE) on intestinal morphology, gene expression, and the cecal microbiome. The BCE intra-amniotic administration was evaluated by an animal model in Gallus gallus. The eggs (n = 8 per group) were divided into: (1) no injection; (2) 18 MΩ H2O; (3) 5% black corn extract (BCE); and (4) 0.38% cyanidin-3-glucoside (C3G). A total of 1 mL of each component was injected intra-amniotic on day 17 of incubation. On day 21, the animals were euthanized after hatching, and the duodenum and cecum content were collected. The cecal microbiome changes were attributed to BCE administration, increasing the population of Bifidobacterium and Clostridium, and decreasing E. coli. The BCE did not change the gene expression of intestinal inflammation and functionality. The BCE administration maintained the villi height, Paneth cell number, and goblet cell diameter (in the villi and crypt), similar to the H2O injection but smaller than the C3G. Moreover, a positive correlation was observed between Bifidobacterium, Clostridium, E. coli, and villi GC diameter. The BCE promoted positive changes in the cecum microbiome and maintained intestinal morphology and functionality.},
}
@article {pmid36364915,
year = {2022},
author = {Lavallee, CM and Bruno, A and Ma, C and Raman, M},
title = {The Role of Intermittent Fasting in the Management of Nonalcoholic Fatty Liver Disease: A Narrative Review.},
journal = {Nutrients},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/nu14214655},
pmid = {36364915},
issn = {2072-6643},
mesh = {Animals ; Humans ; *Fasting/adverse effects ; *Non-alcoholic Fatty Liver Disease/therapy ; Weight Loss ; Obesity/metabolism ; Adipokines ; },
abstract = {Intermittent fasting is a non-pharmacological dietary approach to management of obesity and metabolic syndrome, involving periodic intervals of complete or near-complete abstinence from food and energy-containing fluids. This dietary strategy has recently gained significant popularity in mainstream culture and has been shown to induce weight loss in humans, reduce gut and systemic inflammation, and improve gut microbial diversity and dysbiosis (largely in animal models). It has been hypothesized that intermittent fasting could be beneficial in the management of nonalcoholic fatty liver disease, given the condition's association with obesity. This review summarizes protocols, potential mechanisms of action, and evidence for intermittent fasting in nonalcoholic fatty liver disease. It also highlights practical considerations for implementing intermittent fasting in clinical practice. A search of the literature for English-language articles related to intermittent fasting or time-restricted feeding and liver disease was completed in PubMed and Google Scholar. Potential mechanisms of action for effects of intermittent fasting included modulation of circadian rhythm, adipose tissue and adipokines, gut microbiome, and autophagy. Preclinical, epidemiological, and clinical trial data suggested clinical benefits of intermittent fasting on metabolic and inflammatory markers in humans. However, there was a paucity of evidence of its effects in patients with nonalcoholic fatty liver disease. More clinical studies are needed to determine mechanisms of action and to evaluate safety and efficacy of intermittent fasting in this population.},
}
@article {pmid36364844,
year = {2022},
author = {Lin, H and Chen, J and Ma, S and An, R and Li, X and Tan, H},
title = {The Association between Gut Microbiome and Pregnancy-Induced Hypertension: A Nested Case-Control Study.},
journal = {Nutrients},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/nu14214582},
pmid = {36364844},
issn = {2072-6643},
support = {81773535//National Natural Science Foundation of China/ ; 2018SK2061//Key Research and Development Program of Hunan Province/ ; },
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; Case-Control Studies ; *Hypertension, Pregnancy-Induced ; Blood Pressure/physiology ; Bacteria/genetics ; },
abstract = {(1) Background: Pregnancy-induced hypertension (PIH) is associated with obvious microbiota dysbiosis in the third trimester of pregnancy. However, the mechanisms behind these changes remain unknown. Therefore, this study aimed to explore the relationship between the gut microbiome in early pregnancy and PIH occurrence. (2) Methods: A nested case-control study design was used based on the follow-up cohort. Thirty-five PIH patients and thirty-five matched healthy pregnant women were selected as controls. The gut microbiome profiles were assessed in the first trimester using metagenomic sequencing. (3) Results: Diversity analyses showed that microbiota diversity was altered in early pregnancy. At the species level, eight bacterial species were enriched in healthy controls: Alistipes putredinis, Bacteroides vulgatus, Ruminococcus torques, Oscillibacter unclassified, Akkermansia muciniphila, Clostridium citroniae, Parasutterella excrementihominis and Burkholderiales bacterium_1_1_47. Conversely, Eubacterium rectale, and Ruminococcus bromii were enriched in PIH patients. The results of functional analysis showed that the changes in these different microorganisms may affect the blood pressure of pregnant women by affecting the metabolism of vitamin K2, sphingolipid, lipid acid and glycine. (4) Conclusion: Microbiota dysbiosis in PIH patients begins in the first trimester of pregnancy, and this may be associated with the occurrence of PIH. Bacterial pathway analyses suggest that the gut microbiome might lead to the development of PIH through the alterations of function modules.},
}
@article {pmid36364814,
year = {2022},
author = {Chudzicka-Strugała, I and Gołębiewska, I and Banaszewska, B and Brudecki, G and Zwoździak, B},
title = {The Role of Individually Selected Diets in Obese Women with PCOS-A Review.},
journal = {Nutrients},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/nu14214555},
pmid = {36364814},
issn = {2072-6643},
mesh = {Humans ; Female ; *Polycystic Ovary Syndrome/metabolism ; Overweight/therapy ; Obesity/metabolism ; Diet ; Life Style ; },
abstract = {Polycystic ovarian syndrome (PCOS) is one of the most common heterogeneous endocrine and metabolic disorders in premenopausal women. It is a complex multifactorial disorder with strong epigenetic and environmental influences, including factors related to eating habits and lifestyle. There is a close relationship between obesity and PCOS. Weight gain and obesity are often clinical symptoms manifested by biochemical markers. Moreover, abdominal obesity in women with PCOS is involved in the development of inflammatory changes. A significant share of balanced therapies correcting the lifestyle of patients is suggested, e.g., with the implementation of appropriate diets to minimize exposure to inflammatory factors and prevent abnormal immune system stimulation. In the case of obese patients with PCOS, planning a diet program and supporting the motivation to change eating habits play an important role to lose weight and lower BMI. Probiotics/synbiotic supplementation may enhance weight loss during the diet program and additionally positively affect metabolic and inflammatory factors by improving the intestinal microbiome.},
}
@article {pmid36364799,
year = {2022},
author = {Moriki, D and Francino, MP and Koumpagioti, D and Boutopoulou, B and Rufián-Henares, JÁ and Priftis, KN and Douros, K},
title = {The Role of the Gut Microbiome in Cow's Milk Allergy: A Clinical Approach.},
journal = {Nutrients},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/nu14214537},
pmid = {36364799},
issn = {2072-6643},
mesh = {Cattle ; Animals ; Female ; Child, Preschool ; Humans ; *Milk Hypersensitivity/prevention &amp; control ; *Gastrointestinal Microbiome ; Ecosystem ; Dysbiosis ; *Food Hypersensitivity ; },
abstract = {Cow's milk allergy (CMA) is the most prevalent food allergy (FA) in infancy and early childhood and can be present with various clinical phenotypes. The significant increase in FA rates recorded in recent decades has been associated with environmental and lifestyle changes that limit microbial exposure in early life and induce changes in gut microbiome composition. Gut microbiome is a diverse community of microbes that colonize the gastrointestinal tract (GIT) and perform beneficial functions for the host. This complex ecosystem interacts with the immune system and has a pivotal role in the development of oral tolerance to food antigens. Emerging evidence indicates that alterations of the gut microbiome (dysbiosis) in early life cause immune dysregulation and render the host susceptible to immune-mediated diseases later in life. Therefore, the colonization of the gut by "healthy" microbes that occurs in the first years of life determines the lifelong health of the host. Here, we present current data on the possible role of the gut microbiome in the development of CMA. Furthermore, we discuss how gut microbiome modification might be a potential strategy for CMA prevention and treatment.},
}
@article {pmid36364779,
year = {2022},
author = {Speciani, MC and Cintolo, M and Marino, M and Oren, M and Fiori, F and Gargari, G and Riso, P and Ciafardini, C and Mascaretti, F and Parpinel, M and Airoldi, A and Vangeli, M and Leone, P and Cantù, P and Lagiou, P and Del Bo', C and Vecchi, M and Carnevali, P and Oreggia, B and Guglielmetti, S and Bonzi, R and Bonato, G and Ferraroni, M and La Vecchia, C and Penagini, R and Mutignani, M and Rossi, M},
title = {Flavonoid Intake in Relation to Colorectal Cancer Risk and Blood Bacterial DNA.},
journal = {Nutrients},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/nu14214516},
pmid = {36364779},
issn = {2072-6643},
support = {My First AIRC grant No.17070//Italian Foundation for Cancer Research (AIRC)/ ; },
mesh = {Humans ; Flavonoids ; Anthocyanins ; DNA, Bacterial/genetics ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; *Flavanones ; Diet ; *Colorectal Neoplasms/epidemiology/prevention &amp; control ; },
abstract = {Flavonoids have been inversely associated to colorectal cancer (CRC) and are plausible intermediaries for the relation among gut microbiome, intestinal permeability and CRC. We analyzed the relation of flavonoid intake with CRC and blood bacterial DNA. We conducted a case-control study in Italy involving 100 incident CRC cases and 200 controls. A valid and reproducible food-frequency questionnaire was used to assess dietary habits and to estimate six flavonoid subclass intakes. We applied qPCR and 16S rRNA gene profiling to assess blood bacterial DNA. We used multiple logistic regression to derive odds ratios (ORs) of CRC and Mann-Whitney and chi--square tests to evaluate abundance and prevalence of operational taxonomic units (OTUs) according to flavonoid intakes. Inverse associations with CRC were found for anthocyanidins (OR for the highest versus the lowest tertile = 0.24, 95% confidence interval, CI = 0.11-0.52) and flavanones (OR = 0.18, 95% CI = 0.08-0.42). We found different abundance and prevalence according to anthocyanidin and flavanone intake for OTUs referring to Oligoflexales order, Diplorickettsiaceae family, Staphylococcus, Brevundimonas, Pelomonas and Escherischia-Shigella genera, and Flavobacterium and Legionella species. The study provides evidence to a protective effect of dietary anthocyanidins and flavanones on CRC and suggests an influence of flavonoids on blood bacterial DNA, possibly through intestinal permeability changes.},
}
@article {pmid36364776,
year = {2022},
author = {Basak, S and Das, RK and Banerjee, A and Paul, S and Pathak, S and Duttaroy, AK},
title = {Maternal Obesity and Gut Microbiota Are Associated with Fetal Brain Development.},
journal = {Nutrients},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/nu14214515},
pmid = {36364776},
issn = {2072-6643},
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; *Obesity, Maternal ; Placenta/metabolism ; Fetal Development ; Obesity/metabolism ; Brain/metabolism ; Inflammation/metabolism ; },
abstract = {Obesity in pregnancy induces metabolic syndrome, low-grade inflammation, altered endocrine factors, placental function, and the maternal gut microbiome. All these factors impact fetal growth and development, including brain development. The lipid metabolic transporters of the maternal-fetal-placental unit are dysregulated in obesity. Consequently, the transport of essential long-chain PUFAs for fetal brain development is disturbed. The mother's gut microbiota is vital in maintaining postnatal energy homeostasis and maternal-fetal immune competence. Obesity during pregnancy changes the gut microbiota, affecting fetal brain development. Obesity in pregnancy can induce placental and intrauterine inflammation and thus influence the neurodevelopmental outcomes of the offspring. Several epidemiological studies observed an association between maternal obesity and adverse neurodevelopment. This review discusses the effects of maternal obesity and gut microbiota on fetal neurodevelopment outcomes. In addition, the possible mechanisms of the impacts of obesity and gut microbiota on fetal brain development are discussed.},
}
@article {pmid36364752,
year = {2022},
author = {Araujo, R and Borges-Canha, M and Pimentel-Nunes, P},
title = {Microbiota Modulation in Patients with Metabolic Syndrome.},
journal = {Nutrients},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/nu14214490},
pmid = {36364752},
issn = {2072-6643},
support = {CEECIND/01070/2018//Fundação para a Ciência e Tecnologia/ ; },
mesh = {Adult ; Humans ; *Metabolic Syndrome/complications ; *Synbiotics ; *Probiotics/therapeutic use ; *Gastrointestinal Microbiome ; Dysbiosis/complications ; Prebiotics ; },
abstract = {Metabolic syndrome (MS) comprises a vast range of metabolic dysfunctions, which can be associated to cardiovascular disease risk factors. MS is reaching pandemic levels worldwide and it currently affects around 25% in the adult population of developed countries. The definition states for the diagnosis of MS may be clear, but it is also relevant to interpret the patient data and realize whether similar criteria were used by different clinicians. The different criteria explain, at least in part, the controversies on the theme. Several studies are presently focusing on the microbiota changes according to the components of MS. It is widely accepted that the gut microbiota is a regulator of metabolic homeostasis, being the gut microbiome in MS described as dysbiotic and certain taxonomic groups associated to metabolic changes. Probiotics, and more recently synbiotics, arise as promising therapeutic alternatives that can mitigate some metabolic disturbances, namely by correcting the microbiome and bringing homeostasis to the gut. The most recent studies were revised and the promising results and perspectives revealed in this review.},
}
@article {pmid36364328,
year = {2022},
author = {Baćmaga, M and Wyszkowska, J and Borowik, A and Kucharski, J},
title = {Effects of Tebuconazole Application on Soil Microbiota and Enzymes.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {21},
pages = {},
doi = {10.3390/molecules27217501},
pmid = {36364328},
issn = {1420-3049},
support = {30.610.006-110//University of Warmia and Mazury in Olsztyn, Faculty of Agriculture and Forestry, Department of Soil Science and Microbiology/ ; 010/RID/2018/19//Minister of Education and Science in the range of the program entitled "Regional Initiative of Excellence" for the years 2019-2023/ ; },
mesh = {*Soil/chemistry ; Soil Microbiology ; *Microbiota ; Triazoles/pharmacology ; Bacteria ; RNA, Ribosomal, 16S ; },
abstract = {Identification of pesticide impact on the soil microbiome is of the utmost significance today. Diagnosing the response of bacteria to tebuconazole, used for plant protection, may help isolate the most active bacteria applicable in the bioaugmentation of soils contaminated with this preparation. Bearing in mind the above, a study was undertaken to test the effect of tebuconazole on the diversity of bacteria at all taxonomic levels and on the activity of soil enzymes. It was conducted by means of standard and metagenomic methods. Its results showed that tebuconazole applied in doses falling within the ranges of good agricultural practice did not significantly disturb the biological homeostasis of soil and did not diminish its fertility. Tebuconazole was found to stimulate the proliferation of organotrophic bacteria and fungi, and also the activities of soil enzymes responsible for phosphorus, sulfur, and carbon metabolism. It did not impair the activity of urease responsible for urea hydrolysis, or cause any significant changes in the structure of bacterial communities. All analyzed soil samples were mainly populated by bacteria from the phylum Proteobacteria, Actinobacteria, Firmicutes, Gemmatimonadetes, Acidobacteria, Planctomycetes, and Chloroflexi. Bacteria from the genera Kaistobacter, Arthrobacter, and Streptomyces predominated in the soils contaminated with tebuconazole, whereas these from the Gemmata genus were inactivated by this preparation.},
}
@article {pmid36363813,
year = {2022},
author = {Ortega-Santos, CP and Al-Nakkash, L and Whisner, CM},
title = {Exercise and/or Genistein Do Not Revert 24-Week High-Fat, High-Sugar Diet-Induced Gut Microbiota Diversity Changes in Male C57BL/6J Adult Mice.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/microorganisms10112221},
pmid = {36363813},
issn = {2076-2607},
support = {AZ0163//Midwestern-Arizona Alzheimer's Consortium/ ; 334469//GPSA Arizona State University Termination Grant Spring 2021/ ; },
abstract = {The gut microbiota (GM) has been hypothesized to be a potential mediator in the health benefits of exercise and diet. The current literature is focused on the prevention effects of exercise and diet and could benefit from exploring whether these treatments alone or combined can treat obesity via the gut microbiome. This study aimed to explore the effects of genistein, exercise, and their synergistic effect to revert diet-induced obesity and gut microbiota changes. A total of 57 male adult C57BL/6 mice were randomized to 24 weeks of unpurified diet (chow) or a high-fat, high-sugar diet (HFD; 60% fat total energy). After the first 12 weeks, animals on the HFD were randomized into: HFD + chow, HFD, HFD + exercise (HFD + Exe), HFD + genistein (HFD + Gen), and HFD + Exe + Gen. We compared the body weight change between groups after 24 weeks. GM (α-diversity and ß-diversity) was profiled after sequencing the 16S rRNA gene by Illumina MiSeq. HFD + Exe + Gen significantly (p < 0.05) decreased weight gain relative to the HFD with only HFD + chow reverting the body weight change to that of chow. All diets including HFD reduced the GM richness (observed amplicon sequence variants) relative to chow with the HFD + Gen and HFD + Exe resulting in significantly lower phylogenetic diversity compared to the HFD. Data did not support an additive benefit to the GM for HFD + Gen + Exe. HFD + Exe + Gen showed a greater capacity to revert diet-induced obesity in adult male mice, but it was not as effective as switching from HFD to chow. Lifestyle treatment of HFD-induced obesity including exercise and genistein resulted in a reduction in weight gain and GM richness, but switching from HFD to chow had the greatest potential to revert these characteristics toward that of lean controls.},
}
@article {pmid36363791,
year = {2022},
author = {Șchiopu, CG and Ștefănescu, C and Boloș, A and Diaconescu, S and Gilca-Blanariu, GE and Ștefănescu, G},
title = {Functional Gastrointestinal Disorders with Psychiatric Symptoms: Involvement of the Microbiome-Gut-Brain Axis in the Pathophysiology and Case Management.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/microorganisms10112199},
pmid = {36363791},
issn = {2076-2607},
abstract = {Functional Gastrointestinal Disorders have been an important cause of poor life quality in affected populations. The unclear etiology and pathophysiological mechanism alter the clinical evolution of the patient. Although a strong connection with psychological stress has been observed, it was not until recently that the gut-brain axis involvement has been revealed. Furthermore, the current literature not only promotes the gut-brain axis modulation as a therapeutical target for functional digestive disorders but also states that the gut microbiome has a main role in this bi-directional mechanism. Psychiatric symptoms are currently recognized as an equally important aspect of the clinical manifestation and modulation of both the digestive and central nervous systems and could be the best approach in restoring the balance. As such, this article proposes a detailed description of the physiology of the microbiome-gut-brain axis, the pathophysiology of the functional gastrointestinal disorders with psychiatric symptoms and current perspectives for therapeutical management, as revealed by the latest studies in the scientific literature.},
}
@article {pmid36363788,
year = {2022},
author = {Lu, C and Zhang, Q and Huang, Q and Wang, S and Qin, X and Ren, T and Xie, R and Su, H},
title = {Significant Shifts in Microbial Communities Associated with Scleractinian Corals in Response to Algae Overgrowth.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/microorganisms10112196},
pmid = {36363788},
issn = {2076-2607},
support = {Nos. 41706158//National Natural Science Foundation of China/ ; Nos. AD19245121//Science and Technology Project of Guangxi/ ; 2018GXNSFBA281101//Natural Science Foundation of Guangxi Province/ ; },
abstract = {Microbes play a key role in reef dynamics, mediating the competition between scleractinian corals and benthic algae; however, major shifts in bacterial communities among coral species in response to increases in the abundance of algae are not well understood. We investigated the taxonomic composition of coral-associated microbial communities under algae-overgrowth conditions using 16S rRNA gene sequencing. The results showed that non-algal (i.e., healthy) tissue (HH) had lower bacterial abundance and diversity than tissue collected from the coral-algae interface boundary (HA) and areas of algae growth (AA). Specifically, the HA and AA samples had higher relative abundances of Saprospiraceae, Rhodobacteraceae, and Alteromonadaceae. Compared with Platygyra sp. and Montipora sp., the physiological response of Pocillopora sp. was more intense under algae-induced stress based on microbial gene function prediction. Our results indicate that algal pressure can significantly alter the microbial community structure and function of coral ecosystems. Our data thus provide new insight into the relationship between corals and their microbiome under environmental stress.},
}
@article {pmid36363781,
year = {2022},
author = {Solazzo, G and Iodice, S and Mariani, J and Persico, N and Bollati, V and Ferrari, L and , },
title = {Upper Respiratory Microbiome in Pregnant Women: Characterization and Influence of Parity.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/microorganisms10112189},
pmid = {36363781},
issn = {2076-2607},
support = {0152T74ZL_004//Italian Ministry of Education, University, and Research "Progetti di Rilevante Interesse Nazionale" (PRIN)/ ; },
abstract = {During pregnancy, the woman's immune system changes to support fetal development. These immunological modifications can increase the risk of respiratory diseases. Because the respiratory microbiome is involved in airway homeostasis, it is important to investigate how it changes during pregnancy. Additionally, since parity is associated with immune system alterations and cohabitants shared a similar microbiome, we investigated whether having a child may influence the respiratory microbiome of pregnant women. We compared the microbiome of 55 pregnant with 26 non-pregnant women using 16S rRNA gene sequencing and analyzed taxonomy, diversity, and metabolic pathways to evaluate the differences among nulliparous, primiparous, and multiparous women. The microbiome was similar in pregnant and non-pregnant women, but pregnant women had higher alpha diversity (Chao1 p-value = 0.001; Fisher p-value = 0.005) and a lower abundance of several metabolic pathways. Multiparous pregnant women had a higher relative abundance of Moraxella (p-value = 0.003) and a lower abundance of Corynebacterium (p-value = 0.002) compared with primiparous women. Both multiparous (pregnant) and primiparous/multiparous (non-pregnant) women reported a higher abundance of Moraxella compared with primiparous (pregnant) or nulliparous ones (p-value = 0.001). In conclusion, we characterized for the first time the upper airway microbiome of pregnant women and observed the influence of parity on its composition.},
}
@article {pmid36363763,
year = {2022},
author = {Kravchenko, I and Rayko, M and Tikhonova, E and Konopkin, A and Abakumov, E and Lapidus, A},
title = {Agricultural Crops Grown in Laboratory Conditions on Chernevaya Taiga Soil Demonstrate Unique Composition of the Rhizosphere Microbiota.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/microorganisms10112171},
pmid = {36363763},
issn = {2076-2607},
support = {19-16-00049//Russian Science Foundation/ ; FFEN-2022-0022//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Chernevaya taiga in West Siberia is a unique environment, with gigantism of grasses and shrubs. Exceptionally high productivity of plants is determined by the synergistic interaction of various factors, with a special role belonging to microorganisms colonizing the plant roots. This research explored whether agricultural plants can recruit specific microorganisms from within virgin Chernevaya Umbrisol and thus increase their productivity. Radish and wheat plants were grown on the Umbrisol (T1) and control Retisol of Scotch pine forest stand (T3) soils in the phytotron, and then a bacterial community analysis of the rhizosphere was performed using high-throughput sequencing of the 16S rRNA genes. In laboratory experiments, the plant physiological parameters were significantly higher when growing on the Umbrisol as compared to the Retisol. Bacterial diversity in T1 soil was considerably higher than in the control sample, and the principal coordinate analysis demonstrated apparent differences in the bacterial communities associated with the plants. Agricultural plants growing in the T1 soil form specific prokaryotic communities, with dominant genera Chthoniobacter, Pseudomonas, Burkholderia, and Massilia. These communities also include less abundant but essential for plant growth nitrifiers Cand. Nitrosocosmius and Nitrospira, and representatives of Proteobacteria, Bacilli, and Actinobacteria, known to be gibberellin-producers.},
}
@article {pmid36363762,
year = {2022},
author = {Sawane, K and Hosomi, K and Park, J and Ookoshi, K and Nanri, H and Nakagata, T and Chen, YA and Mohsen, A and Kawashima, H and Mizuguchi, K and Miyachi, M and Kunisawa, J},
title = {Identification of Human Gut Microbiome Associated with Enterolignan Production.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/microorganisms10112169},
pmid = {36363762},
issn = {2076-2607},
support = {22ae0121035s0102//the Japan Agency for Medical Research and Development/ ; 22gm1010006h0004//the Japan Agency for Medical Research and Development/ ; 22ae0121042h0002//the Japan Agency for Medical Research and Development/ ; 22ae0121035s0102//the Japan Agency for Medical Research and Development/ ; 20AC5004//the Ministry of Health and Welfare of Japan and Public /Private R&amp;D Investment Strategic Expansion PrograM/ ; },
abstract = {Dietary plant lignans are converted inside the gut to enterolignans enterodiol (ED) and enterolactone (EL), which have several biological functions, and health benefits. In this study, we characterized the gut microbiome composition associated with enterolignan production using data from a cross-sectional study in the Japanese population. We identified enterolignan producers by measuring ED and EL levels in subject's serum using liquid chromatography-tandem mass spectrometry. Enterolignan producers show more abundant proportion of Ruminococcaceae and Lachnospiraceae than non-enterolignan producers. In particular, subjects with EL in their serum had a highly diverse gut microbiome that was rich in Ruminococcaceae and Rikenellaceae. Moreover, we built a random forest classification model to classify subjects to either EL producers or not using three characteristic bacteria. In conclusion, our analysis revealed the composition of gut microbiome that is associated with lignan metabolism. We also confirmed that it can be used to classify the microbiome ability to metabolize lignan using machine learning approach.},
}
@article {pmid36363755,
year = {2022},
author = {Esposito, P and Ismail, N},
title = {Linking Puberty and the Gut Microbiome to the Pathogenesis of Neurodegenerative Disorders.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/microorganisms10112163},
pmid = {36363755},
issn = {2076-2607},
support = {2020-04302//Natural Sciences and Engineering Research Council/ ; },
abstract = {Puberty is a critical period of development marked by the maturation of the central nervous system, immune system, and hypothalamic-pituitary-adrenal axis. Due to the maturation of these fundamental systems, this is a period of development that is particularly sensitive to stressors, increasing susceptibility to neurodevelopmental and neurodegenerative disorders later in life. The gut microbiome plays a critical role in the regulation of stress and immune responses, and gut dysbiosis has been implicated in the development of neurodevelopmental and neurodegenerative disorders. The purpose of this review is to summarize the current knowledge about puberty, neurodegeneration, and the gut microbiome. We also examine the consequences of pubertal exposure to stress and gut dysbiosis on the development of neurodevelopmental and neurodegenerative disorders. Understanding how alterations to the gut microbiome, particularly during critical periods of development (i.e., puberty), influence the pathogenesis of these disorders may allow for the development of therapeutic strategies to prevent them.},
}
@article {pmid36363749,
year = {2022},
author = {Castro-Mejía, JL and Khakimov, B and Aru, V and Lind, MV and Garne, E and Paulová, P and Tavakkoli, E and Hansen, LH and Smilde, AK and Holm, L and Engelsen, SB and Nielsen, DS},
title = {Gut Microbiome and Its Cofactors Are Linked to Lipoprotein Distribution Profiles.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/microorganisms10112156},
pmid = {36363749},
issn = {2076-2607},
support = {4105-00015B//Innovation Fund Denmark/ ; },
abstract = {Increasing evidence indicates that the gut microbiome (GM) plays an important role in dyslipidemia. To date, however, no in-depth characterization of the associations between GM with lipoproteins distributions (LPD) among adult individuals with diverse BMI has been conducted. To determine such associations, we studied blood-plasma LPD, fecal short-chain fatty acids (SCFA) and GM of 262 Danes aged 19-89 years. Stratification of LPD segregated subjects into three clusters displaying recommended levels of lipoproteins and explained by age and body-mass-index. Higher levels of HDL2a and HDL2b were associated with a higher abundance of Ruminococcaceae and Christensenellaceae. Increasing levels of total cholesterol and LDL-1 and LDL-2 were positively associated with Lachnospiraceae and Coriobacteriaceae, and negatively with Bacteroidaceae and Bifidobacteriaceae. Metagenome-sequencing showed a higher abundance of biosynthesis of multiple B-vitamins and SCFA metabolism genes among healthier LPD profiles. Metagenomic-assembled genomes (MAGs) affiliated to Eggerthellaceae and Clostridiales were contributors of these genes and their relative abundance correlated positively with larger HDL subfractions. The study demonstrates that differences in composition and metabolic traits of the GM are associated with variations in LPD among the recruited subjects. These findings provide evidence for GM considerations in future research aiming to shed light on mechanisms of the GM-dyslipidemia axis.},
}
@article {pmid36363740,
year = {2022},
author = {Sun, L and Dong, X and Wang, Y and Maker, G and Agarwal, M and Ding, Z},
title = {Tea-Soybean Intercropping Improves Tea Quality and Nutrition Uptake by Inducing Changes of Rhizosphere Bacterial Communities.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/microorganisms10112149},
pmid = {36363740},
issn = {2076-2607},
support = {SD2019ZZ010//the Significant Application Project of Agriculture Technology Innovation in Shandong Province/ ; SDAIT-19-01//the Technology System of Modern Agricultural Industry in Shandong Province/ ; No.ts201712057//the Special Foundation for Distinguished Taishan Scholars of Shandong Province/ ; 19-6-1-64-nsh//the Livelihood Project of Qingdao City/ ; 2019LY002, 2019YQ010, 2019TSLH0802//the Project of Agricultural Science and Technology Fund in Shandong Province/ ; },
abstract = {The positive aspects of the tea plant/legume intercropping system draw attention to the Chinese tea industry for its benefit for soil fertility improvement with low fertilizer input. However, limited information exists as to the roles of intercropped legumes in the rhizosphere microbiome and tea quality. Hereby, soybean was selected as the intercropped plant to investigate its effect on bacterial communities, nutrient competition, tea plant development, and tea quality. Our data showed that intercropped soybean boosted the uptake of nitrogen in tea plants and enhanced the growth of young tea shoots. Nutrient competition for phosphorus and potassium in soil existed between soybeans and tea plants. Moreover, tea/soybean intercropping improved tea quality, manifested by a significantly increased content of non-ester type catechins (C, EGC, EC), total catechins and theanine, and decreased content of ester type catechins (EGCG). Significant differences in rhizobacterial composition were also observed under different systems. At the genus level, the relative abundance of beneficial bacteria, such as Bradyrhizobium, Saccharimonadales and Mycobacterium, was significantly increased with the intercropping system, while the relative abundance of denitrifying bacteria, Pseudogulbenkiania, was markedly decreased. Correlation analysis showed that Pseudogulbenkiania, SBR1031, and Burkholderiaceae clustered together showing a similar correlation with soil physicochemical and tea quality characteristics; however, other differential bacteria showed the opposite pattern. In conclusion, tea/soybean intercropping improves tea quality and nutrition uptake by increasing the relative abundance of beneficial rhizosphere bacteria and decreasing denitrifying bacteria. This study strengthens our understanding of how intercropping system regulate the soil bacterial community to maintain the health of soils in tea plantations and provides the basis for replacing chemical fertilizers and improving the ecosystem in tea plantations.},
}
@article {pmid36363738,
year = {2022},
author = {Zhou, B and Mobberley, J and Shi, K and Chen, IA},
title = {Effects of Preservation and Propagation Methodology on Microcosms Derived from the Oral Microbiome.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/microorganisms10112146},
pmid = {36363738},
issn = {2076-2607},
support = {DP2GM123457/NH/NIH HHS/United States ; Teacher-Scholar Awards Program//Camille and Henry Dreyfus Foundation/ ; SSP//Searle Scholars Program/ ; },
abstract = {The creation of oral microcosms with reproducible composition is important for developing model systems of the oral microbiome. However, oral microbiomes vary substantially across individuals. To derive a reproducible composition from inocula sourced from different individuals, we tested whether selective conditions from cold storage and culturing in defined media would generate a reproducible community composition despite individual variations. In this pilot study, we collected dental plaque scrapings from three individuals, inoculated media under anaerobic conditions, and characterized the bacterial community compositions after cold storage and subsequent propagation in liquid media. Harvested cultures were extracted and bacterial composition was determined by 16S rRNA gene amplicon sequencing and the mothur pipeline. Our results show that samples from two out of three individuals clustered into a specific compositional type (termed "attractor" here). In addition, the samples from the third individual could adopt this attractor compositional type after propagation in vitro, even though its original composition did not display this type. These results indicate that simple selective environments could help create reproducible microcosms despite variation among dental plaque samples sourced from different individuals. The findings illustrate important parameters to consider for creating reproducible microcosms from the human oral microbiome.},
}
@article {pmid36363728,
year = {2022},
author = {Wenger, NM and Qiao, L and Nicola, T and Nizami, Z and Xu, X and Willis, KA and Ambalavanan, N and Gaggar, A and Lal, CV},
title = {Efficacy of a Probiotic and Herbal Supplement in Models of Lung Inflammation.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/microorganisms10112136},
pmid = {36363728},
issn = {2076-2607},
support = {K08 HL141652 (CVL)//National Institute of Health/ ; NA//ResBiotic Nutrition, Inc./ ; },
abstract = {BACKGROUND: Gut microbiome dysbiosis is associated with lung disease through the gut-lung axis. Abundant proteobacteria increase MMP-9 and contribute to tissue proteolysis followed by neutrophil recruitment, lung tissue injury, and perpetuation of chronic lung disease. We sought to determine if a scientifically formulated probiotic and herbal supplement could attenuate neutrophilic inflammation and improve lung structure and function in models of lung inflammation.<br><br>METHODS: For in vitro experiments, epithelial cells exposed to proteobacteria were treated with resB-a blend of three probiotic Lactobacillus strains and turmeric, holy basil, and vasaka herbal extracts. For in vivo experimentation, mice exposed to pulmonary proteobacteria-derived lipopolysaccharide were treated by gavage with resB.<br><br>RESULTS: In vitro, the bacterial and herbal components of resB decreased activity of the MMP-9 pathway. Mice exposed to LPS and pre- and post-treated with resB had decreased neutrophil recruitment and inflammatory biomarkers in bronchoalveolar lavage fluid, serum, and lung tissue compared to untreated mice.<br><br>CONCLUSIONS: This study describes the mechanisms and efficacy of probiotic and herbal blend in pre-clinical models of lung injury and inflammation.},
}
@article {pmid36363713,
year = {2022},
author = {Hurtado-McCormick, V and Trevathan-Tackett, SM and Bowen, JL and Connolly, RM and Duarte, CM and Macreadie, PI},
title = {Pathways for Understanding Blue Carbon Microbiomes with Amplicon Sequencing.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/microorganisms10112121},
pmid = {36363713},
issn = {2076-2607},
support = {DP200100575//Australian Research Council/ ; DE210101029//Australian Research Council/ ; DEB2203322//National Science Foundation/ ; },
abstract = {The capacity of Blue Carbon Ecosystems to act as carbon sinks is strongly influenced by the metabolism of soil-associated microbes, which ultimately determine how much carbon is accumulated or returned to the atmosphere. The rapid evolution of sequencing technologies has facilitated the generation of tremendous amounts of data on what taxa comprise belowground microbial assemblages, largely available as isolated datasets, offering an opportunity for synthesis research that informs progress on understanding Blue Carbon microbiomes. We identified questions that can be addressed with a synthesis approach, including the high variability across datasets, space, and time due to differing sampling techniques, ecosystem or vegetation specificity, and the relationship between microbiome community and edaphic properties, particularly soil carbon. To address these questions, we collated 34 16S rRNA amplicon sequencing datasets, including bulk soil or rhizosphere from seagrass, mangroves, and saltmarshes within publicly available repositories. We identified technical and theoretical challenges that precluded a synthesis of multiple studies with currently available data, and opportunities for addressing the knowledge gaps within Blue Carbon microbial ecology going forward. Here, we provide a standardisation toolbox that supports enacting tasks for the acquisition, management, and integration of Blue Carbon-associated sequencing data and metadata to potentially elucidate novel mechanisms behind Blue Carbon dynamics.},
}
@article {pmid36363699,
year = {2022},
author = {Song, H and Kim, WS and Park, JW and Kwak, IS},
title = {Identification of Bacterial Communities in Laboratory-Adapted Glyptotendipes tokunagai and Wild-Stream-Inhabiting Chironomus flaviplumus.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/microorganisms10112107},
pmid = {36363699},
issn = {2076-2607},
support = {NRF2020R1A2C1013936//National Research Foundation of Korea/ ; NRF-2018R1A6A1A03024314//National Research Foundation of Korea/ ; NRF-2016R1A6A1A03012862//National Research Foundation of Korea/ ; },
abstract = {Chironomidae (chironomid) are one of the dominant families in freshwater ecosystems, and they plays an important role in the food web. They have been used as an indicator for water quality assessment, as they are resistant to diverse environmental pollutants. In this study, we identified the microbiomes of two chironomid species to see if there are any endogenous bacterial groups which could contribute to the host survival. The studied species are Glyptotendipes tokunagai, a model species cultivated in a laboratory-controlled environment, and Chironomus flaviplumus captured in a field stream in Yeosu, Korea. DNAs were extracted from the whole body of the individual species, and the 16S rRNA gene was amplified. The amplified products were sequenced using an Illumina MiSeq platform. The microbiomes of G. tokunagai were homogeneous, having 20% of the core amplicon sequence variants overlapping between replicates sampled from different water tanks. In contrast, none of the core amplicon sequence variants overlapped in C.flaviplumus. In both chironomid groups, potential symbionts were identified. Dysgonomonas, which can degrade complex carbon sources, was found in more than half of the total microbiomes of G. tokunagai. Tyzzerella and Dechloromonas, which have been suggested to detoxify environmental pollutants, were identified in the microbiome of C.flaviplumus. This study can help elucidate the life strategies of chironomids in polluted or organic-rich environments.},
}
@article {pmid36363684,
year = {2022},
author = {Sarkar, S and Magne, F and Venugopal, G and Purkait, S and Mutha, NVR and Maiti, R and Sharma, P and Ramadass, B},
title = {Altered Nasal Microbiome in Atrophic Rhinitis: A Novel Theory of Etiopathogenesis and Therapy.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/microorganisms10112092},
pmid = {36363684},
issn = {2076-2607},
support = {T/IM-F/17-18/18//All India Institute of Medical Sciences Bhubaneswar/ ; },
abstract = {BACKGROUND: Atrophic rhinitis (AtR) is a chronic nasal condition with polygenic and polybacterial etiology. We investigated the clinical outcomes of honey therapy and the associated nasal microbiome in AtR.<br><br>METHODS: For eight weeks, a nonrandomized control trial using a nasal spray of 10% manuka honey and saline on the right and left sides of the nose was conducted on 19 primary AtR patients. A nasal endoscopy was performed and a mucosal biopsy were taken before and after the intervention. Five of the nineteen patients were selected for microbiome and GPR43 expression studies.<br><br>RESULTS: We used manuka honey to describe an effective prebiotic treatment for atrophic rhinitis. There were nine males and ten females with an average (±SD) age of 33.8 (±10.7) years. Endoscopic scores and clinical symptoms improved in honey-treated nasal cavities (p < 0.003). There was a significant decrease in inflammation, restoration of mucus glands, and increased expression of GPR43 in the nasal cavities with honey therapy. The nasal microbiome composition before and after treatment was documented. Particularly, short chain fatty acid (SCFA) producers were positively enriched after honey therapy and correlated with improved clinical outcomes like nasal crusting, congestion, and discharge.<br><br>CONCLUSION: Our approach to treating AtR patients with manuka honey illustrated effective clinical outcomes such as (1) decreased fetid smell, (2) thickening of the mucosa, (3) decreased inflammation with healed mucosal ulcers, (4) increased concentration of the mucosal glands, (5) altered nasal microbiome, and (6) increased expression of SCFA receptors. These changes are consequent to resetting the nasal microbiome due to honey therapy.},
}
@article {pmid36362427,
year = {2022},
author = {Shi, H and Lu, L and Ye, J and Shi, L},
title = {Effects of Two Bacillus Velezensis Microbial Inoculants on the Growth and Rhizosphere Soil Environment of Prunus davidiana.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232113639},
pmid = {36362427},
issn = {1422-0067},
support = {G191208//the Research and Application of Microbial Fertilizer of Shanghai Landscaping and Appearance of the City Management Bureau/ ; 22N51900400//Shanghai Science and Technology Plan Project/ ; },
mesh = {Rhizosphere ; *Agricultural Inoculants ; Soil ; Soil Microbiology ; *Prunus ; Plant Roots ; Bacteria ; Plants ; },
abstract = {Microbial inoculants, as harmless, efficient, and environmentally friendly plant growth promoters and soil conditioners, are attracting increasing attention. In this study, the effects of Bacillus velezensis YH-18 and B. velezensis YH-20 on Prunus davidiana growth and rhizosphere soil bacterial community in continuously cropped soil were investigated by inoculation tests. The results showed that in a pot seedling experiment, inoculation with YH-18 and YH-20 resulted in a certain degree of increase in diameter growth, plant height, and leaf area at different time periods of 180 days compared with the control. Moreover, after 30 and 90 days of inoculation, the available nutrients in the soil were effectively improved, which protected the continuously cropped soil from acidification. In addition, high-throughput sequencing showed that inoculation with microbial inoculants effectively slowed the decrease in soil microbial richness and diversity over a one-month period. At the phylum level, Proteobacteria and Bacteroidetes were significantly enriched on the 30th day. At the genus level, Sphingomonas and Pseudomonas were significantly enriched at 15 and 30 days, respectively. These bacterial phyla and genera can effectively improve the soil nutrient utilization rate, antagonize plant pathogenic bacteria, and benefit the growth of plants. Furthermore, inoculation with YH-18 and inoculation with YH-20 resulted in similar changes in the rhizosphere microbiome. This study provides a basis for the short-term effect of microbial inoculants on the P. davidiana rhizosphere microbiome and has application value for promoting the cultivation and production of high-quality fruit trees.},
}
@article {pmid36362334,
year = {2022},
author = {Krawczyk, K and Szabelska-Beręsewicz, A and Przemieniecki, SW and Szymańczyk, M and Obrępalska-Stęplowska, A},
title = {Insect Gut Bacteria Promoting the Growth of Tomato Plants (Solanum lycopersicum L.).},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232113548},
pmid = {36362334},
issn = {1422-0067},
support = {UMO-2016/23/B/NZ9/03503//Polish National Science Centre/ ; },
mesh = {Animals ; *Lycopersicon esculentum/microbiology ; *Coleoptera ; Insecta ; Zea mays ; *Pseudomonas putida ; },
abstract = {We investigated gut bacteria from three insect species for the presence of plant growth properties (PGP). Out of 146 bacterial strains obtained from 20 adult specimens of Scolytidae sp., 50 specimens of Oulema melanopus, and 150 specimens of Diabrotica virgifera, we selected 11 strains displaying the following: PGP, phosphate solubility, production of cellulase, siderophore, lipase, protease, and hydrogen cyanide. The strains were tested for growth promotion ability on tomato (Lycopersicon&amp;nbsp;esculentum) plants. Each strain was tested individually, and all strains were tested together as a bacterial consortium. Tomato fruit yield was compared with the negative control. The plants treated with bacterial consortium showed a significant increase in fruit yield, in both number of fruits (+41%) and weight of fruits (+44%). The second highest yield was obtained for treatment with Serratia&amp;nbsp;liquefaciens Dv032 strain, where the number and weight of yielded fruits increased by 35% and 30%, respectively. All selected 11 strains were obtained from Western Corn Rootworm (WCR), Diabrotica virgifera. The consortium comprised: Ewingella americana, Lactococcus garvieae, L. lactis, Pseudomonas putida, Serratia liquefaciens, and S. plymuthica. To our knowledge, this is the first successful application of D. virgifera gut bacteria for tomato plant growth stimulation that has been described.},
}
@article {pmid36362265,
year = {2022},
author = {Nirmalkar, K and Qureshi, F and Kang, DW and Hahn, J and Adams, JB and Krajmalnik-Brown, R},
title = {Shotgun Metagenomics Study Suggests Alteration in Sulfur Metabolism and Oxidative Stress in Children with Autism and Improvement after Microbiota Transfer Therapy.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232113481},
pmid = {36362265},
issn = {1422-0067},
support = {GR37996//Finch Therapuetics, MA, USA and Arizona Board of regents/ ; },
mesh = {Child ; Humans ; *Autistic Disorder ; RNA, Ribosomal, 16S/genetics/metabolism ; *Autism Spectrum Disorder/genetics/therapy/metabolism ; *Microbiota ; Metagenomics ; Oxidative Stress ; Sulfur ; },
abstract = {Links between gut microbiota and autism spectrum disorder (ASD) have been explored in many studies using 16S rRNA gene amplicon and shotgun sequencing. Based on these links, microbiome therapies have been proposed to improve gastrointestinal (GI) and ASD symptoms in ASD individuals. Previously, our open-label microbiota transfer therapy (MTT) study provided insight into the changes in the gut microbial community of children with ASD after MTT and showed significant and long-term improvement in ASD and GI symptoms. Using samples from the same study, the objective of this work was to perform a deeper taxonomic and functional analysis applying shotgun metagenomic sequencing. Taxonomic analyses revealed that ASD Baseline had many bacteria at lower relative abundances, and their abundance increased after MTT. The relative abundance of fiber consuming and beneficial microbes including Prevotella (P. dentalis, P. enoeca, P. oris, P. meloninogenica), Bifidobacterium bifidum, and a sulfur reducer Desulfovibrio piger increased after MTT-10wks in children with ASD compared to Baseline (consistent at genus level with the previous 16S rRNA gene study). Metabolic pathway analysis at Baseline compared to typically developing (TD) children found an altered abundance of many functional genes but, after MTT, they became similar to TD or donors. Important functional genes that changed included: genes encoding enzymes involved in folate biosynthesis, sulfur metabolism and oxidative stress. These results show that MTT treatment not only changed the relative abundance of important genes involved in metabolic pathways, but also seemed to bring them to a similar level to the TD controls. However, at a two-year follow-up, the microbiota and microbial genes shifted into a new state, distinct from their levels at Baseline and distinct from the TD group. Our current findings suggest that microbes from MTT lead to initial improvement in the metabolic profile of children with ASD, and major additional changes at two years post-treatment. In the future, larger cohort studies, mechanistic in vitro experiments and metatranscriptomics studies are recommended to better understand the role of these specific microbes, functional gene expression, and metabolites relevant to ASD.},
}
@article {pmid36362236,
year = {2022},
author = {Sawicka-Gutaj, N and Gruszczyński, D and Zawalna, N and Nijakowski, K and Muller, I and Karpiński, T and Salvi, M and Ruchała, M},
title = {Microbiota Alterations in Patients with Autoimmune Thyroid Diseases: A Systematic Review.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232113450},
pmid = {36362236},
issn = {1422-0067},
mesh = {Humans ; *Hashimoto Disease/pathology ; *Graves Disease ; *Autoimmune Diseases ; *Microbiota ; },
abstract = {Autoimmune thyroid diseases (AITDs) are chronic autoimmune disorders that cause impaired immunoregulation, leading to specific immune responses against thyroid antigens. Graves' disease (GD) and Hashimoto's thyroiditis (HT) are the major forms of AITDs. Increasing evidence suggests a possible role of microbiota alterations in the pathogenesis and progression of AITDs. This systematic review was designed to address the following question: "Is microbiota altered in patients with AITDs?" After screening the selected studies using the inclusion and exclusion criteria, 16 studies were included in this review (in accordance with PRISMA statement guidelines). A meta-analysis revealed that patients with HT showed significantly higher values of diversity indices (except for the Simpson index) and that patients with GD showed significant tendencies toward lower values of all assessed indices compared with healthy subjects. However, the latter demonstrated a higher relative abundance of Bacteroidetes and Actinobacteria at the phylum level and thus Prevotella and Bifidobacterium at the genus level, respectively. Thyroid peroxidase antibodies showed the most significant positive and negative correlations between bacterial levels and thyroid functional parameters. In conclusion, significant alterations in the diversity and composition of the intestinal microbiota were observed in both GD and HT patients.},
}
@article {pmid36362150,
year = {2022},
author = {Sterling, KG and Dodd, GK and Alhamdi, S and Asimenios, PG and Dagda, RK and De Meirleir, KL and Hudig, D and Lombardi, VC},
title = {Mucosal Immunity and the Gut-Microbiota-Brain-Axis in Neuroimmune Disease.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232113328},
pmid = {36362150},
issn = {1422-0067},
support = {N/A//C.E. Hudig UNR Foundation Award for Undergraduate Research/ ; U54 GM104944/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Immunity, Mucosal ; *Gastrointestinal Microbiome/physiology ; *Enteric Nervous System/physiology ; *Parkinson Disease ; Brain/physiology ; },
abstract = {Recent advances in next-generation sequencing (NGS) technologies have opened the door to a wellspring of information regarding the composition of the gut microbiota. Leveraging NGS technology, early metagenomic studies revealed that several diseases, such as Alzheimer's disease, Parkinson's disease, autism, and myalgic encephalomyelitis, are characterized by alterations in the diversity of gut-associated microbes. More recently, interest has shifted toward understanding how these microbes impact their host, with a special emphasis on their interactions with the brain. Such interactions typically occur either systemically, through the production of small molecules in the gut that are released into circulation, or through signaling via the vagus nerves which directly connect the enteric nervous system to the central nervous system. Collectively, this system of communication is now commonly referred to as the gut-microbiota-brain axis. While equally important, little attention has focused on the causes of the alterations in the composition of gut microbiota. Although several factors can contribute, mucosal immunity plays a significant role in shaping the microbiota in both healthy individuals and in association with several diseases. The purpose of this review is to provide a brief overview of the components of mucosal immunity that impact the gut microbiota and then discuss how altered immunological conditions may shape the gut microbiota and consequently affect neuroimmune diseases, using a select group of common neuroimmune diseases as examples.},
}
@article {pmid36362106,
year = {2022},
author = {Piccioni, A and Rosa, F and Manca, F and Pignataro, G and Zanza, C and Savioli, G and Covino, M and Ojetti, V and Gasbarrini, A and Franceschi, F and Candelli, M},
title = {Gut Microbiota and Clostridium difficile: What We Know and the New Frontiers.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232113323},
pmid = {36362106},
issn = {1422-0067},
mesh = {Humans ; *Clostridioides difficile ; *Gastrointestinal Microbiome/physiology ; *Enterocolitis, Pseudomembranous/microbiology ; *Clostridium Infections/microbiology ; *Microbiota ; },
abstract = {Our digestive system, particularly our intestines, harbors a vast amount of microorganisms, whose genetic makeup is referred to as the microbiome. Clostridium difficile is a spore-forming Gram-positive bacterium, which can cause an infection whose symptoms range from asymptomatic colonization to fearsome complications such as the onset of toxic megacolon. The relationship between gut microbiota and Clostridium difficile infection has been studied from different perspectives. One of the proposed strategies is to be able to specifically identify which types of microbiota alterations are most at risk for the onset of CDI. In this article, we understood once again how crucial the role of the human microbiota is in health and especially how crucial it becomes, in the case of its alteration, for the individual's disease. Clostridium difficile infection is an emblematic example of how a normal and physiological composition of the human microbiome can play a very important role in immune defense against such a fearsome disease.},
}
@article {pmid36362056,
year = {2022},
author = {Ustianowska, K and Ustianowski, Ł and Machaj, F and Gorący, A and Rosik, J and Szostak, B and Szostak, J and Pawlik, A},
title = {The Role of the Human Microbiome in the Pathogenesis of Pain.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232113267},
pmid = {36362056},
issn = {1422-0067},
mesh = {Female ; Humans ; *Visceral Pain/pathology ; Brain/pathology ; Dysbiosis/pathology ; *Microbiota ; *Gastrointestinal Microbiome/physiology ; *Probiotics ; *Chronic Pain ; },
abstract = {Understanding of the gut microbiome's role in human physiology developed rapidly in recent years. Moreover, any alteration of this microenvironment could lead to a pathophysiological reaction of numerous organs. It results from the bidirectional communication of the gastrointestinal tract with the central nervous system, called the gut-brain axis. The signals in the gut-brain axis are mediated by immunological, hormonal, and neural pathways. However, it is also influenced by microorganisms in the gut. The disturbances in the gut-brain axis are associated with gastrointestinal syndromes, but recently their role in the development of different types of pain was reported. The gut microbiome could be the factor in the central sensitization of chronic pain by regulating microglia, astrocytes, and immune cells. Dysbiosis could lead to incorrect immune responses, resulting in the development of inflammatory pain such as endometriosis. Furthermore, chronic visceral pain, associated with functional gastrointestinal disorders, could result from a disruption in the gut microenvironment. Any alteration in the gut-brain axis could also trigger migraine attacks by affecting cytokine expression. Understanding the gut microbiome's role in pain pathophysiology leads to the development of analgetic therapies targeting microorganisms. Probiotics, FODMAP diet, and fecal microbiota transplantation are reported to be beneficial in treating visceral pain.},
}
@article {pmid36362038,
year = {2022},
author = {Chakladar, J and John, D and Magesh, S and Uzelac, M and Li, WT and Dereschuk, K and Apostol, L and Brumund, KT and Rodriguez, JW and Ongkeko, WM},
title = {The Intratumor Bacterial and Fungal Microbiome Is Characterized by HPV, Smoking, and Alcohol Consumption in Head and Neck Squamous Cell Carcinoma.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232113250},
pmid = {36362038},
issn = {1422-0067},
support = {RG096651//University of California, San Diego/ ; },
mesh = {Humans ; Squamous Cell Carcinoma of Head and Neck/complications ; *Papillomavirus Infections ; Papillomaviridae/genetics ; *Head and Neck Neoplasms/complications ; *Mycobiome ; Smoking/adverse effects ; Alcohol Drinking/adverse effects ; },
abstract = {Head and neck squamous cell carcinoma (HNSCC) tumor phenotypes and clinical outcomes are significantly influenced by etiological agents, such as HPV infection, smoking, and alcohol consumption. Accordingly, the intratumor microbiome has been increasingly implicated in cancer progression and metastasis. However, few studies characterize the intratumor microbial landscape of HNSCC with respect to these etiological agents. In this study, we aimed to investigate the bacterial and fungal landscape of HNSCC in association with HPV infection, smoking, and alcohol consumption. RNA-sequencing data were extracted from The Cancer Genome Atlas (TCGA) regarding 449 tissue samples and 44 normal samples. Pathoscope 2.0 was used to extract the microbial reads. Microbe abundance was compared to clinical variables, oncogenic signatures, and immune-associated pathways. Our results demonstrated that a similar number of dysregulated microbes was overabundant in smokers and nonsmokers, while heavy drinkers were characterized by an underabundance of dysregulated microbes. Conversely, the majority of dysregulated microbes were overabundant in HPV+ tumor samples when compared to HPV- tumor samples. Moreover, we observed that many dysregulated microbes were associated with oncogenic and metastatic pathways, suggesting their roles in influencing carcinogenesis. These microbes provide insights regarding potential mechanisms for tumor pathogenesis and progression with respect to the three etiological agents.},
}
@article {pmid36361976,
year = {2022},
author = {Zeng, X and Liu, Z and Dong, Y and Zhao, J and Wang, B and Xiao, H and Li, Y and Chen, Z and Liu, X and Liu, J and Dong, J and Fan, S and Cui, M},
title = {Social Hierarchy Dictates Intestinal Radiation Injury in a Gut Microbiota-Dependent Manner.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232113189},
pmid = {36361976},
issn = {1422-0067},
support = {20JCJQJC00100//Science Foundation for Distinguished Young Scholars of Tianjin/ ; CIFMS, 2021-I2M-1-060//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-042//CAMS Innovation Fund for Medical Sciences/ ; },
mesh = {Mice ; Animals ; *Gastrointestinal Microbiome/physiology ; Hierarchy, Social ; *Probiotics/pharmacology ; Verrucomicrobia/physiology ; *Radiation Injuries ; Mice, Inbred C57BL ; },
abstract = {Social hierarchy governs the physiological and biochemical behaviors of animals. Intestinal radiation injuries are common complications connected with radiotherapy. However, it remains unclear whether social hierarchy impacts the development of radiation-induced intestinal toxicity. Dominant mice exhibited more serious intestinal toxicity following total abdominal irradiation compared with their subordinate counterparts, as judged by higher inflammatory status and lower epithelial integrity. Radiation-elicited changes in gut microbiota varied between dominant and subordinate mice, being more overt in mice of higher status. Deletion of gut microbes by using an antibiotic cocktail or restructuring of the gut microecology of dominant mice by using fecal microbiome from their subordinate companions erased the difference in radiogenic intestinal injuries. Lactobacillus murinus and Akkermansia&amp;nbsp;muciniphila were both found to be potential probiotics for use against radiation toxicity in mouse models without social hierarchy. However, only Akkermansia muciniphila showed stable colonization in the digestive tracts of dominant mice, and significantly mitigated their intestinal radiation injuries. Our findings demonstrate that social hierarchy impacts the development of radiation-induced intestinal injuries, in a manner dependent on gut microbiota. The results also suggest that the gut microhabitats of hosts determine the colonization and efficacy of foreign probiotics. Thus, screening suitable microbial preparations based on the gut microecology of patients might be necessary in clinical application.},
}
@article {pmid36361857,
year = {2022},
author = {Lee, HJ and Kim, M},
title = {Skin Barrier Function and the Microbiome.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232113071},
pmid = {36361857},
issn = {1422-0067},
mesh = {Humans ; *Microbiota ; *Dermatitis, Atopic ; Skin ; *Psoriasis/genetics ; Dysbiosis ; },
abstract = {Human skin is the largest organ and serves as the first line of defense against environmental factors. The human microbiota is defined as the total microbial community that coexists in the human body, while the microbiome refers to the collective genome of these microorganisms. Skin microbes do not simply reside on the skin but interact with the skin in a variety of ways, significantly affecting the skin barrier function. Here, we discuss recent insights into the symbiotic relationships between the microbiome and the skin barrier in physical, chemical, and innate/adaptive immunological ways. We discuss the gut-skin axis that affects skin barrier function. Finally, we examine the effects of microbiome dysbiosis on skin barrier function and the role of these effects in inflammatory skin diseases, such as acne, atopic dermatitis, and psoriasis. Microbiome cosmetics can help restore skin barrier function and improve these diseases.},
}
@article {pmid36361844,
year = {2022},
author = {Kiruba N, JM and Saeid, A},
title = {An Insight into Microbial Inoculants for Bioconversion of Waste Biomass into Sustainable "Bio-Organic" Fertilizers: A Bibliometric Analysis and Systematic Literature Review.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232113049},
pmid = {36361844},
issn = {1422-0067},
mesh = {Fertilizers/analysis ; Biomass ; *Agricultural Inoculants ; Food ; *Refuse Disposal ; Sewage/microbiology ; Bibliometrics ; Soil ; },
abstract = {The plant-microbe holobiont has garnered considerable attention in recent years, highlighting its importance as an ecological unit. Similarly, manipulation of the microbial entities involved in the rhizospheric microbiome for sustainable agriculture has also been in the limelight, generating several commercial bioformulations to enhance crop yield and pest resistance. These bioformulations were termed biofertilizers, with the consistent existence and evolution of different types. However, an emerging area of interest has recently focused on the application of these microorganisms for waste valorization and the production of "bio-organic" fertilizers as a result. In this study, we performed a bibliometric analysis and systematic review of the literature retrieved from Scopus and Web of Science to determine the type of microbial inoculants used for the bioconversion of waste into "bio-organic" fertilizers. The Bacillus, Acidothiobacillus species, cyanobacterial biomass species, Aspergillus sp. and Trichoderma sp. were identified to be consistently used for the recovery of nutrients and bioconversion of wastes used for the promotion of plant growth. Cyanobacterial strains were used predominantly for wastewater treatment, while Bacillus, Acidothiobacillus, and Aspergillus were used on a wide variety of wastes such as sawdust, agricultural waste, poultry bone meal, crustacean shell waste, food waste, and wastewater treatment plant (WWTP) sewage sludge ash. Several bioconversion strategies were observed such as submerged fermentation, solid-state fermentation, aerobic composting, granulation with microbiological activation, and biodegradation. Diverse groups of microorganisms (bacteria and fungi) with different enzymatic functionalities such as chitinolysis, lignocellulolytic, and proteolysis, in addition to their plant growth promoting properties being explored as a consortium for application as an inoculum waste bioconversion to fertilizers. Combining the efficiency of such functional and compatible microbial species for efficient bioconversion as well as higher plant growth and crop yield is an enticing opportunity for "bio-organic" fertilizer research.},
}
@article {pmid36361763,
year = {2022},
author = {Mahalak, KK and Firrman, J and Bobokalonov, J and Narrowe, AB and Bittinger, K and Daniel, S and Tanes, C and Mattei, LM and Zeng, WB and Soares, JW and Kobori, M and Lemons, JMS and Tomasula, PM and Liu, L},
title = {Persistence of the Probiotic Lacticaseibacillus rhamnosus Strain GG (LGG) in an In Vitro Model of the Gut Microbiome.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232112973},
pmid = {36361763},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Lactobacillus rhamnosus ; *Probiotics ; Fatty Acids, Volatile ; },
abstract = {The consumption of probiotics is widely encouraged due to reports of their positive effects on human health. In particular, Lacticaseibacillus rhamnosus strain GG (LGG) is an approved probiotic that has been reported to improve health outcomes, especially for gastrointestinal disorders. However, how LGG cooperates with the gut microbiome has not been fully explored. To understand the interaction between LGG and its ability to survive and grow within the gut microbiome, this study introduced LGG into established microbial communities using an in vitro model of the colon. LGG was inoculated into the simulated ascending colon and its persistence in, and transit through the subsequent transverse and descending colon regions was monitored over two weeks. The impact of LGG on the existing bacterial communities was investigated using 16S rRNA sequencing and short-chain fatty acid analysis. LGG was able to engraft and proliferate in the ascending region for at least 10 days but was diminished in the transverse and descending colon regions with little effect on short-chain fatty acid abundance. These data suggest that the health benefits of the probiotic LGG rely on its ability to transiently engraft and modulate the host microbial community.},
}
@article {pmid36361736,
year = {2022},
author = {Graindorge, S and Villette, C and Koechler, S and Groh, C and Comtet-Marre, S and Mercier, P and Magerand, R and Peyret, P and Heintz, D and Schaller, H and Arsène-Ploetze, F},
title = {The Arabidopsis thaliana-Streptomyces Interaction Is Controlled by the Metabolic Status of the Holobiont.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232112952},
pmid = {36361736},
issn = {1422-0067},
support = {Projet International de Cooperation Scientifique//French National Centre for Scientific Research/ ; },
mesh = {*Arabidopsis/metabolism ; *Streptomyces/metabolism ; Plant Diseases/genetics/microbiology ; Pseudomonas syringae/metabolism ; *Arabidopsis Proteins/metabolism ; },
abstract = {How specific interactions between plant and pathogenic, commensal, or mutualistic microorganisms are mediated and how bacteria are selected by a plant are important questions to address. Here, an Arabidopsis thaliana mutant called chs5 partially deficient in the biogenesis of isoprenoid precursors was shown to extend its metabolic remodeling to phenylpropanoids and lipids in addition to carotenoids, chlorophylls, and terpenoids. Such a metabolic profile was concomitant to increased colonization of the phyllosphere by the pathogenic strain Pseudomonas syringae pv. tomato DC3000. A thorough microbiome analysis by 16S sequencing revealed that Streptomyces had a reduced colonization potential in chs5. This study revealed that the bacteria-Arabidopsis interaction implies molecular processes impaired in the chs5 mutant. Interestingly, our results revealed that the metabolic status of A. thaliana was crucial for the specific recruitment of Streptomyces into the microbiota. More generally, this study highlights specific as well as complex molecular interactions that shape the plant microbiota.},
}
@article {pmid36361709,
year = {2022},
author = {Torres-Sánchez, A and Ruiz-Rodríguez, A and Ortiz, P and Moreno, MA and Ampatzoglou, A and Gruszecka-Kosowska, A and Monteoliva-Sánchez, M and Aguilera, M},
title = {Exploring Next Generation Probiotics for Metabolic and Microbiota Dysbiosis Linked to Xenobiotic Exposure: Holistic Approach.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232112917},
pmid = {36361709},
issn = {1422-0067},
support = {PI20/01278//Instituto de Salud Carlos III/ ; IE_2019-198//FEDER Project Infrastructure/ ; },
mesh = {Animals ; Humans ; Dysbiosis/therapy ; Xenobiotics ; *Probiotics/therapeutic use ; *Microbiota ; *Gastrointestinal Microbiome ; },
abstract = {Variation of gut microbiota in metabolic diseases seems to be related to dysbiosis induced by exposure to multiple substances called Microbiota Disrupting Chemicals (MDCs), which are present as environmental and dietary contaminants. Some recent studies have focused on elucidating the alterations of gut microbiota taxa and their metabolites as a consequence of xenobiotic exposures to find possible key targets involved in the severity of the host disease triggered. Compilation of data supporting the triad of xenobiotic-microbiota-metabolic diseases would subsequently allow such health misbalances to be prevented or treated by identifying beneficial microbe taxa that could be Next Generation Probiotics (NGPs) with metabolic enzymes for MDC neutralisation and mitigation strategies. In this review, we aim to compile the available information and reports focused on variations of the main gut microbiota taxa in metabolic diseases associated with xenobiotic exposure and related microbial metabolite profiles impacting the host health status. We performed an extensive literature search using SCOPUS, Web of Science, and PubMed databases. The data retrieval and thorough analyses highlight the need for more combined metagenomic and metabolomic studies revealing signatures for xenobiotics and triggered metabolic diseases. Moreover, metabolome and microbiome compositional taxa analyses allow further exploration of how to target beneficial NGP candidates according to their alleged variability abundance and potential therapeutic significance. Furthermore, this holistic approach has identified limitations and the need of future directions to expand and integrate key knowledge to design appropriate clinical and interventional studies with NGPs. Apart from human health, the beneficial microbes and metabolites identified could also be proposed for various applications under One Health, such as probiotics for animals, plants and environmental bioremediation.},
}
@article {pmid36361668,
year = {2022},
author = {Cadau, S and Gault, M and Berthelemy, N and Hsu, CY and Danoux, L and Pelletier, N and Goudounèche, D and Pons, C and Leprince, C and André-Frei, V and Simon, M and Pain, S},
title = {An Inflamed and Infected Reconstructed Human Epidermis to Study Atopic Dermatitis and Skin Care Ingredients.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232112880},
pmid = {36361668},
issn = {1422-0067},
mesh = {Humans ; *Dermatitis, Atopic/metabolism ; Staphylococcus aureus/metabolism ; Epidermis/metabolism ; Skin/metabolism ; Cytokines/metabolism ; *Staphylococcal Infections/metabolism ; Skin Care ; },
abstract = {Atopic dermatitis (AD), the most common inflammatory skin disorder, is a multifactorial disease characterized by a genetic predisposition, epidermal barrier disruption, a strong T helper (Th) type 2 immune reaction to environmental antigens and an altered cutaneous microbiome. Microbial dysbiosis characterized by the prevalence of Staphylococcus aureus (S. aureus) has been shown to exacerbate AD. In recent years, in vitro models of AD have been developed, but none of them reproduce all of the pathophysiological features. To better mimic AD, we developed reconstructed human epidermis (RHE) exposed to a Th2 pro-inflammatory cytokine cocktail and S. aureus. This model well reproduced some of the vicious loops involved in AD, with alterations at the physical, microbial and immune levels. Our results strongly suggest that S. aureus acquired a higher virulence potential when the epidermis was challenged with inflammatory cytokines, thus later contributing to the chronic inflammatory status. Furthermore, a topical application of a Castanea sativa extract was shown to prevent the apparition of the AD-like phenotype. It increased filaggrin, claudin-1 and loricrin expressions and controlled S. aureus by impairing its biofilm formation, enzymatic activities and inflammatory potential.},
}
@article {pmid36361666,
year = {2022},
author = {Madany, AM and Hughes, HK and Ashwood, P},
title = {Prenatal Maternal Antibiotics Treatment Alters the Gut Microbiota and Immune Function of Post-Weaned Prepubescent Offspring.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232112879},
pmid = {36361666},
issn = {1422-0067},
support = {90120/NH/NIH HHS/United States ; 123456/NH/NIH HHS/United States ; 123456//Autism Research Institute/ ; },
mesh = {Animals ; Mice ; Pregnancy ; Female ; *Gastrointestinal Microbiome ; Weaning ; Vancomycin ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice, Inbred C57BL ; Immunity ; },
abstract = {This study aimed to investigate the immediate and continual perturbation to the gut microbiota of offspring in the weeks post-weaning and how these may be modulated by treating pregnant C57BL/6J dams with antibiotics (ABX). We used a broad-spectrum antibiotic cocktail consisting of ampicillin 1 mg/mL, neomycin 1 mg/mL, and vancomycin 0.5 mg/mL, or vancomycin 0.5 mg/mL alone, administered ad-lib orally to dams via drinking water during gestation and stopped after delivery. We analyzed the gut microbiota of offspring, cytokine profiles in circulation, and the brain to determine if there was evidence of a gut-immune-brain connection. Computationally predicted metabolic pathways were calculated from 16s rRNA sequencing data. ABX treatment can negatively affect the gut microbiota, including reduced diversity, altered metabolic activity, and immune function. We show that the maternal ABX-treatment continues to alter the offspring's gut microbiota diversity, composition, and metabolic pathways after weaning, with the most significant differences evident in 5-week-olds as opposed to 4-week-olds. Lower levels of chemokines and inflammatory cytokines, such as interleukin (IL)-1α and IL-2, are also seen in the periphery and brains of offspring, respectively. In conclusion, this study shows maternal antibiotic administration alters gut microbiome profiles in offspring, which undergoes a continuous transformation, from week to week, at an early age after weaning.},
}
@article {pmid36361626,
year = {2022},
author = {Ionescu, RF and Enache, RM and Cretoiu, SM and Gaspar, BS},
title = {Gut Microbiome Changes in Gestational Diabetes.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
doi = {10.3390/ijms232112839},
pmid = {36361626},
issn = {1422-0067},
mesh = {Humans ; Female ; Infant, Newborn ; Pregnancy ; *Diabetes, Gestational ; *Gastrointestinal Microbiome/physiology ; Dysbiosis ; *Insulin Resistance ; *Diabetes Mellitus, Type 2 ; Obesity ; Inflammation/prevention &amp; control ; },
abstract = {Gestational diabetes mellitus (GDM), one of the most common endocrine pathologies during pregnancy, is defined as any degree of glucose intolerance with onset or first discovery in the perinatal period. Physiological changes that occur in pregnant women can lead to inflammation, which promotes insulin resistance. In the general context of worldwide increasing obesity in young females of reproductive age, GDM follows the same ascending trend. Changes in the intestinal microbiome play a decisive role in obesity and the development of insulin resistance and chronic inflammation, especially in patients with type 2 diabetes mellitus (T2D). To date, various studies have also associated intestinal dysbiosis with metabolic changes in women with GDM. Although host metabolism in women with GDM has not been fully elucidated, it is of particular importance to analyze the available data and to discuss the actual knowledge regarding microbiome changes with potential impact on the health of pregnant women and newborns. We analyzed peer-reviewed journal articles available in online databases in order to summarize the most recent findings regarding how variations in diet and metabolic status of GDM patients can contribute to alteration of the gut microbiome, in the same way that changes of the gut microbiota can lead to GDM. The most frequently observed alteration in the microbiome of patients with GDM was either an increase of the Firmicutes phylum, respectively, or a decrease of the Bacteroidetes and Actinobacteria phyla. Gut dysbiosis was still present postpartum and can impact the development of the newborn, as shown in several studies. In the evolution of GDM, probiotic supplementation and regular physical activity have the strongest evidence of proper blood glucose control, favoring fetal development and a healthy outcome for the postpartum period. The current review aims to summarize and discuss the most recent findings regarding the correlation between GDM and dysbiosis, and current and future methods for prevention and treatment (lifestyle changes, pre- and probiotics administration). To conclude, by highlighting the role of the gut microbiota, one can change perspectives about the development and progression of GDM and open up new avenues for the development of innovative therapeutic targets in this disease.},
}
@article {pmid36361318,
year = {2022},
author = {Przemieniecki, SW and Oćwieja, M and Ciesielski, S and Halecki, W and Matras, E and Gorczyca, A},
title = {Chemical Structure of Stabilizing Layers of Negatively Charged Silver Nanoparticles as an Effector of Shifts in Soil Bacterial Microbiome under Short-Term Exposure.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {21},
pages = {},
doi = {10.3390/ijerph192114438},
pmid = {36361318},
issn = {1660-4601},
mesh = {Soil/chemistry ; Soil Microbiology ; *Metal Nanoparticles/chemistry ; *Fungicides, Industrial ; Silver ; Bacteria ; *Microbiota ; Ions ; },
abstract = {In this work, we have assessed the exposure of soil bacteria from potato monoculture to three types of silver nanoparticles (AgNPs) as well as silver ions (Ag[+] ions) delivered in the form of silver nitrate and a commercially available fungicide. The diversity of the soil microbial community, enzymatic activity, and carbon source utilization were evaluated. It was found that only the fungicide significantly limited the abundance and activity of soil bacteria. Silver ions significantly reduced bacterial metabolic activity. In turn, one type of AgNPs prepared with the use of tannic acid (TA) increased bacterial load and activity. There was found in all AgNPs treated soils (1) a greater proportion of all types of persistent bacteria, i.e., Bacillus, Paenibacillus, and Clostridium; (2) a visible decrease in the proportion of Nocardioides, Arthrobacter, and Candidatus Solibacter; (3) almost complete depletion of Pseudomonas; (4) increase in the number of low-frequency taxa and decrease in dominant taxa compared to the control soil. Despite the general trend of qualitative changes in the bacterial community, it was found that the differences in the chemical structure of the AgNP stabilizing layers had a significant impact on the specific metabolic activity resulting from qualitative changes in the microbiome.},
}
@article {pmid36360970,
year = {2022},
author = {Sousa, V and Spratt, D and Davrandi, M and Mardas, N and Beltrán, V and Donos, N},
title = {Oral Microcosm Biofilms Grown under Conditions Progressing from Peri-Implant Health, Peri-Implant Mucositis, and Peri-Implantitis.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {21},
pages = {},
doi = {10.3390/ijerph192114088},
pmid = {36360970},
issn = {1660-4601},
mesh = {Humans ; *Peri-Implantitis/microbiology ; RNA, Ribosomal, 16S/genetics ; *Mucositis ; Biofilms ; *Microbiota/genetics ; Bacteria/genetics ; },
abstract = {Peri-implantitis is a disease influenced by dysbiotic microbial communities that play a role in the short- and long-term outcomes of its clinical treatment. The ecological triggers that establish the progression from peri-implant mucositis to peri-implantitis remain unknown. This investigation describes the development of a novel in vitro microcosm biofilm model. Biofilms were grown over 30 days over machined titanium discs in a constant depth film fermentor (CDFF), which was inoculated (I) with pooled human saliva. Following longitudinal biofilm sampling across peri-implant health (PH), peri-implant mucositis (PM), and peri-implantitis (PI) conditions, the characterisation of the biofilms was performed. The biofilm analyses included imaging by confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM), selective and non-selective culture media of viable biofilms, and 16S rRNA gene amplification and sequencing. Bacterial qualitative shifts were observed by CLSM and SEM across conditions, which were defined by characteristic phenotypes. A total of 9 phyla, 83 genera, and 156 species were identified throughout the experiment. The phyla Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Actinobacteria showed the highest prevalence in PI conditions. This novel in vitro microcosm model provides a high-throughput alternative for growing microcosm biofilms resembling an in vitro progression from PH-PM-PI conditions.},
}
@article {pmid36360258,
year = {2022},
author = {Beheshti, R and Stone, S and Chandran, D and Hicks, SD},
title = {Multi-Omic Profiles in Infants at Risk for Food Reactions.},
journal = {Genes},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/genes13112024},
pmid = {36360258},
issn = {2073-4425},
support = {(#5295).//Gerber Foundation/ ; },
mesh = {Infant ; Humans ; Longitudinal Studies ; Allergens ; Food ; *MicroRNAs/genetics ; *Microbiota ; },
abstract = {Food reactions (FR) are multifactorial and impacted by medical, demographic, environmental, and immunologic factors. We hypothesized that multi-omic analyses of host-microbial factors in saliva would enhance our understanding of FR development. This longitudinal cohort study included 164 infants followed from birth through two years. The infants were identified as FR (n = 34) or non-FR (n = 130) using the Infant Feeding Practice II survey and medical record confirmation. Saliva was collected at six months for the multi-omic assessment of cytokines, mRNAs, microRNAs, and the microbiome/virome. The levels of one miRNA (miR-203b-3p, adj. p = 0.043, V = 2913) and one viral phage (Proteus virus PM135, adj. p = 0.027, V = 2955) were lower among infants that developed FRs. The levels of one bacterial phylum (Cyanobacteria, adj. p = 0.048, V = 1515) were higher among infants that developed FR. Logistical regression models revealed that the addition of multi-omic features (miR-203b-3p, Cyanobacteria, and Proteus virus PM135) improved predictiveness for future FRs in infants (p = 0.005, X[2] = 12.9), predicting FRs with 72% accuracy (AUC = 0.81, sensitivity = 72%, specificity = 72%). The multi-omic analysis of saliva may enhance the accurate identification of infants at risk of FRs and provide insights into the host/microbiome interactions that predispose certain infants to FRs.},
}
@article {pmid36360204,
year = {2022},
author = {Qin, C and Chen, Z and Cao, R and Shi, M and Tian, Y},
title = {Integrated Analysis of the Fecal Metagenome and Metabolome in Bladder Cancer in a Chinese Population.},
journal = {Genes},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/genes13111967},
pmid = {36360204},
issn = {2073-4425},
support = {bhz2020-4//the Research Foundation of Beijing Friendship Hospital, Capital Medical University/ ; 2021-ZZ-009//Beijing Postdoctoral Research Foundation/ ; },
mesh = {Humans ; *Metagenome ; *Urinary Bladder Neoplasms/genetics ; Metabolome ; Metabolomics ; China ; },
abstract = {Bladder cancer (BLCA) is a common malignancy of the urinary system. The gut microbiome produces various metabolites that play functional roles in tumorigenesis and tumor progression. However, the integrative analysis of the gut microbiome and metabolome in BLCA has still been lacking. Thus, the aim of this study was to identify microbial and functional characteristics and metabolites in BLCA in a Chinese population. Metagenomics, targeted metabolomics, bioinformatics, and integrative analysis were used in fecal samples of BLCA patients and healthy individuals. We found gut microbiomes were significantly dysregulated in BLCA patients, including Bifidobacterium, Lactobacillus, Streptococcus, Blautia, and Eubacterium. We also found 11Z-eicosenoic acid, 3-methoxytyrosine, abrine, aniline-2-sulfonate, arachidic acid, conjugated linoleic acids, elaidic acid, glycylleucine, glycylproline, leucyl-glycine, linoelaidic acid, linoleic acid, nicotinamide hypoxanthine dinucleotide, oleic acid, petroselinic acid, and ricinoleic acid to be significantly decreased, while cholesterol sulfate was significantly increased in BLCA patients. Integration of metagenomics and metabolomics revealed interactions between gut microbiota and metabolites and the host. We identified the alterations of gut microbiomes and metabolites in BLCA in a Chinese population. Moreover, we preliminarily revealed the associations between specific gut microbiomes and metabolites. These findings determined potential causative links among gut dysbiosis, dysregulated metabolites, and BLCA.},
}
@article {pmid36360018,
year = {2022},
author = {Zhang, J and Wang, W and Guo, D and Bai, B and Bo, T and Fan, S},
title = {Antidiabetic Effect of Millet Bran Polysaccharides Partially Mediated via Changes in Gut Microbiome.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {21},
pages = {},
doi = {10.3390/foods11213406},
pmid = {36360018},
issn = {2304-8158},
support = {20210302124511//General Youth Fund Project of Shanxi Province/ ; XCSXU-KF-202201, XCSXU-KF-202203, XCSXU-KF-202208, XCSXU-KF-202211//Xinghuacun College Open Project Foundation/ ; },
abstract = {Diabetes is a type of metabolic disease associated with changes in the intestinal flora. In this study, the regulatory effect of millet bran on intestinal microbiota in a model of type 2 diabetes (T2DM) was investigated in an effort to develop new approaches to prevent and treat diabetes and its complications in patients. The effect of purified millet bran polysaccharide (MBP) with three different intragastric doses (400 mg/kg, 200 mg/kg, and 100 mg/kg) combined with a high-fat diet was determined in a streptozotocin (STZ)-induced model of T2DM. By analyzing the changes in indicators, weight, fasting blood sugar, and other bio-physiological parameters, the changes in gut microbiota were analyzed via high-throughput sequencing to establish the effect of MBP on the intestinal flora. The results showed that MBP alleviated symptoms of high-fat diet-induced T2DM. A high dosage of MBP enhanced the hypoglycemic effects compared with low and medium dosages. During gavage, the fasting blood glucose (FBG) levels of rats in the MBP group were significantly reduced (p < 0.05). The glucose tolerance of rats in the MBP group was significantly improved (p < 0.05). In diabetic mice, MBP significantly increased the activities of CAT, SOD, and GSH-Px. The inflammatory symptoms of liver cells and islet cells in the MBP group were alleviated, and the anti-inflammatory effect was partially correlated with the dose of MBP. After 4 weeks of treatment with MBP, the indices of blood lipid in the MBP group were significantly improved compared with those of the DM group (p < 0.05). Treatment with MBP (400 mg/kg) increases the levels of beneficial bacteria and decreases harmful bacteria in the intestinal tract of rats, thus altering the intestinal microbial community and antidiabetic effect on mice with T2DM by modulating gut microbiota. The findings suggest that MBP is a potential pharmaceutical supplement for preventing and treating diabetes.},
}
@article {pmid36359885,
year = {2022},
author = {Min, SH and Kwon, J and Do, EJ and Kim, SH and Kim, ES and Jeong, JY and Bae, SM and Kim, SY and Park, DH},
title = {Duodenal Dual-Wavelength Photobiomodulation Improves Hyperglycemia and Hepatic Parameters with Alteration of Gut Microbiome in Type 2 Diabetes Animal Model.},
journal = {Cells},
volume = {11},
number = {21},
pages = {},
doi = {10.3390/cells11213490},
pmid = {36359885},
issn = {2073-4409},
support = {NRF-2020R1A2C2099718//National Research Foundation of Korea/ ; 2021R1A6A1A03040260//National Research Foundation of Korea/ ; 2021IP0015//Asan Medical Center/ ; },
mesh = {Animals ; Rats ; *Diabetes Mellitus, Type 2/metabolism ; Disease Models, Animal ; Duodenum/metabolism/pathology ; *Gastrointestinal Microbiome ; Glucagon-Like Peptide 1 ; *Glucose Intolerance ; *Hyperglycemia ; Insulin ; *Insulin Resistance ; Liver/metabolism ; },
abstract = {BACKGROUND: Recently, the duodenum has garnered interest for its role in treating metabolic diseases, including type 2 diabetes (T2DM). Multiple sessions of external photobiomodulation (PBM) in previous animal studies suggested it resulted in improved hyperglycemia, glucose intolerance, and insulin resistance with a multifactorial mechanism of action, despite the target organ of PBM not being clearly proven. This study aimed to determine whether a single session of a duodenal light-emitting diode (LED) PBM may impact the T2DM treatment in an animal model.<br><br>METHODS: Goto-Kakizaki rats as T2DM models were subjected to PBM through duodenal lumen irradiation, sham procedure, or control in 1-week pilot (630 nm, 850 nm, or 630/850 nm) and 4-week follow-up (630 nm or 630/850 nm) studies. Oral glucose tolerance tests; serum glucagon-like peptide 1 (GLP-1), glucose-dependent insulinotropic polypeptide, and insulin levels; liver chemistry and histology; and gut microbiome in the PBM, sham control, and control groups were evaluated.<br><br>RESULTS: In the 1-week study, duodenal dual-wavelength (D, 630/850 nm) LED PBM showed improved glucose intolerance, alkaline phosphatase and cholesterol levels, and weight gain than other groups. The D-LED PBM group in the 4-week study also showed improved hyperglycemia and liver enzyme levels, with relatively preserved pancreatic islets and increased serum insulin and GLP-1 levels. Five genera (Bacteroides, Escherichia, Parabacteroides, Allobaculum, and Faecalibaculum) were significantly enriched 1 week after the D-LED PBM. Bacteroides acidifaciens significantly increased, while Lachnospiraceae significantly decreased after 1 week.<br><br>CONCLUSION: A single session of D-LED PBM improved hyperglycemia and hepatic parameters through the change of serum insulin, insulin resistance, insulin expression in the pancreatic β-cells, and gut microbiome in T2DM animal models.},
}
@article {pmid36359553,
year = {2022},
author = {Yasuo, T and Kitaya, K},
title = {Challenges in Clinical Diagnosis and Management of Chronic Endometritis.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/diagnostics12112711},
pmid = {36359553},
issn = {2075-4418},
abstract = {Chronic endometritis (CE) is a local mucosal infectious and inflammatory disorder characterized by unusual filtration of CD138(+) endometrial stromal plasmacytes. CE is attracting attention due to its potential association with infertility of unknown etiology, repeated implantation failure, recurrent pregnancy loss, and several maternal/neonatal complications. Due to the variance in study design among researchers, universal diagnostic criteria remain to be established for the clinical diagnosis and management of CE. This review article aims to summarize current knowledge and provide insights into unsolved questions on CE to establish clinical guidelines for the disease from the viewpoint of human reproduction.},
}
@article {pmid36359484,
year = {2022},
author = {Tozzo, P and Amico, I and Delicati, A and Toselli, F and Caenazzo, L},
title = {Post-Mortem Interval and Microbiome Analysis through 16S rRNA Analysis: A Systematic Review.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/diagnostics12112641},
pmid = {36359484},
issn = {2075-4418},
abstract = {The determination of the Post-Mortem Interval (PMI) is an issue that has always represented a challenge in the field of forensic science. Different innovative approaches, compared to the more traditional ones, have been tried over the years, without succeeding in being validated as successful methods for PMI estimation. In the last two decades, innovations in sequencing technologies have made it possible to generate large volumes of data, allowing all members of a bacterial community to be sequenced. The aim of this manuscript is to provide a review regarding new advances in PMI estimation through cadaveric microbiota identification using 16S rRNA sequencing, in order to correlate specific microbiome profiles obtained from different body sites to PMI. The systematic review was performed according to PRISMA guidelines. For this purpose, 800 studies were identified through database searching (Pubmed). Articles that dealt with PMI estimation in correlation with microbiome composition and contained data about species, body site of sampling, monitoring time and sequencing method were selected and ultimately a total of 25 studies were considered. The selected studies evaluated the contribution of the various body sites to determine PMI, based on microbiome sequencing, in human and animal models. The results of this systematic review highlighted that studies conducted on both animals and humans yielded results that were promising. In order to fully exploit the potential of the microbiome in the estimation of PMI, it would be desirable to identify standardized body sampling sites and specific sampling methods in order to align data obtained by different research groups.},
}
@article {pmid36359311,
year = {2022},
author = {Righi, E and Lambertenghi, L and Gorska, A and Sciammarella, C and Ivaldi, F and Mirandola, M and Sartor, A and Tacconelli, E},
title = {Impact of COVID-19 and Antibiotic Treatments on Gut Microbiome: A Role for Enterococcus spp.},
journal = {Biomedicines},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/biomedicines10112786},
pmid = {36359311},
issn = {2227-9059},
support = {Enact-React_2020//Fondazione Cariverona/ ; },
abstract = {OBJECTIVE: Several studies showed the substantial use of antibiotics and increased risk of antimicrobial resistant infections in patients with COVID-19. The impact of COVID-19-related treatments and antibiotics on gut dysbiosis has not been clarified.<br><br>DESIGN: The prospective cohort study included hospitalized COVID-19 patients (April-December 2020). The gut microbiome composition was analysed by 16S sequencing. The gut diversity and changes in opportunistic bacteria (OBs) or symbionts were analysed according to clinical parameters, laboratory markers of disease progression, type of non-antibiotic COVID-19 treatments (NACT) and type, WHO AWaRe group, and duration of antibiotic therapy (AT).<br><br>RESULTS: A total of 82 patients (mean age 66 ± 13 years, 70% males) were enrolled. The relative abundance of Enterococcus was significantly correlated with duration of hospitalization, intensive care unit stay, O2 needs, and D-dimer, ferritin, and IL-6 blood levels. The presence of Enterococcus showed the highest number of correlations with NACT, AT, and AT + NACT (e.g., hydroxychloroquine ± lopinavir/ritonavir) and increased relative abundance with AWaRe Watch/Reserve antibiotics, AT duration, and combinations. Abundance of Dorea, Agathobacter, Roseburia, and Barnesiella was negatively correlated with AT and corticosteroids use. Patients with increased IL-6, D-dimer, and ferritin levels receiving AT were more likely to show dysbiosis with increased abundance of Enterococcus and Bilophila bacteria and decreased abundance of Roseburia compared with those not receiving AT.<br><br>CONCLUSION: Microbiome diversity is affected by COVID-19 severity. In this context, antibiotic treatment may shift the gut microbiome composition towards OBs, particularly Enterococcus. The impact of treatment-driven dysbiosis on OBs infections and long-term consequences needs further study to define the role of gut homeostasis in COVID-19 recovery and inform targeted interventions.},
}
@article {pmid36359282,
year = {2022},
author = {Drapkina, OM and Ashniev, GA and Zlobovskaya, OA and Yafarova, AA and Dementeva, EV and Kaburova, AN and Meshkov, IO and Sheptulina, AF and Kiselev, AR and Kontsevaya, AV and Zhamalov, LM and Koretskiy, SN and Pokrovskaya, MS and Akinshina, AI and Zagaynova, AV and Lukashina, MV and Kirillov, AV and Abramov, IA and Tolkacheva, LR and Bikaeva, IO and Glazunova, EV and Shipulin, GA and Bobrova, MM and Makarov, VV and Keskinov, AA and Yudin, VS and Yudin, SM},
title = {Diversities in the Gut Microbial Patterns in Patients with Atherosclerotic Cardiovascular Diseases and Certain Heart Failure Phenotypes.},
journal = {Biomedicines},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/biomedicines10112762},
pmid = {36359282},
issn = {2227-9059},
support = {388-00154-22-00//Federal Medical Biological Agency/ ; },
abstract = {To continue progress in the treatment of cardiovascular disease, there is a need to improve the overall understanding of the processes that contribute to the pathogenesis of cardiovascular disease (CVD). Exploring the role of gut microbiota in various heart diseases is a topic of great interest since it is not so easy to find such reliable connections despite the fact that microbiota undoubtedly affect all body systems. The present study was conducted to investigate the composition of gut microbiota in patients with atherosclerotic cardiovascular disease (ASCVD) and heart failure syndromes with reduced ejection fraction (HFrEF) and HF with preserved EF (HFpEF), and to compare these results with the microbiota of individuals without those diseases (control group). Fecal microbiota were evaluated by three methods: living organisms were determined using bacterial cultures, total DNA taxonomic composition was estimated by next generation sequencing (NGS) of 16S rRNA gene (V3-V4) and quantitative assessment of several taxa was performed using qPCR (quantitative polymerase chain reaction). Regarding the bacterial culture method, all disease groups demonstrated a decrease in abundance of Enterococcus faecium and Enterococcus faecalis in comparison to the control group. The HFrEF group was characterized by an increased abundance of Streptococcus sanguinus and Streptococcus parasanguinis. NGS analysis was conducted at the family level. No significant differences between patient's groups were observed in alpha-diversity indices (Shannon, Faith, Pielou, Chao1, Simpson, and Strong) with the exception of the Faith index for the HFrEF and control groups. Erysipelotrichaceae were significantly increased in all three groups; Streptococcaceae and Lactobacillaceae were significantly increased in ASCVD and HFrEF groups. These observations were indirectly confirmed with the culture method: two species of Streptococcus were significantly increased in the HFrEF group and Lactobacillus plantarum was significantly increased in the ASCVD group. The latter observation was also confirmed with qPCR of Lactobacillus sp. Acidaminococcaceae and Odoribacteraceae were significantly decreased in the ASCVD and HFrEF groups. Participants from the HFpEF group showed the least difference compared to the control group in all three study methods. The patterns found expand the knowledge base on possible correlations of gut microbiota with cardiovascular diseases. The similarities and differences in conclusions obtained by the three methods of this study demonstrate the need for a comprehensive approach to the analysis of microbiota.},
}
@article {pmid36359118,
year = {2022},
author = {Liu, J and Bai, Y and Liu, F and Kohn, RA and Tadesse, DA and Sarria, S and Li, RW and Song, J},
title = {Rumen Microbial Predictors for Short-Chain Fatty Acid Levels and the Grass-Fed Regimen in Angus Cattle.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {21},
pages = {},
doi = {10.3390/ani12212995},
pmid = {36359118},
issn = {2076-2615},
support = {2017//Jorgenson Fund/ ; },
abstract = {The health benefits of grass-fed beef are well documented. However, the rumen microbiome features in beef steers raised in a grass-fed regimen have yet to be identified. This study examined the rumen microbiome profile in the feeding regimes. Our findings show that the rumen microbiome of the grass-fed cattle demonstrated greater species diversity and harbored significantly higher microbial alpha diversity, including multiple species richness and evenness indices, than the grain-fed cattle. Global network analysis unveiled that grass-fed cattle's rumen microbial interaction networks had higher modularity, suggesting a more resilient and stable microbial community under this feeding regimen. Using the analysis of compositions of microbiomes with a bias correction (ANCOM-BC) algorithm, the abundance of multiple unclassified genera, such as those belonging to Planctomycetes, LD1-PB3, SR1, Lachnospira, and Sutterella, were significantly enriched in the rumen of grass-fed steers. Sutterella was also the critical genus able to distinguish the two feeding regimens by Random Forest. A rumen microbial predictor consisting of an unclassified genus in the candidate division SR1 (numerator) and an unclassified genus in the order Bacteroidales (denominator) accurately distinguished the two feeding schemes. Multiple microbial signatures or balances strongly correlated with various levels of SCFA in the rumen. For example, a balance represented by the log abundance ratio of Sutterella to Desulfovibrio was strongly associated with acetate-to-propionate proportions in the rumen (R[2] = 0.87), which could be developed as a valuable biomarker for optimizing milk fat yield and cattle growth. Therefore, our findings provided novel insights into microbial interactions in the rumen under different feed schemes and their ecophysiological implications. These findings will help to develop rumen manipulation strategies to improve feed conversion ratios and average daily weight gains for grass- or pasture-fed cattle production.},
}
@article {pmid36359115,
year = {2022},
author = {Zhang, Q and Guo, T and Wang, X and Zhang, X and Geng, Y and Liu, H and Xu, T and Hu, L and Zhao, N and Xu, S},
title = {Rumen Microbiome Reveals the Differential Response of CO2 and CH4 Emissions of Yaks to Feeding Regimes on the Qinghai-Tibet Plateau.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {21},
pages = {},
doi = {10.3390/ani12212991},
pmid = {36359115},
issn = {2076-2615},
support = {2021YFD1600205//the National Key Research and Development Program of China/ ; 2019-ZJ-974Q//the Qinghai Province Natural Science Foundation/ ; U21A20250//the Joint fund project of NSFC/ ; CASLWC-2021//the CAS "Light of West China" for Interdisciplinary Innovation Team/ ; XDA20050104, XDA23060603//the Strategic Priority Research Program of Chinese Academy of Sciences/ ; },
abstract = {Shifts in feeding regimes are important factors affecting greenhouse gas (GHG) emissions from livestock farming. However, the quantitative values and associated drivers of GHG emissions from yaks (Bos grunniens) following shifts in feeding regimes have yet to be fully described. In this study, we aimed to investigate CH4 and CO2 emissions differences of yaks under different feeding regimes and their potential microbial mechanisms. Using static breathing chamber and Picarro G2508 gas concentration analyzer, we measured the CO2 and CH4 emissions from yaks under traditional grazing (TG) and warm-grazing and cold-indoor feeding (WGCF) regimes. Microbial inventories from the ruminal fluid of the yaks were determined via Illumina 16S rRNA and ITS sequencing. Results showed that implementing the TG regime in yaks decreased their CO2 and CH4 emissions compared to the WGCF regime. The alpha diversity of ruminal archaeal community was higher in the TG regime than in the WGCF regime. The beta diversity showed that significant differences in the rumen microbial composition of the TG regime and the WGCF regime. Changes in the rumen microbiota of the yaks were driven by differences in dietary nutritional parameters. The relative abundances of the phyla Neocallimastigomycota and Euryarchaeota and the functional genera Prevotella, Ruminococcus, Orpinomyces, and Methanobrevibacter were significantly higher in the WGCF regime than in the TG regime. CO2 and CH4 emissions from yaks differed mainly because of the enrichment relationship of functional H2- and CO2-producing microorganisms, hydrogen-consuming microbiota, and hydrogenotrophic methanogenic microbiota. Our results provided a view that it is ecologically important to develop GHG emissions reduction strategies for yaks on the Qinghai-Tibet Plateau based on traditional grazing regime.},
}
@article {pmid36358990,
year = {2022},
author = {Scott, E and De Paepe, K and Van de Wiele, T},
title = {Postbiotics and Their Health Modulatory Biomolecules.},
journal = {Biomolecules},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/biom12111640},
pmid = {36358990},
issn = {2218-273X},
support = {HBC.2021.0969//VLAIO/ ; BOF/GOA 01G03122//Ghent University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics ; Fatty Acids, Volatile ; Vitamins ; Inflammation ; },
abstract = {Postbiotics are a new category of biotics that have the potential to confer health benefits but, unlike probiotics, do not require living cells to induce health effects and thus are not subject to the food safety requirements that apply to live microorganisms. Postbiotics are defined as a "preparation of inanimate microorganisms and/or their components that confers a health benefit on the host". Postbiotic components include short-chain fatty acids, exopolysaccharides, vitamins, teichoic acids, bacteriocins, enzymes and peptides in a non-purified inactivated cell preparation. While research into postbiotics is in its infancy, there is increasing evidence that postbiotics have the potential to modulate human health. Specifically, a number of postbiotics have been shown to improve gut health by strengthening the gut barrier, reducing inflammation and promoting antimicrobial activity against gut pathogens. Additionally, research is being conducted into the potential application of postbiotics to other areas of the body, including the skin, vagina and oral cavity. The purpose of this review is to set out the current research on postbiotics, demonstrate how postbiotics are currently used in commercial products and identify a number of knowledge gaps where further research is needed to identify the potential for future applications of postbiotics.},
}
@article {pmid36358859,
year = {2022},
author = {Mauceri, R and Coppini, M and Vacca, D and Bertolazzi, G and Panzarella, V and Di Fede, O and Tripodo, C and Campisi, G},
title = {Salivary Microbiota Composition in Patients with Oral Squamous Cell Carcinoma: A Systematic Review.},
journal = {Cancers},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/cancers14215441},
pmid = {36358859},
issn = {2072-6694},
support = {PON-AIM Line 1 (Id. AIM1892002)//Ministry of Education, Universities and Research/ ; },
abstract = {BACKGROUND: Oral squamous cell carcinoma (OSCC) is one of the most prevalent cancers worldwide. Despite recent advances in diagnosis and treatment, in recent years, an increase in the incidence of OSCC has been registered, and the mortality rate is still high. This systematic review aims to identify a potential association between the composition of salivary microbiota and OSCC.<br><br>MATERIALS AND METHODS: The protocol for this study was designed following the PRISMA guidelines. Records were identified using different search engines (e.g., Medline/PubMed). Observational studies, in human subjects with histological diagnosis of OSCC, concerning the analysis of salivary microbiota, were selected.<br><br>RESULTS: Eleven papers were included. The salivary microbiomes of 1335 patients were analysed (n.687 OSCC and n.648 controls). Due to the great heterogeneity of the studies, it was not possible to profile a specific microbiota associated with OSCC. However, periodontal pathogens were the most common bacteria detected in patients with OSCC (i.e., Fusobacterium, Prevotella).<br><br>CONCLUSIONS: Although there are evident alterations in the salivary microbiota composition in OSCC patients, it is still a challenge to identify a specific microbiota pattern in OSCC patients. If the associations between specific salivary microorganisms and OSCC are confirmed, microbiome analysis could be a useful tool for the screening and follow-up of patients affected by OSCC.},
}
@article {pmid36358821,
year = {2022},
author = {Hakozaki, T and Nolin-Lapalme, A and Kogawa, M and Okuma, Y and Nakamura, S and Moreau-Amaru, D and Tamura, T and Hosomi, Y and Takeyama, H and Richard, C and Hosokawa, M and Routy, B},
title = {Cancer Cachexia among Patients with Advanced Non-Small-Cell Lung Cancer on Immunotherapy: An Observational Study with Exploratory Gut Microbiota Analysis.},
journal = {Cancers},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/cancers14215405},
pmid = {36358821},
issn = {2072-6694},
support = {JP19K16820//Japan Society for the Promotion of Science/ ; },
abstract = {Cancer cachexia exerts a negative clinical influence on patients with advanced non-small-cell lung cancer (NSCLC) treated with immune checkpoint inhibitors (ICI). The prognostic impact of body weight change during ICI treatment remains unknown. The gut microbiota (GM) is a key contributor to the response to ICI therapy in cancer patients. However, the association between cancer cachexia and GM and their association with the response to ICIs remains unexplored. This study examined the association of cancer cachexia with GM composition and assessed the impact of GM on clinical outcomes in patients with NSCLC treated with ICIs. In this observational, prospective study, which included 113 Japanese patients with advanced NSCLC treated with ICIs, the prevalence of cachexia was 50.4% (57/113). The median progression-free survival (PFS) and overall survival (OS) were significantly shorter in the cachexia group than in the non-cachexia group (4.3 vs. 11.6 months (p = 0.003) and 12.0 months vs. not reached (p = 0.02), respectively). A multivariable analysis revealed that baseline cachexia was independently associated with a shorter PFS. Moreover, a gain in body weight from the baseline (reversible cachexia) was associated with a significantly longer PFS and OS compared to irreversible cachexia. Microbiome profiling with 16S rRNA analysis revealed that the cachexia group presented an overrepresentation of the commensal bacteria, Escherichia-Shigella and Hungatella, while the non-cachexia group had a preponderance of Anaerostipes,&amp;nbsp;Blautia, and Eubacterium ventriosum. Anaerostipes and E. ventriosum were associated with longer PFS and OS. Moreover, a cachexia status correlated with the systemic inflammatory marker-derived-neutrophil-to-lymphocytes ratio (dNLR) and Lung Immune Prognostic Index (LIPI) indexes. Our study demonstrates that cachexia and longitudinal bodyweight change have a prognostic impact on patients with advanced NSCLC treated with ICI therapy. Moreover, our study demonstrates that bacteria associated with ICI resistance are also linked to cachexia. Targeted microbiota interventions may represent a new type of treatment to overcome cachexia in patients with NSCLC.},
}
@article {pmid36358819,
year = {2022},
author = {Liu, B and Chau, J and Dai, Q and Zhong, C and Zhang, J},
title = {Exploring Gut Microbiome in Predicting the Efficacy of Immunotherapy in Non-Small Cell Lung Cancer.},
journal = {Cancers},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/cancers14215401},
pmid = {36358819},
issn = {2072-6694},
support = {DBI-1943291//National Science Foundation/ ; //the University of Kansas Start-Up/ ; //the "Play with a Pro" Lung Cancer Research Fund/ ; //the Pilot Grant for Cancer Research of the University of Kansas Cancer Center/ ; },
abstract = {We performed various analyses on the taxonomic and functional features of the gut microbiome from NSCLC patients treated with immunotherapy to establish a model that may predict whether a patient will benefit from immunotherapy. We collected 65 published whole metagenome shotgun sequencing samples along with 14 samples from our previous study. We systematically studied the taxonomical characteristics of the dataset and used both the random forest (RF) and the multilayer perceptron (MLP) neural network models to predict patients with progression-free survival (PFS) above 6 months versus those below 3 months. Our results showed that the RF classifier achieved the highest F-score (85.2%) and the area under the receiver operating characteristic curve (AUC) (95%) using the protein families (Pfam) profile, and the MLP neural network classifier achieved a 99.9% F-score and 100% AUC using the same Pfam profile. When applying the model trained in the Pfam profile directly to predict the treatment response, we found that both trained RF and MLP classifiers significantly outperformed the stochastic predictor in F-score. Our results suggested that such a predictive model based on functional (e.g., Pfam) rather than taxonomic profile might be clinically useful to predict whether an NSCLC patient will benefit from immunotherapy, as both the F-score and AUC of functional profile outperform that of taxonomic profile. In addition, our model suggested that interactive biological processes such as methanogenesis, one-carbon, and amino acid metabolism might be important in regulating the immunotherapy response that warrants further investigation.},
}
@article {pmid36358812,
year = {2022},
author = {Wang, H and Hu, J and Wu, J and Ji, P and Shang, A and Li, D},
title = {The Function and Molecular Mechanism of Commensal Microbiome in Promoting Malignant Progression of Lung Cancer.},
journal = {Cancers},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/cancers14215394},
pmid = {36358812},
issn = {2072-6694},
support = {82072362//National Natural Science Foundation of China/ ; 8200223//National Natural Science Foundation of China/ ; 8200222//National Natural Science Foundation of China/ ; 2020M681399//China Postdoctoral Science Foundation/ ; },
abstract = {The human commensal microbiome existing in an internal environment is relatively consistent with that of the host. The presence of bacterial dysbiosis, on the other hand, promptly results in the termination of this symbiotic association. The altered microbial structure in the lung may be responsible for the development of lung cancer by controlling the host's inflammatory response and influencing a variety of immunological pathways. More and more studies have pointed to the fact that the commensal microbiota plays a vital role in both the development of tumors and the body's response to lung cancer treatment. Microbiome dysbiosis, genotoxicity, virulence effect, and epigenetic dysregulations are some of the potential mechanisms that may lie behind the process of tumorigenesis that is mediated by microbiome. Other potential mechanisms include regulating host immune activity through a variety of pathogenic factors, dysregulating host metabolism as a result of microbiome alterations, and microbiome dysbiosis. In this historical overview, we go through some of the more recent mechanistic discoveries into the biological processes that are involved in lung cancer that are caused by bacteria. Without a question, obtaining a greater knowledge of the dynamic link between the lung microbiome and lung cancer has the potential to inspire the development of innovative early detection and customized treatment methods for lung cancer.},
}
@article {pmid36358789,
year = {2022},
author = {Pietrzak, B and Tomela, K and Olejnik-Schmidt, A and Galus, Ł and Mackiewicz, J and Kaczmarek, M and Mackiewicz, A and Schmidt, M},
title = {A Clinical Outcome of the Anti-PD-1 Therapy of Melanoma in Polish Patients Is Mediated by Population-Specific Gut Microbiome Composition.},
journal = {Cancers},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/cancers14215369},
pmid = {36358789},
issn = {2072-6694},
support = {2017/25/B/NZ5/01949//National Science Center/ ; },
abstract = {The gut microbiota is considered a key player modulating the efficacy of immune checkpoint inhibitor therapy. The study investigated the association between the response to anti-PD-1 therapy and the baseline gut microbiome in a Polish cohort of melanoma patients, alongside selected agents modifying the microbiome. Sixty-four melanoma patients enrolled for the anti-PD-1 therapy, and ten healthy subjects were recruited. The response to the treatment was assessed according to the response evaluation criteria in solid tumors, and patients were classified as responders or non-responders. The association between selected extrinsic factors and response was investigated using questionnaire-based analysis and the metataxonomics of the microbiota. In the responders, the Bacteroidota to Firmicutes ratio was higher, and the richness was decreased. The abundance of Prevotella&amp;nbsp;copri and Bacteroides&amp;nbsp;uniformis was related to the response, whereas the non-responders' gut microbiota was enriched with Faecalibacterium&amp;nbsp;prausnitzii and Desulfovibrio&amp;nbsp;intestinalis and some unclassified Firmicutes. Dietary patterns, including plant, dairy, and fat consumption as well as gastrointestinal tract functioning were significantly associated with the therapeutic effects of the therapy. The specific gut microbiota along with diet were found to be associated with the response to the therapy in the population of melanoma patients.},
}
@article {pmid36358736,
year = {2022},
author = {He, Y and Huang, J and Li, Q and Xia, W and Zhang, C and Liu, Z and Xiao, J and Yi, Z and Deng, H and Xiao, Z and Hu, J and Li, H and Zu, X and Quan, C and Chen, J},
title = {Gut Microbiota and Tumor Immune Escape: A New Perspective for Improving Tumor Immunotherapy.},
journal = {Cancers},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/cancers14215317},
pmid = {36358736},
issn = {2072-6694},
support = {81873626, 81902592, 82070785//the National Natural Science Foundation of China/ ; 2020JJ5884//Hunan Natural Science Foundation/ ; 2021RC3027//Hunan Province Young talents Program/ ; },
abstract = {The gut microbiota is a large symbiotic community of anaerobic and facultative aerobic bacteria inhabiting the human intestinal tract, and its activities significantly affect human health. Increasing evidence has suggested that the gut microbiome plays an important role in tumor-related immune regulation. In the tumor microenvironment (TME), the gut microbiome and its metabolites affect the differentiation and function of immune cells regulating the immune evasion of tumors. The gut microbiome can indirectly influence individual responses to various classical tumor immunotherapies, including immune checkpoint inhibitor therapy and adoptive immunotherapy. Microbial regulation through antibiotics, prebiotics, and fecal microbiota transplantation (FMT) optimize the composition of the gut microbiome, improving the efficacy of immunotherapy and bringing a new perspective and hope for tumor treatment.},
}
@article {pmid36358626,
year = {2022},
author = {Romanov, VA and Karasev, IA and Klimenko, NS and Koshechkin, SI and Tyakht, AV and Malikhova, OA},
title = {Luminal and Tumor-Associated Gut Microbiome Features Linked to Precancerous Lesions Malignancy Risk: A Compositional Approach.},
journal = {Cancers},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/cancers14215207},
pmid = {36358626},
issn = {2072-6694},
support = {No//PENTAX Europe GmbH/ ; },
abstract = {Colorectal cancer is the third most commonly diagnosed cancer worldwide. Human gut microbiome plays important roles in protecting against it, as well as contributing to its onset and progression. Identification of specific bacterial taxa associated with early stages of colorectal cancer may help develop effective microbiome-based diagnostics. For precancerous lesions, links of their characteristics to luminal and tumor-associated microbiome composition are to be elucidated. Paired stool and tumor brush biopsy samples were collected from 50 patients with precancerous lesions and early forms of colon cancer; their microbial communities were profiled using high-throughput 16S rRNA sequencing. We showed that the microbiome differences between stool and biopsy samples can be to a high extent computationally corrected. Compositionality-aware statistical analysis of microbiome composition revealed its associations with the number of lesions, lesion type, location and malignization pathway. A major determinant of precancerous lesions malignancy risk-the number of lesions-was positively associated with the abundance of H2S-producing taxa. Our results contribute to the basis for developing early non-invasive colorectal cancer diagnostics via identifying microorganisms likely participating in early stages of cancer pathogenesis.},
}
@article {pmid36358596,
year = {2022},
author = {Huang, Q and Wei, X and Li, W and Ma, Y and Chen, G and Zhao, L and Jiang, Y and Xie, S and Chen, Q and Chen, T},
title = {Endogenous Propionibacterium acnes Promotes Ovarian Cancer Progression via Regulating Hedgehog Signalling Pathway.},
journal = {Cancers},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/cancers14215178},
pmid = {36358596},
issn = {2072-6694},
support = {20202ACB206008//Key R&amp;D Project of Jiangxi Science and Technology Department/ ; 81960470//the National Natural Science Founda tion of China/ ; },
abstract = {BACKGROUND: The oncogenesis and progression of epithelial ovarian cancer (EOC) is a complicated process involving several key molecules and factors, yet whether microbiota are present in EOC, and their role in the development of EOC, remains greatly unknown.<br><br>METHODS: In this study, 30 patients were enrolled to compare the similarities and differences of intratumour microbiota among patients with epithelial benign ovarian tumours (EBOTs) and patients with EOC based on the high-throughput sequencing method. Subsequently, we further isolated the specific EOC-related bacteria and defined Propionibacterium acnes as a key strain in facilitating EOC progression. More importantly, we constructed a mouse EOC model to evaluate the effect of the P. acnes strain on EOC using immunohistochemistry, Western blotting, and RT-qPCR.<br><br>RESULTS: The high-throughput sequencing showed that the intratumour microbiota in EOC tissues had a higher microbial diversity and richness compared to EBOT tissues. The abundance of previously considered pathogens, Actinomycetales, Acinetobacter, Streptococcus, Ochrobacterium, and Pseudomonadaceae Pseudomonas, was increased in the EOC tissues. Meanwhile, we discovered the facilitating role of the P. acnes strain in the progression of EOC, which may be partially associated with the increased inflammatory response to activate the hedgehog (Hh) signalling pathway. This microbial-induced EOC progression mechanism is further confirmed using the inhibitor GANT61.<br><br>CONCLUSIONS: This study profiled the intratumour microbiota of EBOT and EOC tissues and demonstrated that the diversity and composition of the intratumour microbiota were significantly different. Furthermore, through in vivo and in vitro experiments, we confirmed the molecular mechanism of intratumour microbiota promotion of EOC progression in mice, which induces inflammation to activate the Hh signalling pathway. This could provide us clues for improving EOC treatment.},
}
@article {pmid36358513,
year = {2022},
author = {Silva, DF and Empadinhas, N and Cardoso, SM and Esteves, AR},
title = {Neurodegenerative Microbially-Shaped Diseases: Oxidative Stress Meets Neuroinflammation.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/antiox11112141},
pmid = {36358513},
issn = {2076-3921},
support = {EXPL/MED-NEU/1515/2021//Fundação para a Ciência e Tecnologia/ ; PTDC/MED-NEU/3644/2020//Fundação para a Ciência e Tecnologia/ ; UIDB/04539/2020//Fundação para a Ciência e Tecnologia/ ; UIDP/04539/2020//Fundação para a Ciência e Tecnologia/ ; LA/P/0058/2020//Fundação para a Ciência e Tecnologia/ ; COMPETE 2020 - Operational Programme for Competitiveness and Internationalization//European Regional Development Fund (ERDF)/ ; },
abstract = {Inflammation and oxidative stress characterize a number of chronic conditions including neurodegenerative diseases and aging. Inflammation is a key component of the innate immune response in Alzheimer's disease and Parkinson's disease of which oxidative stress is an important hallmark. Immune dysregulation and mitochondrial dysfunction with concomitant reactive oxygen species accumulation have also been implicated in both diseases, both systemically and within the Central Nervous System. Mitochondria are a centrally positioned signalling hub for inflammatory responses and inflammatory cells can release reactive species at the site of inflammation often leading to exaggerated oxidative stress. A growing body of evidence suggests that disruption of normal gut microbiota composition may induce increased permeability of the gut barrier leading to chronic systemic inflammation, which may, in turn, impair the blood-brain barrier function and promote neuroinflammation and neurodegeneration. The gastrointestinal tract is constantly exposed to myriad exogenous substances and microbial pathogens, which are abundant sources of reactive oxygen species, oxidative damage and pro-inflammatory events. Several studies have demonstrated that microbial infections may also affect the balance in gut microbiota composition (involving oxidant and inflammatory processes by the host and indigenous microbiota) and influence downstream Alzheimer's disease and Parkinson's disease pathogenesis, in which blood-brain barrier damage ultimately occurs. Therefore, the oxidant/inflammatory insults triggered by a disrupted gut microbiota and chronic dysbiosis often lead to compromised gut barrier function, allowing inflammation to "escape" as well as uncontrolled immune responses that may ultimately disrupt mitochondrial function upwards the brain. Future therapeutic strategies should be designed to "restrain" gut inflammation, a goal that could ideally be attained by microbiota modulation strategies, in alternative to classic anti-inflammatory agents with unpredictable effects on the microbiota architecture itself.},
}
@article {pmid36358343,
year = {2022},
author = {Siddiqui, R and Boghossian, A and Alharbi, AM and Alfahemi, H and Khan, NA},
title = {The Pivotal Role of the Gut Microbiome in Colorectal Cancer.},
journal = {Biology},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/biology11111642},
pmid = {36358343},
issn = {2079-7737},
abstract = {Colorectal cancer is the third most diagnosed cancer worldwide and the second most prevalent cause of cancer-related mortality. It is believed that alterations within the gut microbiome may impact the development and progression of cancer. Additionally, the diet an individual maintains and the amount of alcohol consumed can alter the microbiome, thus impacting the development of colorectal cancer. A diet focused on fiber intake is considered beneficial, as it contains short-chain fatty acids such as butyrate, which have antitumor properties. Furthermore, current treatment strategies, such as chemotherapy, have various side effects. In this review, we discuss the role of the gut microbiome and oral bacteria in relation to colorectal cancer. We also deliberate on the role of diet and alcohol consumption in the development of colorectal cancer. Moreover, the influence of the various metabolites within the gut and the importance of gut inflammation in the development of colorectal cancer are explained. Finally, potential therapies such as fecal microbiota transfer and post/prebiotics are elaborated on. To further comprehend risk factors in the development of colorectal cancer, future studies are warranted to determine the precise mechanisms of action between the gut microbiome and carcinogenesis in order to develop therapies that may target gut microbial dysbiosis.},
}
@article {pmid36358323,
year = {2022},
author = {Pezzino, S and Sofia, M and Faletra, G and Mazzone, C and Litrico, G and La Greca, G and Latteri, S},
title = {Gut-Liver Axis and Non-Alcoholic Fatty Liver Disease: A Vicious Circle of Dysfunctions Orchestrated by the Gut Microbiome.},
journal = {Biology},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/biology11111622},
pmid = {36358323},
issn = {2079-7737},
abstract = {Non-alcoholic fatty liver disease (NAFLD) is a prevalent, multifactorial, and poorly understood liver disease with an increasing incidence worldwide. NAFLD is typically asymptomatic and coupled with other symptoms of metabolic syndrome. The prevalence of NAFLD is rising in tandem with the prevalence of obesity. In the Western hemisphere, NAFLD is one of the most prevalent causes of liver disease and liver transplantation. Recent research suggests that gut microbiome dysbiosis may play a significant role in the pathogenesis of NAFLD by dysregulating the gut-liver axis. The so-called "gut-liver axis" refers to the communication and feedback loop between the digestive system and the liver. Several pathological mechanisms characterized the alteration of the gut-liver axis, such as the impairment of the gut barrier and the increase of the intestinal permeability which result in endotoxemia and inflammation, and changes in bile acid profiles and metabolite levels produced by the gut microbiome. This review will explore the role of gut-liver axis disruption, mediated by gut microbiome dysbiosis, on NAFLD development.},
}
@article {pmid36358303,
year = {2022},
author = {Xu, X and De Mandal, S and Wu, H and Zhu, S and Kong, J and Lin, S and Jin, F},
title = {Effect of Diet on the Midgut Microbial Composition and Host Immunity of the Fall Armyworm, Spodoptera frugiperda.},
journal = {Biology},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/biology11111602},
pmid = {36358303},
issn = {2079-7737},
support = {31972345//National Natural Science Foundation of China/ ; },
abstract = {The fall armyworm (Spodoptera frugiperda, J.E. Smith) is one of the most important agricultural pests in the world and causes serious damage to many significant crops. Insect gut microbiota plays a vital role in host immunity, digestion, and development, helping the higher organism colonize in a new environment. However, the effects of different diets on midgut microbial composition and host immunity in S. frugiperda remain unclear. So far, no reports have compared the gut microbiota of fall armyworm reared using an artificial diet compared to corn leaf in Guangzhou, China. High-throughput 16S rRNA sequencing technology was applied to gain insight into the composition of the gut microbiota of S. frugiperda feeding on corn leaf (field diet) and on a starch-rich artificial diet (lab diet). The fall armyworm gut microbiota was dominated by the bacterial phyla Firmicutes and Proteobacteria. Despite the difference in diet, the core bacterial community was represented by the genus Enterococcus. However, the bacterial community is dominated by a few phylotypes, namely operational taxonomical units 1 (OTU1) (Enterococcus casseliflavus), OTU3 (Enterobacteriaceae), OTU2 (Weissella), and OTU4 (Clostridium), accounting for 97.43% of the total OTUs in the complete dataset. A significant difference was identified in the bacterial communities between the "lab diet" and the "field diet" groups. OTU1 and OTU2 were significantly higher in the "field diet" group, whereas OTU3 and OTU4 were higher in the "lab diet" group. A phylogenetic investigation of the communities by reconstruction of unobserved states (PICRUSt) predicted functional analysis indicates the presence of several genes associated with plant biomass degradation. Importantly, antibiotic-mediated perturbation of the midgut microbial community significantly impacts the expression profile of the important immune genes of the host. Furthermore, the oral reintroduction of gut bacterial isolates (E. mundtii and E. gallinarum) significantly enhances host resistance to AcMNPV infection. Taken together, our results indicate that diet composition is an important driver in shaping insect gut microbiome and immune gene expression, ultimately playing an important role in the pest defense system.},
}
@article {pmid36358296,
year = {2022},
author = {Stavridou, E and Karamichali, I and Lagiotis, G and Patsea, E and Osathanunkul, M and Madesis, P},
title = {Seasonal Shifts in Soil Microbiome Structure Are Associated with the Cultivation of the Local Runner Bean Variety around the Lake Mikri Prespa.},
journal = {Biology},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/biology11111595},
pmid = {36358296},
issn = {2079-7737},
abstract = {Leguminous crops play a key role in food production and agroecosystem sustainability. However, climate change and agricultural intensification have a significant impact on the available arable land, soil microbiome functions, and ultimately, crop productivity. The "Prespa bean" (Phaseolous coccineous L.) is an important leguminous crop for the agricultural economy of the rural areas surrounding the lake, Mikri Prespa, which is of significant ecological importance. The seasonal effects on soil microbiome structure, diversity and functions associated with the runner bean cultivation were investigated using 16S rRNA amplicon sequencing. The results indicated that the presence of the runner bean differentially shaped the soil microbial community structure. The runner bean was implicated in the recruitment of specific bacteria, by favouring or excluding specific classes or even phyla. Soil functions involved in nutrient availability and carbon metabolism, among other pathways, were associated with microbiome-plant interactions. The temporal relative abundance shifts could be explained by the impact of soil organic matter, the fertilization regime, and the equilibrium in carbon metabolic processes. This research has shown the effect of runner bean cultivation on the soil microbiome which, in future, may potentially contribute to research into sustainable agricultural productivity and the protection of soil ecosystem services.},
}
@article {pmid36358294,
year = {2022},
author = {Simon, C and McHale, M and Sulpice, R},
title = {Applications of Ulva Biomass and Strategies to Improve Its Yield and Composition: A Perspective for Ulva Aquaculture.},
journal = {Biology},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/biology11111593},
pmid = {36358294},
issn = {2079-7737},
support = {19/FFP/6841/SFI_/Science Foundation Ireland/Ireland ; project number 366//European Union Northern Periphery and Arctic Programme/ ; CA 20106//European Union, COST action/ ; project Atlantis//Nestlé Foundation/ ; },
abstract = {Sea lettuce (Ulva spp.), with its worldwide distribution and remarkable ability to grow rapidly under various conditions, represents an important natural resource that is still under-exploited. Its biomass can be used for a wide range of applications in the food/feed, pharmaceutical, nutraceutical, biofuel, and bioremediation industries. However, knowledge of the factors affecting Ulva biomass yield and composition is far from complete. Indeed, the respective contributions of the microbiome, natural genetic variation in Ulva species, environmental conditions and importantly, the interactions between these three factors on the Ulva biomass, have been only partially elucidated. Further investigation is important for the implementation of large-scale Ulva aquaculture, which requires stable and controlled biomass composition and yields. In this review, we document Ulva biomass composition, describe the uses of Ulva biomass and we propose different strategies for developing a sustainable and profitable Ulva aquaculture industry.},
}
@article {pmid36358286,
year = {2022},
author = {Yang, X and Yu, B and Song, C and Feng, C and Zhang, J and Wang, X and Cheng, G and Yang, R and Wang, W and Zhu, Y},
title = {The Effect of Long-Term Moderate Static Magnetic Field Exposure on Adult Female Mice.},
journal = {Biology},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/biology11111585},
pmid = {36358286},
issn = {2079-7737},
support = {2008085MC105//Anhui Provincial Natural Science Foundation/ ; KJ2021A0925; KJ2020A0095//Anhui Provincial Natural Science Research Project of Higher Education/ ; 2020rcjj46//Research Foundation for Talented Scholars of Hefei Normal University/ ; 2022rcjj21//Research Foundation for Talented Scholars of Hefei Normal University/ ; },
abstract = {Because of the high cost and safety of ultra-high magnetic resonance imaging (MRI), its application has certain limitations. Whereas 0.5-3 T MRI has been widely applied in hospitals, static magnetic fields (SMFs) have been shown to improve mice mental health and have anti-tumor potentials. Here, we compared the effects of the upward and downward 150 mT SMF groups with the sham group on C57BL/6J adult female mice. Locomotor and exploratory activity were also measured by behavioral tests, including the open field and elevated plus test. Additionally, physiology, pathology indicators and gut microbiota were examined. We found that 150 mT SMFs long-term exposure enhanced locomotive and exploratory activity of mice, especially the downward 150 mT SMF. Compared with the downward 150 mT SMF group, the movement speed and distance in the center area of the sham group were increased by 65.99% (p < 0.0001) and 68.58% (p = 0.0038), respectively. Moreover, compared to the sham group, downward 150 mT SMF increased the number of entrances to the center area by 67.0% (p = 0.0082) and time in the center area by 77.12% (p = 0.0054). Additionally, we observed that upward 150 mT SMF improved the number of follicles (~2.5 times, p = 0.0325) and uterine glands through increasing the total antioxidant capacity and reducing lipid peroxidation level in mice. Gut microbiome analysis showed that 150 mT SMFs long-term exposure improved the microbiota abundance (Clostridium, Bifidobacterium, Ralstonia and Yaniella) in the genus level, which may affect metabolism, anxiety and behavior in adult female mice. Our results demonstrated that 150 mT SMFs long-term exposure not only had good biosafety, but also improved athletic performance, emotion and the function of ovarian, uterine and gut microbiota abundance in adult female mice, which unraveled the potential of moderate long-term SMF exposure in clinical applications.},
}
@article {pmid36358176,
year = {2022},
author = {Sági, V and Makra, N and Csoszánszki, N and Decmann, A and Szabó, D and Garami, M},
title = {The Influence of the Gut Microbiome in Paediatric Cancer Origin and Treatment.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/antibiotics11111521},
pmid = {36358176},
issn = {2079-6382},
abstract = {Knowledge of the complexity of the gut microbiota is expanding, and its importance in physiological processes and disease development is widely studied. The aim of this review is to present the most relevant and recent research on the associations between gut microbiota and oncologic disease. Recently, a number of associations between the gut microbiome and neoplasms-regarding tumorigenesis, prognosis and therapeutic efficacy-have been reported. The effects of the gut microbiome on these processes are via the direct and indirect immunomodulating effects of bacteria. Studies have been done mainly in adult populations, where its effect on immunomodulating therapies was unambiguous. In paediatric populations, however, due to the low number of cases and the complex therapeutic approaches, there have been only a few studies. Among them, children with acute lymphoblastic leukaemia were mainly involved. Significant alterations in the abundance of certain bacteria were associated with altered therapeutic responses. Regarding solid tumours, studies with low case numbers have been reported; no significant discoveries have been described so far. In the future, studies with larger cohorts are needed in order to better understand the associations between bacteria and neoplasms and to improve prognosis in the paediatric oncologic population.},
}
@article {pmid36358125,
year = {2022},
author = {Xu, X and Huang, P and Cui, X and Li, X and Sun, J and Ji, Q and Wei, Q and Huang, Y and Li, Z and Bao, G and Liu, Y},
title = {Effects of Dietary Coated Lysozyme on the Growth Performance, Antioxidant Activity, Immunity and Gut Health of Weaned Piglets.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/antibiotics11111470},
pmid = {36358125},
issn = {2079-6382},
support = {No. CARS-43-C-2//China Agriculture Research System of MOF and MARA/ ; No. 2021C02007 and No. 2019C02052//Zhejiang Provincial Key Research and Development Program/ ; No. 31672598//National Natural Science Foundation of China/ ; },
abstract = {The purpose of this study was to evaluate the effects of dietary coated lysozyme on growth performance, serum biochemical indexes, antioxidant activity, digestive enzyme activity, intestinal permeability, and the cecal microbiota in weaned piglets. In total, 144 weaned Large White × Landrace piglets were divided into six treatment groups, with 3 replicates and 8 piglets per replicate: CN, a basal diet; CL-L, CL-M, and CL-H, basal diet supplemented with 100, 150, 500 mg/kg coated lysozyme; UL, basal diet supplemented with 150 mg/kg lysozyme; and Abs, basal diet supplemented with 150 mg/kg guitaromycin for 6 weeks. Compared with the CN and UL diets, dietary CL-H inclusion increased the average daily gain (ADG) and decreased the feed/gain (F/G) ratio of piglets (p < 0.05). The addition of 500 mg/kg coated lysozyme to the diet significantly increased the total protein (TP) and globulin (Glob) plasma levels of weaned piglets (p < 0.05). Supplementation with 500 mg/kg coated lysozyme significantly increased the serum IgM concentration and increased lipase activity in the duodenum (p < 0.05). The addition of coated lysozyme and lysozyme significantly decreased the malondialdehyde (MDA) content, while the superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and total antioxidant capacity (T-AOC) levels all increased (p < 0.05). High-throughput sequencing results showed that CL-H treatment effectively improved the intestinal microbiome. The relative abundance of Terrisporobacter in the CL-H and CL-M groups was significantly lower than that in the other groups (p < 0.05). LEfSe analysis results showed that the relative abundance of Coprococcus_3 was higher in the CL-M treatment group. The marker species added to the CL-H treatment group was Anaerofilum. In summary, as a potential substitute for feed antibiotics, lysozyme is directly used as a dietary additive, which is inefficient. Therefore, we used palm oil as the main coating material to coat lysozyme. Lysozyme after coating can more effectively improve the growth performance of piglets by improving the intestinal flora, improving the activity of digestive enzymes, reducing the damage to intestinal permeability and oxidative stress in piglets caused by weaning stress, and improving the immunity of piglets.},
}
@article {pmid36358119,
year = {2022},
author = {Calatayud, M and Duysburgh, C and Van den Abbeele, P and Franckenstein, D and Kuchina-Koch, A and Marzorati, M},
title = {Long-Term Lactulose Administration Improves Dysbiosis Induced by Antibiotic and C. difficile in the PathoGut[TM] SHIME Model.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/antibiotics11111464},
pmid = {36358119},
issn = {2079-6382},
abstract = {Clostridioides difficile infection (CDI) is the leading cause of antibiotic-associated diarrhea and an important nosocomial infection with different severity degrees. Disruption of the gut microbiota by broad-spectrum antibiotics creates a proper environment for C. difficile colonization, proliferation, and clinical disease onset. Restoration of the gut microbial ecosystem through prebiotic interventions can constitute an effective complementary treatment of CDI. Using an adapted simulator of the human gut microbial ecosystem, the PathoGut[TM] SHIME, the effect of different long-term and repeated dose lactulose treatments was tested on C. difficile germination and growth in antibiotic-induced dysbiotic gut microbiota environments. The results showed that lactulose reduced the growth of viable C. difficile cells following clindamycin treatment, shifted the antibiotic-induced dysbiotic microbial community, and stimulated the production of health-promoting metabolites (especially butyrate). Recovery of the gut microenvironment by long-term lactulose administration following CDI was also linked to lactate production, decrease in pH and modulation of bile salt metabolism. At a structural level, lactulose showed a significant bifidogenic potential and restored key commensal members of the gut ecosystem such as Lactobacillaceae, Veillonellaceae and Lachnospiraceae. These results support further human intervention studies aiming to validate the in vitro beneficial effects of lactulose on gut microbiome recovery during antibiotic exposure and CDI.},
}
@article {pmid36357898,
year = {2022},
author = {Zhang, Z and Yu, W and Li, G and He, Y and Shi, Z and Wu, J and Ma, X and Zhu, Y and Zhao, L and Liu, S and Wei, Y and Xue, J and Guo, S and Gao, Z},
title = {Characteristics of oral microbiome of healthcare workers in different clinical scenarios: a cross-sectional analysis.},
journal = {BMC oral health},
volume = {22},
number = {1},
pages = {481},
pmid = {36357898},
issn = {1472-6831},
support = {2021XM19//Key Medical Research Project of Shanxi Province/ ; 2021XM19//Key Medical Research Project of Shanxi Province/ ; 2111//Key Research and Development Plan of Linfen Science and technology/ ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; *Bacteria/genetics ; Prospective Studies ; *Microbiota ; Health Personnel ; },
abstract = {The environment of healthcare institutes (HCIs) potentially affects the internal microecology of medical workers, which is reflected not only in the well-studied gut microbiome but also in the more susceptible oral microbiome. We conducted a prospective cross-sectional cohort study in four hospital departments in Central China. Oropharyngeal swabs from 65 healthcare workers were collected and analyzed using 16S rRNA gene amplicon sequencing. The oral microbiome of healthcare workers exhibited prominent deviations in diversity, microbial structure, and predicted function. The coronary care unit (CCU) samples exhibited robust features and stability, with significantly higher abundances of genera such as Haemophilus, Fusobacterium, and Streptococcus, and a lower abundance of Prevotella. Functional prediction analysis showed that vitamin, nucleotide, and amino acid metabolisms were significantly different among the four departments. The CCU group was at a potential risk of developing periodontal disease owing to the increased abundance of F. nucleatum. Additionally, oral microbial diversification of healthcare workers was related to seniority. We described the oral microbiome profile of healthcare workers in different clinical scenarios and demonstrated that community diversity, structure, and potential functions differed markedly among departments. Intense modulation of the oral microbiome of healthcare workers occurs because of their original departments, especially in the CCU.},
}
@article {pmid36356944,
year = {2022},
author = {Liu, K and Yang, L and Wang, X and Huang, Q and Tuerhong, K and Yang, M and Zhang, R and Li, Y and Yang, S},
title = {Electroacupuncture regulates macrophage, neutrophil, and oral microbiota to alleviate alveolar bone loss and inflammation in experimental ligature-induced periodontitis.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.13748},
pmid = {36356944},
issn = {1600-051X},
abstract = {AIM: Electroacupuncture (EA) regulates distant body physiology through somatic sensory autonomic reflexes, balances the microbiome and can promote the release of immune cells into bloodstream, thereby inhibits severe systemic inflammation. This makes it possible to use EA as an integrated treatment for periodontitis.<br><br>MATERIALS AND METHODS: In this study, EA was applied to the ST36 acupoints in a ligature-induced periodontitis (LIP) mouse model. Then the effects of EA on periodontal myeloid cells, cytokines and microbiome were comprehensively analyzed using flow cytometry, qPCR and 16S sequencing.<br><br>RESULTS: Results demonstrated that EA could significantly relieve periodontal bone resorption. EA also suppressed infiltration of macrophages and neutrophils, reduced gene expression of the pro-inflammatory cytokines IL-1β, IL-6, IL-17 and TNF-α, while increased expression of anti-inflammatory factors IL-4 and IL-10 in periodontal tissues. Moreover, composition of the periodontal microbiome was regulated by EA, finding that complex of microbiota, including supragingival Veillonella, subgingival Streptococcus, and subgingival Erysipelatoclostridium, were significantly reduced. Meanwhile, nitrate and nitrate-related activities of subgingival microbiota were reversed. Network analysis revealed close relationships among Veillonella, Streptococcus, and Bacteroides.<br><br>CONCLUSION: Our study indicated that EA effectively alleviated inflammation and bone resorption in LIP mice, potentially via regulation of myeloid cells, cytokines, and periodontal microbiome.},
}
@article {pmid36356938,
year = {2022},
author = {Zhu, R and Tian, P and Zhang, H and Wang, G and Chen, W},
title = {Gut microbiome-brain interactions in anorexia nervosa: Potential mechanisms and regulatory strategies.},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {109315},
doi = {10.1016/j.neuropharm.2022.109315},
pmid = {36356938},
issn = {1873-7064},
abstract = {Anorexia nervosa (AN) is a psychiatric disorder characterised by malnutrition, fear of weight gain, and body image disturbances. The aetiology of AN is complex, and may involve environmental factors, genetic factors, and biochemical factors, with the latter meaning that AN may be closely associated with neurons, neurotransmitters, and hormones related to appetite and emotional regulation. In addition, an increasing number of studies have shown there is a link between the intestinal microbiota and psychiatric disorders, such as depression. However, few studies and reviews have focused on AN and gut microbes. Accordingly, in this review, we examine the potential pathogenesis of AN in terms of changes in the gut microbiota and its metabolites, and their effects on AN. The neurobiological function of the nervous system in relation to AN are also been mentioned. Furthermore, we suggest future research directions for this field, and note that probiotics may be developed for use as dietary supplements to help alleviate AN in patients.},
}
@article {pmid36356926,
year = {2022},
author = {Pechlivanis, S and Depner, M and Kirjavainen, PV and Roduit, C and Täubel, M and Frei, R and Skevaki, C and Hose, A and Barnig, C and Schmausser-Hechfellner, E and Ege, MJ and Schaub, B and Divaret-Chauveau, A and Lauener, R and Karvonen, AM and Pekkanen, J and Riedler, J and Illi, S and von Mutius, E and , },
title = {Continuous rather than solely early farm exposure protect from hay fever development.},
journal = {The journal of allergy and clinical immunology. In practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaip.2022.10.035},
pmid = {36356926},
issn = {2213-2201},
abstract = {BACKGROUND: An important 'window of opportunity' for early life exposures has been proposed for the development of atopic eczema and asthma.<br><br>OBJECTIVE: However it is, unknown whether hay fever with a peak incidence around late school age to adolescence is similarly determined very early in life.<br><br>METHODS: In the PASTURE birth cohort potentially relevant exposures such as farm milk consumption and exposure to animal sheds were assessed at multiple time points from infancy to age 10.5 years and classified by repeated measure latent class analyses (N=769). Fecal samples at age 2 and 12 months were sequenced by 16S rRNA. Hay fever was defined by parental reported symptoms and/or physician's diagnosis of hay fever in the last 12 months using questionnaires at age 10.5 years.<br><br>RESULTS: Farm children had half the risk of hay fever at age 10.5 years (adjusted odds-ratio (aOR) [95% CI]=0.50 [0.31; 0.79]) compared to non-farm children. While early life events such as gut microbiome richness at age 12 months (aOR=0.66 [0.46; 0.96]) and exposure to animal sheds in the first three years of life (aOR=0.26 [0.06; 1.15]) were determinants of hay fever, the continuous consumption of farm milk from infancy up-to school age was necessary to exert the protective effect (aOR=0.35 [0.17; 0.72]).<br><br>CONCLUSION: While early life events determine the risk of subsequent hay fever, continuous exposure is necessary to achieve protection. These findings argue against the notion that only early life exposures set long-lasting trajectories.},
}
@article {pmid36356636,
year = {2022},
author = {Ahmed, RU and Knibbe, CA and Wilkins, F and Sherwood, LC and Howland, DR and Boakye, M},
title = {Porcine spinal cord injury model for translational research across multiple functional systems.},
journal = {Experimental neurology},
volume = {359},
number = {},
pages = {114267},
doi = {10.1016/j.expneurol.2022.114267},
pmid = {36356636},
issn = {1090-2430},
abstract = {Animal models are necessary to identify pathological changes and help assess therapeutic outcomes following spinal cord injury (SCI). Small animal models offer value in research in terms of their easily managed size, minimal maintenance requirements, lower cost, well-characterized genomes, and ability to power research studies. However, despite these benefits, small animal models have neurologic and anatomical differences that may influence translation of results to humans and thus limiting the success of their use in preclinical studies as a direct pipeline to clinical studies. Large animal models, offer an attractive intermediary translation model that may be more successful in translating to the clinic for SCI research. This is largely due to their greater neurologic and anatomical similarities to humans. The physical characteristics of pig spinal cord, gut microbiome, metabolism, proportions of white to grey matter, bowel anatomy and function, and urinary system are strikingly similar and provide great insight into human SCI conditions. In this review, we address the variety of existing porcine injury models and their translational relevance, benefits, and drawbacks in modeling human systems and functions for neurophysiology, cardiovascular, gastrointestinal and urodynamic functions.},
}
@article {pmid36356566,
year = {2022},
author = {Tian, S and Bisanz, JE},
title = {Making gut microbiomes from scratch.},
journal = {Cell host &amp; microbe},
volume = {30},
number = {11},
pages = {1508-1509},
doi = {10.1016/j.chom.2022.10.005},
pmid = {36356566},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {Studying the microbiome presents a challenge: how do we untangle the interactions of microbes at ecologically relevant scales? We highlight research by Afrizal et al. and Cheng et al., which help to solve this problem through the generation and characterization of complex synthetic communities derived from lab-grown microbes.},
}
@article {pmid36356550,
year = {2022},
author = {Berryman, MA and Milletich, PL and Petrone, JR and Roesch, LF and Ilonen, J and Triplett, EW and Ludvigsson, J},
title = {Autoimmune-associated genetics impact probiotic colonization of the infant gut.},
journal = {Journal of autoimmunity},
volume = {133},
number = {},
pages = {102943},
doi = {10.1016/j.jaut.2022.102943},
pmid = {36356550},
issn = {1095-9157},
abstract = {To exemplify autoimmune-associated genetic influence on the colonization of bacteria frequently used in probiotics, microbial composition of stool from 1326 one-year-old infants was analyzed in a prospective general-population cohort, All Babies In Southeast Sweden (ABIS). We show that an individual's HLA haplotype composition has a significant impact on which common Bifidobacterium strains thrive in colonizing the gut. The effect HLA has on the gut microbiome can be more clearly observed when considered in terms of allelic dosage. HLA DR1-DQ5 showed the most significant and most prominent effect on increased Bifidobacterium relative abundance. Therefore, HLA DR1-DQ5 is proposed to act as a protective haplotype in many individuals. Protection-associated HLA haplotypes are more likely to influence the promotion of specific bifidobacteria. In addition, strain-level differences are correlated with colonization proficiency in the gut depending on HLA haplotype makeup. These results demonstrate that HLA genetics should be considered when designing effective probiotics, particularly for those at high genetic risk for autoimmune diseases.},
}
@article {pmid36355832,
year = {2022},
author = {Li, Y and Li, Z and Sun, W and Wang, M and Li, M},
title = {Characteristics of gut microbiota in patients with primary Sjögren's syndrome in Northern China.},
journal = {PloS one},
volume = {17},
number = {11},
pages = {e0277270},
doi = {10.1371/journal.pone.0277270},
pmid = {36355832},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Dysbiosis/microbiology ; *Sjogren's Syndrome/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Clostridiaceae/genetics ; China ; },
abstract = {This study analyzes and compares the structure and diversity of gut microbiota in patients with primary Sjögren's syndrome (pSS) in Northern China to healthy individuals to identify clinical features associated with dysbiosis. We included 60 Chinese pSS patients and 50 age- and gender-matched healthy controls. DNA was extracted from stool samples and subjected to 16S ribosomal RNA gene analysis (V3-V4) for intestinal dysbiosis. In addition, patients were examined for laboratory and serological pSS features. A Spearman's correlation analysis was performed to assess correlations between individual bacteria taxa and clinical characteristics. The alpha-diversity (Chao1 and Shannon Index) and beta-diversity (unweighted UniFrac distances) of the gut microbiota differed significantly between pSS patients and healthy controls. Further analysis showed that several gut opportunistic pathogens (Bacteroides, Megamonas, and Veillonella) were significantly more abundant in pSS patients and positively correlated with their clinical indicators. In contrast, some probiotic genera (Collinsella, unidentified_Ruminococcaceae, Romboutsia, and Dorea) were significantly decreased in pSS patients and negatively correlated with their clinical indicators. Therefore, pSS patients in Northern China showed a dysbiotic intestinal microbiome enriched for potentially pathogenic genera that might be associated with autoimmune disease.},
}
@article {pmid36355185,
year = {2022},
author = {Ryman, S and Vakhtin, AA and Richardson, SP and Lin, HC},
title = {Microbiome-gut-brain dysfunction in prodromal and symptomatic Lewy body diseases.},
journal = {Journal of neurology},
volume = {},
number = {},
pages = {},
pmid = {36355185},
issn = {1432-1459},
support = {P30 GM122734/NS/NINDS NIH HHS/United States ; NS100598/NS/NINDS NIH HHS/United States ; P30 GM122734/GM/NIGMS NIH HHS/United States ; P20 AG068077/AG/NIA NIH HHS/United States ; R03 AG075408/AG/NIA NIH HHS/United States ; R61MH125126/MH/NIMH NIH HHS/United States ; },
abstract = {Lewy body diseases, such as Parkinson's disease and dementia with Lewy bodies, vary in their clinical phenotype but exhibit the same defining pathological feature, α-synuclein aggregation. Microbiome-gut-brain dysfunction may play a role in the initiation or progression of disease processes, though there are multiple potential mechanisms. We discuss the need to evaluate gastrointestinal mechanisms of pathogenesis across Lewy body diseases, as disease mechanisms likely span across diagnostic categories and a 'body first' clinical syndrome may better account for the heterogeneity of clinical presentations across the disorders. We discuss two primary hypotheses that suggest that either α-synuclein aggregation occurs in the gut and spreads in a prion-like fashion to the brain or systemic inflammatory processes driven by gastrointestinal dysfunction contribute to the pathophysiology of Lewy body diseases. Both of these hypotheses posit that dysbiosis and intestinal permeability are key mechanisms and potential treatment targets. Ultimately, this work can identify early interventions targeting initial disease pathogenic processes before the development of overt motor and cognitive symptoms.},
}
@article {pmid36355152,
year = {2022},
author = {Shenker, NS and Perdones-Montero, A and Burke, A and Stickland, S and McDonald, JAK and Cameron, SJS},
title = {Human Milk from Tandem Feeding Dyads Does Not Differ in Metabolite and Metataxonomic Features When Compared to Single Nursling Dyads under Six Months of Age.},
journal = {Metabolites},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/metabo12111069},
pmid = {36355152},
issn = {2218-1989},
support = {MR/S017437/1//UK Research and Innovation/ ; 204786/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Given the long-term advantages of exclusive breastfeeding to infants and their mothers, there is both an individual and public health benefit to its promotion and support. Data on the composition of human milk over the course of a full period of lactation for a single nursling is sparse, but data on human milk composition during tandem feeding (feeding children of different ages from different pregnancies) is almost entirely absent. This leaves an important knowledge gap that potentially endangers the ability of parents to make a fully informed choice on infant feeding. We compared the metataxonomic and metabolite fingerprints of human milk samples from 15 tandem feeding dyads to that collected from ten exclusively breastfeeding single nursling dyads where the nursling is under six months of age. Uniquely, our cohort also included three tandem feeding nursling dyads where each child showed a preferential side for feeding-allowing a direct comparison between human milk compositions for different aged nurslings. Across our analysis of volume, total fat, estimation of total microbial load, metabolite fingerprinting, and metataxonomics, we showed no statistically significant differences between tandem feeding and single nursling dyads. This included comparisons of preferential side nurslings of different ages. Together, our findings support the practice of tandem feeding of nurslings, even when feeding an infant under six months.},
}
@article {pmid36355122,
year = {2022},
author = {Deda, O and Kachrimanidou, M and Armitage, EG and Mouskeftara, T and Loftus, NJ and Zervos, I and Taitzoglou, I and Gika, H},
title = {Metabolic Phenotyping Study of Mouse Brain Following Microbiome Disruption by C.difficile Colonization.},
journal = {Metabolites},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/metabo12111039},
pmid = {36355122},
issn = {2218-1989},
support = {This research is co-financed by Greece and the European Union (European Social Fund- ESF) through the Operational Programme «Human Resources Development, Education and Lifelong Learning» in the context of the project "Reinforcement of Postdoctoral Researc//State Scholarships Foundation/ ; },
abstract = {Clostridioides difficile infection (CDI) is responsible for an increasing number of cases of post-antibiotic diarrhea worldwide, which has high severity and mortality among hospitalized elderly patients. The disruption of gut microbiota due to antibacterial medication facilitates the intestinal colonization of C. difficile. In the present study, a murine model was used to investigate the potential effects of antibiotic administration and subsequent colonization by C. difficile, as well as the effects of three different 10-day treatments (metronidazole, probiotics, and fecal microbiota transplantation), on the brain metabolome for the first time. Four different metabolomic-based methods (targeted HILIC-MS/MS, untargeted RP-LC-HRMS/MS, targeted GC-MS/MS, and untargeted GC-MS) were applied, resulting in the identification of 217 unique metabolites in the brain extracts, mainly glycerophospholipids, glycerolipids, amino acids, carbohydrates, and fatty acids. Univariate and multivariate statistical analysis revealed that CDI, as well as the subsequent treatments, altered significantly several brain metabolites, probably due to gut dysbiosis, and affected the brain through the gut-brain axis. Notably, none of the therapeutic approaches completely restored the brain metabolic profile to the original, healthy, and non-infected phenotype, even after 10 days of treatment.},
}
@article {pmid36355097,
year = {2022},
author = {Silva, AFD and Farias, JR and Franco, DCG and Galiza, AA and Motta, EP and Oliveira, ADS and Vasconcelos, CC and Cartágenes, MDSS and Rocha, CQD and Silva, MCPD and Lopes, AJO and Nascimento, FRFD and Monteiro, CA and Guerra, RNM},
title = {Anti-Candida albicans Activity of Ononin and Other Secondary Metabolites from Platonia Insignis MART.},
journal = {Metabolites},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/metabo12111014},
pmid = {36355097},
issn = {2218-1989},
support = {PAEDT-03230/17//Fundação de Amparo à Pesquisa e ao Desenvolvimento Científico e Tecnológico do Maranhão/ ; },
abstract = {Candida albicans is a human pathogen that is part of the healthy microbiome. However, it is often associated with opportunistic fungal infections. The treatment of these infections is challenging because prolonged exposure to antifungal drugs can culminate in fungal resistance during therapy, and there is a limited number of available drugs. Therefore, this study investigated the antifungal activity of ononin by in silico and in vitro assays, and in Tenebrio molitor as an alternative in vivo model of infection caused by C. albicans. Ononin is an isoflavone glycoside derived from formononetin that has various biological activities. According in silico evaluation, ononin showed the best electron affinity in molecular docking with CaCYP51, with a binding free energy of -10.89 kcal/mol, superior to that of the antifungal drugs fluconazole and posaconazole. The ononin + CaCYP51 complex formed hydrogen bonds with Tyr132, Ser378, Phe380, and Met508, as well as hydrophobic connections with Tyr118, Leu121, Phe126, Leu131, Ile304, and Leu309, and interactions with the heme group. Ononin exerted anti-Candida albicans activity, with MIC between 3.9 and 7.8 µg/mL, and inhibited young and mature biofilms, with a reduction in cell density and metabolic activity of 50 to 80%. The compound was not cytotoxic to sheep red blood cells at concentrations up to 1000 µg/mL. Larvae of the mealworm T. molitor were used as an alternative in vivo model of C. albicans infection. Ononin was able to prolong larval survival at concentrations of 0.5, 1, and 5 mg/kg, and was not toxic up to a concentration of 20 mg/kg. Moreover, ononin reduced the fungal charge in treated animals. In conclusion, our results suggest that ononin has anti-Candida albicans activity and is a potential candidate for the development of new therapeutic alternatives.},
}
@article {pmid36354920,
year = {2022},
author = {Szczepańska, M and Blicharz, L and Nowaczyk, J and Makowska, K and Goldust, M and Waśkiel-Burnat, A and Czuwara, J and Samochocki, Z and Rudnicka, L},
title = {The Role of the Cutaneous Mycobiome in Atopic Dermatitis.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {11},
pages = {},
doi = {10.3390/jof8111153},
pmid = {36354920},
issn = {2309-608X},
abstract = {Atopic dermatitis is a chronic inflammatory skin disorder characterized by eczematous lesions, itch, and a significant deterioration in the quality of life. Recently, microbiome dysbiosis has been implicated in the pathogenesis of atopic dermatitis. Changes in the fungal microbiome (also termed mycobiome) appear to be an important factor influencing the clinical picture of this entity. This review summarizes the available insights into the role of the cutaneous mycobiome in atopic dermatitis and the new research possibilities in this field. The prevalence and characteristics of key fungal species, the most important pathogenesis pathways, as well as classic and emerging therapies of fungal dysbiosis and infections complicating atopic dermatitis, are presented.},
}
@article {pmid36354864,
year = {2022},
author = {Yang, T and Wang, X and Zhou, X},
title = {Microbiome Analysis of the Bamboo Aphid Melanaphis bambusae Infected with the Aphid Obligate Pathogen Conidiobolus obscurus (Entomophthoromycotina).},
journal = {Insects},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/insects13111040},
pmid = {36354864},
issn = {2075-4450},
support = {31870637//National Natural Science Foundation of China/ ; },
abstract = {Insect-associated microbes exert diverse effects on host fitness. This study provides insights into the microbiota of the bamboo aphid, Melanaphis bambusae, and their response to Conidiobolus obscurus infection. 16S rRNA and ITS sequencing data were used to analyze the bacterial and fungal samples associated with healthy, infected, and starved aphids. At ≥97% nucleotide similarity, the total reads were clustered into 79 bacteria and 97 fungi operational Taxonomic Units (OTUs). The phyla Proteobacteria and Ascomycota dominated the bacterial and fungal communities, respectively. The significant divergence in OTU distribution presented differential profiles of the microbiota in response to host conditions. Lower α-diversity indices were found in bacterial and fungal diversity when the aphids were experiencing fungal infection and starvation stresses, respectively. The β-diversity analyses of the communities showed significant differences among the three host conditions, demonstrating that aphid-associated microbiota could significantly shift in response to varying host conditions. Moreover, some OTUs increased under fungal infection, which potentially increased aphid susceptibility. Presumably, C. obscurus infection contributed to this increase by causing the disintegration of host tissues other than host starvation. In conclusion, understanding the differentiation of aphid microbiota caused by fungal entomopathogens helped facilitate the development of novel pest management strategies.},
}
@article {pmid36354779,
year = {2022},
author = {Li, N and Wang, Y and Zhou, J and Chen, R and Li, J and Zhao, X and Zhou, P and Liu, C and Chen, Y and Song, L and Zhao, H and Yan, H and Yan, S},
title = {Association between the Changes in Trimethylamine N-Oxide-Related Metabolites and Prognosis of Patients with Acute Myocardial Infarction: A Prospective Study.},
journal = {Journal of cardiovascular development and disease},
volume = {9},
number = {11},
pages = {},
doi = {10.3390/jcdd9110380},
pmid = {36354779},
issn = {2308-3425},
support = {2016-I2M-1-009//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; SZSM201911017//Fund of &quot;Sanming&quot; Project of Medicine in Shenzhen/ ; SZXK001//Shenzhen Key Medical Discipline Construction Fund/ ; 81970308//National Natural Science Foundation of China/ ; },
abstract = {This study aimed to investigate the association between changes in levels of trimethylamine N-oxide (TMAO) and its precursors and the prognosis of patients with acute myocardial infarction (AMI). Patients diagnosed with AMI were prospectively enrolled at Fuwai Hospital between March 2017 and January 2020. TMAO, betaine, choline, and L-carnitine were measured in 1203 patients at their initial admission and 509 patients at their follow-up of one month. Major adverse cardiovascular events (MACE), a composite of all-cause death, recurrence of MI, rehospitalization caused by HF, ischemic stroke, and any revascularization, were followed up. A decision tree by TMAO levels implicated that compared to those with low levels at admission, patients with high TMAO levels at both time points showed an increased risk of MACE (adjusted hazard ratio (HR) 1.59, 95% confidence interval (CI): 1.03-2.46; p = 0.034), while patients with high TMAO levels at admission and low levels at follow-up exhibited a similar MACE risk (adjusted HR 1.20, 95% CI: 0.69-2.06; p = 0.520). Patients with high choline levels at admission and follow-up showed an elevated MACE risk compared to those with low levels at both time points (HR 1.55, 95% CI: 1.03-2.34; p = 0.034). Repeated assessment of TMAO and choline levels helps to identify the dynamic risk of cardiovascular events.},
}
@article {pmid36354350,
year = {2022},
author = {Zhong, J and Wu, D and Zeng, Y and Wu, G and Zheng, N and Huang, W and Li, Y and Tao, X and Zhu, W and Sheng, L and Shen, X and Zhang, W and Zhu, R and Li, H},
title = {The Microbial and Metabolic Signatures of Patients with Stable Coronary Artery Disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0246722},
doi = {10.1128/spectrum.02467-22},
pmid = {36354350},
issn = {2165-0497},
abstract = {Growing evidence indicates an association between gut dysbiosis and coronary artery disease (CAD). However, the underlying mechanisms relevant to stable CAD (SCAD) pathogenesis, based on microbe-host metabolism interactions, are poorly explored. Here, we constructed a quasi-paired cohort based on the metabolic background of metagenomic samples by the propensity score matching (PSM) principle. Compared to healthy controls (HCs), gut microbiome disturbances were observed in SCAD patients, accompanied by differences in serum metabolome, mainly including elevated acylcarnitine and decreased unsaturated fatty acids in SCAD patients, which implicated the reduced cardiac fatty acid oxidation. Moreover, we identified Ralstonia pickettii as the core strain responsible for impaired microbial homeostasis in SCAD patientsm and may be partly responsible for the decrease of host unsaturated fatty acid levels. These findings highlight the importance of unsaturated fatty acids, R. pickettii, and their interaction in the pathogenesis of SCAD. IMPORTANCE Stable coronary artery disease (SCAD) is an early stage of CAD development. It is important to understand the pathogenesis of SCAD and find out the possible prevention and control targets for delaying the progression of CAD. We observed reduced levels of unsaturated fatty acids (USFAs) in SCAD patients. However, the reduced USFAs may be related to Ralstonia Pickettii, which was the core strain responsible for the impaired gut microbial function in SCAD patients, and further affected the host's cardiovascular health by altering amino acids, vitamin B metabolism, and LPS biosynthesis. These findings not only emphasized the importance of USFAs for cardiovascular health, but also R. Pickettii for maintaining microbial function homeostasis. More importantly, our study revealed, for the first time, that enriched R. Pickettii might be responsible for the reduced USFAs in SCAD patients, which adds new evidence on the role of altered gut microbiota for SCAD formation.},
}
@article {pmid36354216,
year = {2022},
author = {Benucci, GMN and Beschoren da Costa, P and Wang, X and Bonito, G},
title = {Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16269},
pmid = {36354216},
issn = {1462-2920},
abstract = {Sustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant-associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and for evaluating changes in ecosystem functions. Here, we leverage a long-term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil-depth gradient in poplar, restored prairie and switchgrass in order to understand their effects on the microbial communities. High throughput amplicon sequencing of the fungal ITS and prokaryotic 16S DNA regions showed a common trend with depth of root and soil microbial community richness decreasing and evenness increasing. Ecological niche (root vs. soil) had the strongest effect on community structure, followed by depth then crop. Stochastic processes dominated the structuring of fungal communities in deeper soil layers while OTUs in surface soil layers were more likely to co-occur and to be enriched by plant hosts. Prokaryotic communities were dispersal limited at deeper depths. Microbial networks showed a higher density, connectedness, average degree and module size in deeper soils. We observed a decrease in fungal-fungal links and an increase of bacteria-bacteria links with increasing depth in all crops, particularly in the root microbiome. This article is protected by copyright. All rights reserved.},
}
@article {pmid36353996,
year = {2022},
author = {Wang, T and Xing, Y and Peng, B and Yang, K and Zhang, C and Chen, Y and Geng, G and Li, Q and Fu, J and Li, M and Luo, Z and Fu, Z and Wang, J},
title = {Respiratory Microbiome Profile of Pediatric Pulmonary Hypertension Patients Associated With Congenital Heart Disease.},
journal = {Hypertension (Dallas, Tex. : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1161/HYPERTENSIONAHA.122.19182},
pmid = {36353996},
issn = {1524-4563},
abstract = {BACKGROUND: Pulmonary hypertension (PH) associated with congenital heart disease (CHD) is the most common type of PH in pediatric patients. The airway microbiome profile in CHD-PH patients remains rarely studied.<br><br>METHODS: A total of 158 children were recruited for collection of oropharyngeal swabs to sequence the 16S ribosomal RNA (16S rRNA) V3-V4 region of respiratory microbiome, to establish a correlation between these bacterial groups and echocardiography indicators in CHD-PH patients.<br><br>RESULTS: Bacterial α- and β-diversity of the airway microbiome indicated a significantly lower richness in the CHD-PH group and compositional differences associated with the specific taxa and their relative abundances in the upper respiratory tract. Principal coordinate analysis showed that the pharynx microbiota composition in the CHD-PH group varied from that in the CHD or control group. The linear discriminant analysis effect size (LefSe) also highlighted an increased presence of Streptococcus and Rothia in pediatric CHD-PH patients. Comparison of microbial composition between pediatric and adult PH patients showed significant differences and separation of microbiota. The correlation between bacterial abundance and transthoracic echocardiography indexes in CHD-associated PH indicated that different groups of microbiomes may be related to different PH grades.<br><br>CONCLUSIONS: In summary, our study reported the systematic definition and divergent profile of the upper respiratory tract microbiota in pediatric PH patients, CHD and reference subjects, as well as between pediatric and adult PH patients.},
}
@article {pmid36353788,
year = {2022},
author = {Yoon, H and Kim, NE and Park, J and Shin, CM and Kim, N and Lee, DH and Park, JY and Choi, CH and Kim, JG and Park, YS},
title = {Analysis of the gut microbiome using extracellular vesicles in the urine of patients with colorectal cancer.},
journal = {The Korean journal of internal medicine},
volume = {},
number = {},
pages = {},
doi = {10.3904/kjim.2022.112},
pmid = {36353788},
issn = {2005-6648},
abstract = {Background/Aims: We evaluated the gut microbiome using extracellular vesicles (EVs) in the urine of patients with colorectal cancer (CRC) to determine whether gut-microbe-derived EVs could be a potential biomarker for the diagnosis of CRC.<br><br>Methods: EVs were isolated from the urine of patients with CRC and healthy controls. DNA was extracted from the EVs, and the bacterial composition was analyzed using next-generation sequencing of the 16S rRNA.<br><br>Results: A total of 91 patients with CRC and 116 healthy controls were enrolled. We found some specific microbiomes that were more or less abundant in the CRC group than in the control group. The alpha-diversity of the gut microbiome was significantly lower in the CRC group than in the control group. A significant difference was observed in the beta-diversity between the groups. The alpha-diversity indices between patients with early- and late-stage CRC showed conflicting results; however, there was no significant difference in the beta-diversity according to the stage of CRC. There was no difference in the alpha- and beta-diversity of the gut microbiome corresponding to the location of CRC (proximal vs. distal).<br><br>Conclusions: A distinct gut microbiome is reflected in the urine EVs of patients with CRC compared with that in the healthy controls. Microbial signatures from EVs in urine could serve as potential biomarkers for the diagnosis of CRC.},
}
@article {pmid36353731,
year = {2022},
author = {Jensen-Kroll, J and Demetrowitsch, T and Clawin-Rädecker, I and Klempt, M and Waschina, S and Schwarz, K},
title = {Microbiota independent effects of oligosaccharides on Caco-2 cells -A semi-targeted metabolomics approach using DI-FT-ICR-MS coupled with pathway enrichment analysis.},
journal = {Frontiers in molecular biosciences},
volume = {9},
number = {},
pages = {968643},
pmid = {36353731},
issn = {2296-889X},
abstract = {Milk oligosaccharides (MOS) and galactooligosaccharides (GOS) are associated with many benefits, including anti-microbial effects and immune-modulating properties. However, the cellular mechanisms of these are largely unknown. In this study, the effects of enriched GOS and MOS mixtures from caprine and bovine milk consisting mainly 6'-galactosyllactose, 3'-sialyllactose, and 6'-sialyllactose on Caco-2 cells were investigated, and the treatment-specific metabolomes were described. In the control, the cells were treated with a sugar mix consisting of one-third each of glucose, galactose and lactose. A local metabolomics workflow with pathway enrichment was established, which specifically addresses DI-FT-ICR-MS analyses and includes adaptations in terms of measurement technology and sample matrices. By including quality parameters, especially the isotope pattern, we increased the precision of annotation. The independence from online tools, the fast adaptability to changes in databases, and the specific adjustment to the measurement technology and biomaterial used, proved to be a great advantage. For the first time it was possible to find 71 active pathways in a Caco-2 cell experiment. These pathways were assigned to 12 main categories, with amino acid metabolism and carbohydrate metabolism being the most dominant categories in terms of the number of metabolites and metabolic pathways. Treatment of Caco-2 cells with high GOS and glucose contents resulted in significant effects on several metabolic pathways, whereas the MOS containing treatments resulted only for individual metabolites in significant changes. An effect based on bovine or caprine origin alone could not be observed. Thus, it was shown that MOS and GOS containing treatments can exert microbiome-independent effects on the metabolome of Caco-2 cells.},
}
@article {pmid36353544,
year = {2022},
author = {Shi, W and Zhu, H and Yuan, L and Chen, X and Huang, X and Wang, K and Li, Z},
title = {Vaginal microbiota and HPV clearance: A longitudinal study.},
journal = {Frontiers in oncology},
volume = {12},
number = {},
pages = {955150},
pmid = {36353544},
issn = {2234-943X},
abstract = {Although vaginal microbiota (VM) may interact with human papillomavirus (HPV) infection and clearance, longitudinal data remain very limited. We aimed to investigate the association between VM at baseline and the clearance of high-risk HPV (HR-HPV) infection within 12 months. Cervical swabs were collected at diagnosis from 85 patients with HR-HPV infection and histologically confirmed cervical lesions, including cervicitis, low-grade squamous intraepithelial lesion and high-grade squamous intraepithelial lesion. Microbiome analysis was performed using 16S rRNA gene sequencing. Among the 73 women included in the analyses, HPV clearance was observed in 58.9% of the patients within 12 months. No significant difference was observed between the HPV-cleared and HPV-uncleared groups regarding age, disease stage, HPV subtype, VM community state types, and VM diversity (α and β). Women with the depletion of enterococcus ASV_62 and enrichment in Lactobacillus iners at baseline were less likely to have HPV clearance at month 12. Further analysis revealed a significant negative association between high abundance of L. iners and HPV clearance in patients who received non-operative treatment (OR = 3.94, p = 0.041), but not in those who received operative treatment (OR = 1.86, p = 0.660). Our findings provide new evidence for the potential role of VM in the persistent HR-HPV infections.},
}
@article {pmid36353491,
year = {2022},
author = {Rastogi, S and Singh, A},
title = {Gut microbiome and human health: Exploring how the probiotic genus Lactobacillus modulate immune responses.},
journal = {Frontiers in pharmacology},
volume = {13},
number = {},
pages = {1042189},
pmid = {36353491},
issn = {1663-9812},
abstract = {The highest density of microbes resides in human gastrointestinal tract, known as "Gut microbiome". Of note, the members of the genus Lactobacillus that belong to phyla Firmicutes are the most important probiotic bacteria of the gut microbiome. These gut-residing Lactobacillus species not only communicate with each other but also with the gut epithelial lining to balance the gut barrier integrity, mucosal barrier defence and ameliorate the host immune responses. The human body suffers from several inflammatory diseases affecting the gut, lungs, heart, bone or neural tissues. Mounting evidence supports the significant role of Lactobacillus spp. and their components (such as metabolites, peptidoglycans, and/or surface proteins) in modulatingimmune responses, primarily through exchange of immunological signals between gastrointestinal tract and distant organs. This bidirectional crosstalk which is mediated by Lactobacillus spp. promotes anti-inflammatory response, thereby supporting the improvement of symptoms pertaining to asthma, chronic obstructive pulmonary disease (COPD), neuroinflammatory diseases (such as multiple sclerosis, alzheimer's disease, parkinson's disease), cardiovascular diseases, inflammatory bowel disease (IBD) and chronic infections in patients. The metabolic disorders, obesity and diabetes are characterized by a low-grade inflammation. Genus Lactobacillus alleviates metabolic disorders by regulating the oxidative stress response and inflammatory pathways. Osteoporosis is also associated with bone inflammation and resorption. The Lactobacillus spp. and their metabolites act as powerful immune cell controllers and exhibit a regulatory role in bone resorption and formation, supporting bone health. Thus, this review demonstrated the mechanisms and summarized the evidence of the benefit of Lactobacillus spp. in alleviating inflammatory diseases pertaining to different organs from animal and clinical trials. The present narrative review explores in detail the complex interactions between the gut-dwelling Lactobacillus spp. and the immune components in distant organs to promote host's health.},
}
@article {pmid36353464,
year = {2022},
author = {Wu, H and Fang, C and Malacrinò, A and Winkelmann, T and Xiong, W},
title = {Editorial: Rhizosphere conversation among the plant-plant microbiome-soil under consecutive monoculture regimes.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1061427},
pmid = {36353464},
issn = {1664-302X},
}
@article {pmid36353374,
year = {2022},
author = {Kogut, MH and Fernandez-Miyakawa, ME},
title = {Editorial: Functional mechanisms at the avian gut microbiome-intestinal immunity interface and its regulation of avian physiological responses.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {1063102},
doi = {10.3389/fphys.2022.1063102},
pmid = {36353374},
issn = {1664-042X},
}
@article {pmid36353067,
year = {2022},
author = {Bukavina, L and Prunty, M and Isali, I and Calaway, A and Ginwala, R and Sindhani, M and Ghannoum, M and Mishra, K and Kutikov, A and Uzzo, RG and Ponsky, LE and Abbosh, PH},
title = {Human Gut Mycobiome and Fungal Community Interaction: The Unknown Musketeer in the Chemotherapy Response Status in Bladder Cancer.},
journal = {European urology open science},
volume = {43},
number = {},
pages = {5-13},
pmid = {36353067},
issn = {2666-1683},
abstract = {Background: Until recently, the properties of microbiome and mycobiome in humans and its relevance to disease have largely been unexplored. While the interest of microbiome and malignancy over the past few years have burgeoned with advent of new technologies, no research describing the composition of mycobiome in bladder cancer has been done. Deciphering of the metagenome and its aggregate genetic information can be used to understand the functional properties and relationships between the bacteria, fungi, and cancer.<br><br>Objective: The aim of this project is to characterize the compositional range of the normal versus bladder cancer mycobiome of the gut.<br><br>An internal transcribed spacer (ITS) survey of 52 fecal samples was performed to evaluate the gut mycobiome differences between noncancer controls and bladder cancer patients.<br><br>Our study evaluated the differences in mycobiome among patients with bladder cancer, versus matched controls. Our secondary analysis evaluated compositional differences in the gut as a function of response status with neoadjuvant chemotherapy. Data demultiplexing and classification were performed using the QIIME v.1.1.1.1 platform. The Ion Torrent-generated fungal ITS sequence data were processed using QIIME (v.1.9.1), and the reads were demultiplexed, quality filtered, and clustered into operation taxonomic units using default parameters. Alpha and beta diversity were computed and plotted in Phyloseq, principal coordinate analysis was performed on Bray-Curtis dissimilarity indices, and a one-way permutational multivariate analysis of variance was used to test for significant differences between cohorts. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was applied to infer functional categories associated with taxonomic composition.<br><br>Results and limitations: We found distinctive mycobiome differences between control group (n = 32) and bladder cancer (n = 29) gut flora, and identified an increasing abundance of Tremellales, Hypocreales, and Dothideales. Significant differences in alpha and beta diversity were present between the groups (control vs bladder; p = 0.002), noting distinct compositions within each cohort. A subgroup analysis by sex and neoadjuvant chemotherapy status did not show any further differences in mycobiome composition and diversity. Our results indicate that the gut mycobiome may modulate tumor response to preoperative chemotherapy in bladder cancer patients. We propose that patients with a "favorable" mycobiome composition (eg, high diversity, and low abundance of Agaricomycetes and Saccharomycetes) may have enhanced systemic immune response to chemotherapy through antigen presentation.<br><br>Conclusions: Our study is the first to characterize the enteric mycobiome in patients with bladder cancer and describe complex ecological network alterations, indicating complex bacteria-fungi interactions, particularly highlighted among patients with complete neoadjuvant chemotherapy response.<br><br>Patient summary: Our study has demonstrated that the composition of stool mycobiome (fungal inhabitants of the gastrointestinal tract) in patients with bladder cancer is different from that in noncancer individuals. Furthermore, when evaluating how patients respond to chemotherapy given prior to their surgery, our study noted significant differences between patients who responded and those who did not.},
}
@article {pmid36352729,
year = {2022},
author = {Laas, P and Künnis-Beres, K and Talas, L and Tammert, H and Kuprijanov, I and Herlemann, DPR and Kisand, V},
title = {Bacterial communities in ballast tanks of cargo vessels - Shaped by salinity, treatment and the point of origin of the water but "hatch" its typical microbiome.},
journal = {Journal of environmental management},
volume = {324},
number = {},
pages = {116403},
doi = {10.1016/j.jenvman.2022.116403},
pmid = {36352729},
issn = {1095-8630},
mesh = {*Salinity ; RNA, Ribosomal, 16S/genetics ; Water ; Bacteria/genetics ; *Microbiota ; Ships ; },
abstract = {Ballast water is a main vector of introduction of potentially harmful or pathogenic aquatic organisms. The development of genetic tools for ballast water monitoring has been underway and highlighted as a source for accurate and reliable data for decision making. We used 16S rRNA gene amplicon sequencing to analyze the microbial communities found in the ballast water of fifteen commercial ships routed through two Estonian ports. In parallel, samples from the port area were collected at the same time each ship visited. Fluorescence microscopy was utilized to assess the effectiveness of the treatment applied to ballast water. In addition, supplemental samples were collected from Hamburg Port (Germany) and a ballast tank decontamination system used at this port. The composition and diversity of bacterial communities varied greatly between obtained samples. The application of UV treatment did not demonstrate significant reduction in species richness estimates. The composition of microbial communities was significantly influenced by salinity, treatment (mainly untreated or UV treated) and the point of origin of the ballast water. Over a hundred potentially pathogenic bacterial taxa were found in relatively high abundance, including in ballast water that had received UV treatment. These shortcomings of stand-alone UV treatment of ballast water, especially when weak treatment is applied insufficiently, highlight the danger of possible harmful effects arising over time and the need for genetic tools for ballast water monitoring and management.},
}
@article {pmid36352157,
year = {2022},
author = {Hov, JR and Karlsen, TH},
title = {The microbiota and the gut-liver axis in primary sclerosing cholangitis.},
journal = {Nature reviews. Gastroenterology &amp; hepatology},
volume = {},
number = {},
pages = {},
pmid = {36352157},
issn = {1759-5053},
abstract = {Primary sclerosing cholangitis (PSC) offers unique opportunities to explore the gut-liver axis owing to the close association between liver disease and colonic inflammation. It is well established that the gut microbiota in people with PSC differs from that of healthy individuals, but details of the microbial factors that demarcate PSC from inflammatory bowel disease (IBD) without PSC are poorly understood. In this Review, we aim to provide an overview of the latest literature on the gut microbiome in PSC and PSC with IBD, critically examining hypotheses on how microorganisms could contribute to the pathogenesis of PSC. A particular emphasis will be put on pathogenic features of the gut microbiota that might explain the occurrence of bile duct inflammation and liver disease in the context of IBD, and we postulate the potential existence of a specific yet unknown factor related to the gut-liver axis as causative in PSC. Available data are scrutinized in the perspective of therapeutic approaches related to the gut-liver axis.},
}
@article {pmid36352137,
year = {2022},
author = {Graber, LC and Ramalho, MO and Powell, S and Moreau, CS},
title = {Identifying the Role of Elevation, Geography, and Species Identity in Structuring Turtle Ant (Cephalotes Latreille, 1802) Bacterial Communities.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36352137},
issn = {1432-184X},
support = {DEB 1442256//National Science Foundation/ ; DEB 1900357//National Science Foundation/ ; },
abstract = {Bacterial communities in animals are often necessary for hosts to survive, particularly for hosts with nutrient-limited diets. The composition, abundance, and richness of these bacterial communities may be shaped by host identity and external ecological factors. The turtle ants (genus Cephalotes) are predominantly herbivorous and known to rely on bacterial communities to enrich their diet. Cephalotes have a broad Neotropical distribution, with high diversity in the South American Cerrado, a geologically and biologically diverse savanna. Using 16S rRNA amplicon sequencing, we examined the bacterial communities of forty-one Cephalotes samples of sixteen different species collected from multiple locations across two sites in the Cerrado (MG, Brazil) and compared the bacterial communities according to elevation, locality, species, and species group, defined by host phylogeny. Beta diversity of bacterial communities differed with respect to all categories but particularly strongly when compared by geographic location, species, and species group. Differences seen in species and species groups can be partially explained by the high abundance of Mesorhizobium in Cephalotes pusillus and Cephalotes depressus species groups, when compared to other clades via the Analysis of Composition of Microbiome (ANCOM). Though the Cephalotes bacterial community is highly conserved, results from this study indicate that multiple external factors can affect and change bacterial community composition and abundance.},
}
@article {pmid36316276,
year = {2022},
author = {Inserra, A and Giorgini, G and Lacroix, S and Bertazzo, A and Choo, J and Markopolous, A and Grant, E and Abolghasemi, A and De Gregorio, D and Flamand, N and Rogers, G and Comai, S and Silvestri, C and Gobbi, G and Di Marzo, V},
title = {Effects of Repeated Lysergic Acid Diethylamide (LSD) on the Mouse Brain Endocannabinoidome and Gut Microbiome.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.15977},
pmid = {36316276},
issn = {1476-5381},
abstract = {BACKGROUND AND PURPOSE: Psychedelics elicit prosocial, antidepressant, and anxiolytic effects via neuroplasticity, neurotransmission and neuroimmunomodulatory mechanisms. Whether psychedelics affect the brain endocannabinoid system and its extended version, the endocannabinoidome (eCBome), or the gut microbiome, remains unknown.<br><br>EXPERIMENTAL APPROACH: Adult C57BL/6N male mice were administered lysergic acid diethylamide (LSD) or saline for 7 days. Sociability was assessed in the direct social interaction and three chambers tests. Prefrontal cortex (PFC) and hippocampal (HCC) endocannabinoids and endocannabinoid-like mediators and metabolites were quantified via HPLC-MS/MS. Neurotransmitter levels were assessed via HPLC-UV/fluorescence. Gut microbiome changes were investigated by 16S ribosomal DNA sequencing.<br><br>KEY RESULTS: LSD increased social preference and novelty, and decreased hippocampal levels of the N-acylethanolamines, N-linoleoylethanolamine (LEA), N-arachidonoylethanolamine (anandamide, AEA) and N-docosahexaenoylethanolamine (DHEA), the monoacylglycerol ½-docosahexaenoylglycerol (1/2-DHG), the prostaglandins D2 (PGD2) and F2α (PGF2α), thromboxane 2, and kynurenine. Prefrontal eCBome mediator and metabolite levels were less affected by the treatment. LSD decreased Shannon alpha diversity of the gut microbiota, prevented the decrease in the Firmicutes : Bacteroidetes ratio observed in saline-treated mice, and altered the relative abundance of the bacterial taxa Bifidobacterium, Ileibacterium, Dubosiella, and Rikenellaceae RC9.<br><br>CONCLUSIONS AND IMPLICATIONS: The prosocial effects elicited by repeated LSD administration are accompanied by alterations of hippocampal eCBome and kynurenine levels, and the composition of the gut microbiota. Modulation of the hippocampal eCBome and kynurenine pathway might represent a mechanism by which psychedelic compounds elicit prosocial effects and affect the gut microbiome.},
}
@article {pmid36111782,
year = {2022},
author = {de Nies, L and Busi, SB and Kunath, BJ and May, P and Wilmes, P},
title = {Mobilome-driven segregation of the resistome in biological wastewater treatment.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
doi = {10.7554/eLife.81196},
pmid = {36111782},
issn = {2050-084X},
support = {CORE/BM/11333923//Fonds National de la Recherche Luxembourg/ ; PRIDE/11823097//Fonds National de la Recherche Luxembourg/ ; CRSII5_180241//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; CORE/13684739//Fonds National de la Recherche Luxembourg/ ; ERC-CoG 863664/ERC_/European Research Council/International ; },
mesh = {Humans ; Drug Resistance, Microbial/genetics ; Waste Water ; *Fosfomycin ; Bacitracin ; Metagenomics ; *Water Purification ; Anti-Bacterial Agents/pharmacology ; *Bacteriophages/genetics ; Aminoglycosides ; Sulfonamides ; Genes, Bacterial ; },
abstract = {Biological wastewater treatment plants (BWWTP) are considered to be hotspots for the evolution and subsequent spread of antimicrobial resistance (AMR). Mobile genetic elements (MGEs) promote the mobilization and dissemination of antimicrobial resistance genes (ARGs) and are thereby critical mediators of AMR within the BWWTP microbial community. At present, it is unclear whether specific AMR categories are differentially disseminated via bacteriophages (phages) or plasmids. To understand the segregation of AMR in relation to MGEs, we analyzed meta-omic (metagenomic, metatranscriptomic and metaproteomic) data systematically collected over 1.5 years from a BWWTP. Our results showed a core group of 15 AMR categories which were found across all timepoints. Some of these AMR categories were disseminated exclusively (bacitracin) or primarily (aminoglycoside, MLS and sulfonamide) via plasmids or phages (fosfomycin and peptide), whereas others were disseminated equally by both. Combined and timepoint-specific analyses of gene, transcript and protein abundances further demonstrated that aminoglycoside, bacitracin and sulfonamide resistance genes were expressed more by plasmids, in contrast to fosfomycin and peptide AMR expression by phages, thereby validating our genomic findings. In the analyzed communities, the dominant taxon Candidatus Microthrix parvicella was a major contributor to several AMR categories whereby its plasmids primarily mediated aminoglycoside resistance. Importantly, we also found AMR associated with ESKAPEE pathogens within the BWWTP, and here MGEs also contributed differentially to the dissemination of the corresponding ARGs. Collectively our findings pave the way toward understanding the segmentation of AMR within MGEs, thereby shedding new light on resistome populations and their mediators, essential elements that are of immediate relevance to human health.},
}
@article {pmid35876747,
year = {2022},
author = {Salvato, F and Vintila, S and Finkel, OM and Dangl, JL and Kleiner, M},
title = {Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {MPMI05220116TA},
doi = {10.1094/MPMI-05-22-0116-TA},
pmid = {35876747},
issn = {0894-0282},
abstract = {Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species (Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry-based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.},
}
@article {pmid28947284,
year = {2022},
author = {Rutherford, A and Glass, DA and Savory, S},
title = {Dermatology in orbit: Anticipating skin care requirements in the space age.},
journal = {Journal of the American Academy of Dermatology},
volume = {87},
number = {5},
pages = {1223-1224},
doi = {10.1016/j.jaad.2017.09.046},
pmid = {28947284},
issn = {1097-6787},
mesh = {*Dermatitis, Atopic ; *Dermatitis, Occupational ; *Dermatology ; Humans ; Skin Care ; },
}
@article {pmid36351778,
year = {2022},
author = {Connolly, G and Clark, CM and Campbell, RE and Byers, AW and Reed, JB and Campbell, WW},
title = {Poultry Consumption and Human Health: How Much Is Really Known? A Systematically Searched Scoping Review and Research Perspective.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/advances/nmac074},
pmid = {36351778},
issn = {2156-5376},
abstract = {This scoping review was conducted to systematically search and chronicle scientific literature pertinent to poultry intake and human health. The protocol (uploaded to Open Science Framework, https://osf.io/2k7bj/) was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping reviews guidelines. Articles with observational and experimental research, narrative and systematic reviews, and meta-analyses were included. Among 13,141 articles identified, 525 met inclusion criteria. Among these 525 articles, 212 focused on cancer morbidity and mortality; 41 on cardiovascular disease (CVD) morbidity and mortality; 52 on CVD risk factors; 32 on type 2 diabetes mellitus (T2DM) morbidity and mortality; 33 on T2DM risk factors; and 42 on body weight and body composition. An "Other" category (181 articles) included nutrient status, psychological well-being/mental health, cognition, microbiome, chronic kidney disease, nonalcoholic fatty liver disease, skin disorders, and fertility, among others. Among the 525 included articles, 366 were observational, 64 were experimental, and 76 were reviews and meta-analyses. Eighty-three percent of articles focused on adults or older adults. A paucity of research exists to support poultry as health-promoting foods, with most research only indirectly assessing poultry intake compared with other foods of interest (e.g., red meats or plant-based protein foods). No randomized controlled trials and only 1% of OBS assessed the influence of processed poultry intake on human health. In the future, the relative health effects of consuming poultry will be compared with a widening array of traditional and new protein-rich food products, necessitating the need for research to assess poultry as foods of choice. Science and health professionals, the poultry industry, and the public will benefit from new observational and experimental research to address cutting-edge scientific, public policy, and consumer topics pertinent to poultry intake and human health.},
}
@article {pmid36351375,
year = {2022},
author = {Denk, D and Petrocelli, V and Conche, C and Drachsler, M and Ziegler, PK and Braun, A and Kress, A and Nicolas, AM and Mohs, K and Becker, C and Neurath, MF and Farin, HF and Buchholz, CJ and Andreux, PA and Rinsch, C and Greten, FR},
title = {Expansion of T memory stem cells with superior anti-tumor immunity by Urolithin A-induced mitophagy.},
journal = {Immunity},
volume = {55},
number = {11},
pages = {2059-2073.e8},
doi = {10.1016/j.immuni.2022.09.014},
pmid = {36351375},
issn = {1097-4180},
abstract = {T memory stem cells (TSCM) display increased self-renewal and prolonged survival capabilities, thus preventing T cell exhaustion and promoting effective anti-tumor T cell responses. TSCM cells can be expanded by Urolithin A (UA), which is produced by the commensal gut microbiome from foods rich in ellagitannins and is known to improve mitochondrial health. Oral UA administration to tumor-bearing mice conferred strong anti-tumor CD8+ T cell immunity, whereas ex vivo UA pre-treated T cells displayed improved anti-tumor function upon adoptive cell transfer. UA-induced TSCM formation depended on Pink1-mediated mitophagy triggering cytosolic release of the mitochondrial phosphatase Pgam5. Cytosolic Pgam5 dephosphorylated β-catenin, which drove Wnt signaling and compensatory mitochondrial biogenesis. Collectively, we unravel a critical signaling pathway linking mitophagy to TSCM formation and suggest that the well-tolerated metabolic compound UA represents an attractive option to improve immune therapy.},
}
@article {pmid36351361,
year = {2022},
author = {Ramai, D and Salati, M and Pomati, G and Amoroso, C and Facciorusso, A and Botticelli, A and Ghidini, M},
title = {Antibiotics, the microbiome and gastrointestinal cancers: A causal interference?.},
journal = {Current opinion in pharmacology},
volume = {67},
number = {},
pages = {102315},
doi = {10.1016/j.coph.2022.102315},
pmid = {36351361},
issn = {1471-4973},
abstract = {Our understanding of the gut microbiota has significantly evolved over the last two decades. Advances in the analysis of the gut microbiome continues to reveal complex microbial communities and discoveries about their role in health and diseases, including cancer development, are continuously growing. In addition, research has demonstrated that the use of antibiotics can modulate the gut microbiota composition negatively and influence cancer treatment outcomes, suggesting that antibiotics should be avoided if possible. In this article, we review the role of the gut microbiota in the formation of GI cancers. We show that specific bacterial populations can positively or negatively affect cancer formation with specific attention given to gastric and colorectal cancer. We also review the role of microbial-targeted therapies on cancer treatment outcomes.},
}
@article {pmid36351016,
year = {2022},
author = {Chen, J and Zhang, P and Zhao, Y and Zhao, J and Wu, X and Zhang, R and Cha, R and Yao, Q and Gao, Y},
title = {Nitroreductase-instructed supramolecular assemblies for microbiome regulation to enhance colorectal cancer treatments.},
journal = {Science advances},
volume = {8},
number = {45},
pages = {eadd2789},
doi = {10.1126/sciadv.add2789},
pmid = {36351016},
issn = {2375-2548},
abstract = {The development of human microbiome has collectively correlated the sophisticated interactions between Fusobacterium nucleatum and colorectal cancers (CRCs). However, the treatment of CRC via disruption of gastrointestinal flora remains less explored. Aiming at the up-regulated activity of nitroreductase in F. nucleatum-infected tumors, here, we developed the nitroreductase-instructed supramolecular self-assembly. The designed assembly precursors underwent enzymatic transformation to form assemblies, which agglutinated F. nucleatum and eradicated the targeted bacteria. These assemblies with anti-F. nucleatum activity could further alleviate the bacteria-induced drug resistance effect, thus sensitizing CRC cells against chemo-drugs. Eventually, in mice bearing F. nucleatum-infected CRC, the local introduction of nitroreductase-instructed assemblies could efficiently inhibit the tumor growth. Overall, this study incorporated nitroreductase to broaden the toolbox of enzyme-instructed supramolecular self-assembly. The local introduction of nitroreductase-instructed assemblies could target F. nucleatum to eliminate its contribution to CRC drug resistance and ameliorate chemotherapy outcomes.},
}
@article {pmid36350921,
year = {2022},
author = {Zhao, C and Kelly, K and Jabbur, ML and Paguaga, M and Behringer, M and Johnson, CH},
title = {Host circadian behaviors exert only weak selective pressure on the gut microbiome under stable conditions but are critical for recovery from antibiotic treatment.},
journal = {PLoS biology},
volume = {20},
number = {11},
pages = {e3001865},
doi = {10.1371/journal.pbio.3001865},
pmid = {36350921},
issn = {1545-7885},
abstract = {The circadian rhythms of hosts dictate an approximately 24 h transformation in the environment experienced by their gut microbiome. The consequences of this cyclic environment on the intestinal microbiota are barely understood and are likely to have medical ramifications. Can daily rhythmicity in the gut act as a selective pressure that shapes the microbial community? Moreover, given that several bacterial species have been reported to exhibit circadian rhythms themselves, we test here whether a rhythmic environment is a selective pressure that favors clock-harboring bacteria that can anticipate and prepare for consistent daily changes in the environment. We observed that the daily rhythmicity of the mouse gut environment is a stabilizing influence that facilitates microbiotal recovery from antibiotic perturbation. The composition of the microbiome recovers to pretreatment conditions when exposed to consistent daily rhythmicity, whereas in hosts whose feeding and activity patterns are temporally disrupted, microbiotal recovery is incomplete and allows potentially unhealthy opportunists to exploit the temporal disarray. Unexpectedly, we found that in the absence of antibiotic perturbation, the gut microbiome is stable to rhythmic versus disrupted feeding and activity patterns. Comparison of our results with those of other studies reveals an intriguing correlation that a stable microbiome may be resilient to one perturbation alone (e.g., disruption of the daily timing of host behavior and feeding), but not to multiple perturbations in combination. However, after a perturbation of the stable microbiome, a regular daily pattern of host behavior/feeding appears to be essential for the microbiome to recover to the original steady state. Given the inconsistency of daily rhythms in modern human life (e.g., shiftwork, social jet-lag, irregular eating habits), these results emphasize the importance of consistent daily rhythmicity to optimal health not only directly to the host, but also indirectly by preserving the host's microbiome in the face of perturbations.},
}
@article {pmid36350849,
year = {2022},
author = {Coyte, KZ and Stevenson, C and Knight, CG and Harrison, E and Hall, JPJ and Brockhurst, MA},
title = {Horizontal gene transfer and ecological interactions jointly control microbiome stability.},
journal = {PLoS biology},
volume = {20},
number = {11},
pages = {e3001847},
doi = {10.1371/journal.pbio.3001847},
pmid = {36350849},
issn = {1545-7885},
abstract = {Genes encoding resistance to stressors, such as antibiotics or environmental pollutants, are widespread across microbiomes, often encoded on mobile genetic elements. Yet, despite their prevalence, the impact of resistance genes and their mobility upon the dynamics of microbial communities remains largely unknown. Here we develop eco-evolutionary theory to explore how resistance genes alter the stability of diverse microbiomes in response to stressors. We show that adding resistance genes to a microbiome typically increases its overall stability, particularly for genes on mobile genetic elements with high transfer rates that efficiently spread resistance throughout the community. However, the impact of resistance genes upon the stability of individual taxa varies dramatically depending upon the identity of individual taxa, the mobility of the resistance gene, and the network of ecological interactions within the community. Nonmobile resistance genes can benefit susceptible taxa in cooperative communities yet damage those in competitive communities. Moreover, while the transfer of mobile resistance genes generally increases the stability of previously susceptible recipient taxa to perturbation, it can decrease the stability of the originally resistant donor taxon. We confirmed key theoretical predictions experimentally using competitive soil microcosm communities. Here the stability of a susceptible microbial community to perturbation was increased by adding mobile resistance genes encoded on conjugative plasmids but was decreased when these same genes were encoded on the chromosome. Together, these findings highlight the importance of the interplay between ecological interactions and horizontal gene transfer in driving the eco-evolutionary dynamics of diverse microbiomes.},
}
@article {pmid36350780,
year = {2022},
author = {Peng, BY and Sun, Y and Xiao, S and Chen, J and Zhou, X and Wu, WM and Zhang, Y},
title = {Influence of Polymer Size on Polystyrene Biodegradation in Mealworms (Tenebrio molitor): Responses of Depolymerization Pattern, Gut Microbiome, and Metabolome to Polymers with Low to Ultrahigh Molecular Weight.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.2c06260},
pmid = {36350780},
issn = {1520-5851},
abstract = {Biodegradation of polystyrene (PS) in mealworms (Tenebrio molitor lavae) has been identified with commercial PS foams. However, there is currently limited understanding of the influence of molecular weight (MW) on insect-mediated plastic biodegradation and the corresponding responses of mealworms. In this study, we provided the results of PS biodegradation, gut microbiome, and metabolome by feeding mealworms with high-purity PS microplastics with a wide variety of MW. Over 24 days, mealworms (50 individuals) fed with 0.20 g of PS showed decreasing removal of 74.1 ± 1.7, 64.1 ± 1.6, 64.4 ± 4.0, 73.5 ± 0.9, 60.6 ± 2.6, and 39.7 ± 4.3% for PS polymers with respective weight-average molecular weights (Mw) of 6.70, 29.17, 88.63, 192.9, 612.2, and 1346 kDa. The mealworms degraded most PS polymers via broad depolymerization but ultrahigh-MW PS via limited-extent depolymerization. The gut microbiome was strongly associated with biodegradation, but that with low- and medium-MW PS was significantly distinct from that with ultrahigh-MW PS. Metabolomic analysis indicated that PS biodegradation reprogrammed the metabolome and caused intestinal dysbiosis depending on MW. Our findings demonstrate that mealworms alter their gut microbiome and intestinal metabolic pathways in response to in vivo biodegradation of PS polymers of various MWs.},
}
@article {pmid36350750,
year = {2022},
author = {Weber, DA and Weber, M and Meedt, E and Ghimire, S and Wolff, D and Edinger, M and Poeck, H and Hiergeist, A and Gessner, A and Ayuk, FA and Roesler, W and Wolfl, M and Kraus, S and Zeiser, R and Bertrand, H and Bader, P and Ullrich, E and Eder, M and Gleich, S and Young, R and Herr, W and Levine, JE and Ferrara, JL and Holler, E},
title = {Reg3α levels at day of allogeneic stem cell transplantation predict outcome and correlate with early antibiotic use.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2022008480},
pmid = {36350750},
issn = {2473-9537},
abstract = {The intestinal microbiome diversity plays an important role in the pathophysiology of acute gastrointestinal (GI) Graft-versus-Host Disease (aGvHD) and influences the outcome of patients after allogeneic stem cell transplantation (SCT). We analyzed clinical data and blood samples taken pre-conditioning and on the day of allogeneic SCT from 587 patients from seven German centers of the Mount Sinai Acute GvHD International Consortium (MAGIC), dividing them into a single-center test cohort (n=371) and a multicenter validation cohort (n=216). Reg3α serum concentration of day 0 correlated with clinical data as well as urinary 3-Indoxylsulfate and Clostridiales group XIVa, indicators of intestinal microbiome diversity. High Reg3α concentration at day 0 of allogeneic SCT was associated with higher 1-year transplant-related mortality (TRM) in both cohorts (p<0.001). Cox regression analysis revealed high Reg3α at day 0 as an independent prognostic factor for 1-year TRM (HR=2.9, 95%CI=1.8-4.8, p<0.001). Multivariable analysis showed an independent correlation of high Reg3α concentrations at day 0 and early systemic antibiotic treatment (OR=3.1, 95% CI = 2.0-4.8, p<0.001). Urinary 3-Indoxylsulfate (p=0.04) and Clostridiales group XIVa (p=0.004) were lower in patients with high Reg3α day 0 concentrations than in low Reg3α patients. In contrast, Reg3α concentrations prior to conditioning therapy correlated with neither TRM nor disease or treatment-related parameters. Reg3α, a known biomarker of acute GI GvHD correlates with intestinal dysbiosis induced by early antibiotic treatment in the period of pretransplant conditioning. Serum concentrations of Reg3α measured on the day of graft infusion are predictive of the risk for TRM of allogenic SCT recipients.},
}
@article {pmid36350527,
year = {2022},
author = {Shao, X and Chen, Y and Zhang, L and Zhang, Y and Ariyawati, A and Chen, T and Chen, J and Liu, L and Pu, Y and Li, Y and Chen, J},
title = {Effect of 30% Supramolecular Salicylic Acid Peel on Skin Microbiota and Inflammation in Patients with Moderate-to-Severe Acne Vulgaris.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {36350527},
issn = {2193-8210},
support = {n82073462//The National Natural Science Foundation of China/ ; },
abstract = {INTRODUCTION: Thirty-percent supramolecular salicylic acid (SSA), a modified salicylic acid preparation, is a safe and effective treatment for moderate-to-severe acne vulgaris (AV). However, its mechanism of action remains unclear. We aimed to analyze the role of 30% SSA peels on skin microbiota and inflammation in patients with moderate-to-severe AV.<br><br>METHODS: A total of 28 patients were enrolled and received 30% SSA peels biweekly for 2 months. The Global Acne Grading System (GAGS) score, skin water content, transepidermal water loss (TEWL), pH, and sebum levels were assessed. Skin microbial samples and perilesional skin biopsies were obtained at the onset and 2 weeks after treatment completion. Samples were characterized using a high-throughput sequencing approach targeting a portion of the bacterial 16S ribosomal RNA gene.<br><br>RESULTS: After treatment, patients showed a significant improvement in their GAGS score and skin barrier indicators (P < 0.05). The GAGS score was positively associated with both the sebum concentration (R = 0.3, P = 0.027) and pH (R = 0.39, P = 0.003). Increased expression of caveolin-1 and decreased expression of interleukin (IL)-1a, IL-6, IL-17, transforming growth factor beta, and toll-like receptor 2 were observed in the skin tissue after treatment. The richness and evenness of the cutaneous microbiome decreased after treatment and the Staphylococcus proportion decreased significantly (P < 0.05), whereas the Propionibacterium proportion tended to decrease (P = 0.066).<br><br>CONCLUSIONS: On the basis of analyses of the skin barrier and microbiota, we speculate that the 30% SSA peel may have a therapeutic effect in patients with moderate-to-severe AV by improving the skin microenvironment and modulating the skin microbiome, thus reducing local inflammation.},
}
@article {pmid36350434,
year = {2022},
author = {Liang, M and Zhang, J and Yang, Y and Xia, Y and Liu, L and Liu, L and Wang, Q and Gao, X},
title = {Nattokinase enhances the preventive effects of Escherichia coli Nissle 1917 on dextran sulfate sodium-induced colitis in mice.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {39},
number = {1},
pages = {8},
pmid = {36350434},
issn = {1573-0972},
support = {2021ZKMS045//Science Fund Project of Southwest Medical University/ ; },
abstract = {Nattokinase with excellent anti-thrombotic, anti-inflammatory, anti-tumor, and anti-hypertension properties has been used in the development of several healthcare products in many countries. The probiotic Escherichia coli Nissle 1917 (EcN) with anti-inflammatory effect is commonly used to treat inflammatory bowel disease. To determine whether nattokinase could enhance the therapeutic efficacy of EcN in colitis, a recombinant E. coli Nissle 1917 strain (EcNnatto) with nattokinase-expressing ability was successfully constructed, and the protective effect of the engineered strain on mice with experimental chronic colitis was investigated. Although both EcN and EcNnatto strains substantially alleviated the clinical symptoms and pathological abnormalities in colitis mice by regulating gut flora and maintaining intestinal barrier function, the EcNnatto strain was found to perform better than the control strain, based on a further increase in colon length and a downregulation in pro-inflammatory cytokines (IL-6 and TNF-α). Nattokinase expressed in EcN attenuated DSS-induced epithelial damage and restored the mucosal integrity by upregulating the levels of tight junction proteins, including ZO-1 and occludin. The expression level of Lgr5, a marker of intestinal stem cells, was also increased. Moreover, constitutively expressed nattokinase in EcN reversed the gut microbial richness and diversity in colitis mice. Based on our findings, nattokinase could strengthen the capacity of EcN to treat intestinal inflammation.},
}
@article {pmid36350347,
year = {2022},
author = {Ayilara, MS and Adeleke, BS and Babalola, OO},
title = {Correction to: Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-022-02141-2},
pmid = {36350347},
issn = {1432-184X},
}
@article {pmid36350161,
year = {2022},
author = {Li, S and Guo, J and Liu, R and Zhang, F and Wen, S and Liu, Y and Ren, W and Zhang, X and Shang, Y and Gao, M and Lu, J and Pang, Y},
title = {Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0192622},
doi = {10.1128/spectrum.01926-22},
pmid = {36350161},
issn = {2165-0497},
abstract = {Tuberculous meningitis (TBM), the most lethal and disabling form of tuberculosis (TB), may be related to gut microbiota composition, warranting further study. Here we systematically compared gut microbiota compositions and blood cytokine profiles of TBM patients, pulmonary TB patients, and healthy controls. Notably, the significant gut microbiota dysbiosis observed in TBM patients was associated with markedly high proportions of Escherichia-Shigella species as well as increased blood levels of tumor necrosis factor alpha (TNF-α) and interleukin 6 (IL-6). Next, we obtained a fecal bacterial isolate from a TBM patient and administered it via oral gavage to mice in order to develop a murine gut microbiota dysbiosis model for use in exploring mechanisms underlying the observed relationship between gut microbial dysbiosis and TBM. Thereafter, cells of commensal Escherichia coli (E. coli) were isolated and administered to model mice by gavage and then mice were inoculated with Mycobacterium tuberculosis (M. tuberculosis). Subsequently, these mice exhibited increased blood TNF-α levels accompanied by downregulated expression of tight junction protein claudin-5, increased brain tissue bacterial burden, and elevated central nervous system inflammation relative to corresponding indicators in controls administered PBS by gavage. Thus, our results demonstrated that a signature dysbiotic gut microbiome profile containing a high proportion of E. coli was potentially associated with an increased circulating TNF-α level in TBM patients. Collectively, these results suggest that modulation of dysbiotic gut microbiota holds promise as a new strategy for preventing or alleviating TBM. IMPORTANCE As the most severe form of tuberculosis, the pathogenesis of tuberculous meningitis (TBM) is still unclear. Gut microbiota dysbiosis plays an important role in a variety of central nervous system diseases. However, the relationship between gut microbiota and TBM has not been identified. In our study, significant dysbiosis in gut microbiota composition with a high proportion of E. coli and increased levels of TNF-α in plasma was noted in TBM patients. A commensal E. coli was isolated and shown to increase the plasma level of TNF-α and downregulate brain tight junction protein claudin-5 in the murine model. Gavage administration of E. coli aggravated the bacterial burden and increased the inflammatory responses in the central nervous system after M. tuberculosis infection. Dysbiosis of gut microbiota may be a promising therapeutic target and biomarker for TBM prevention or treatment.},
}
@article {pmid36350127,
year = {2022},
author = {Lai, CKC and Cheung, MK and Lui, GCY and Ling, L and Chan, JYK and Ng, RWY and Chan, HC and Yeung, ACM and Ho, WCS and Boon, SS and Chan, PKS and Chen, Z},
title = {Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0219622},
doi = {10.1128/spectrum.02196-22},
pmid = {36350127},
issn = {2165-0497},
abstract = {Numerous studies have reported dysbiosis in the naso- and/or oro-pharyngeal microbiota of COVID-19 patients compared with healthy individuals; however, only a few small-scale studies have also included a disease control group. In this study, we characterized and compared the bacterial communities of pooled nasopharyngeal and throat swabs from hospitalized COVID-19 patients (n = 76), hospitalized non-COVID-19 patients with respiratory symptoms or related illnesses (n = 69), and local community controls (n = 76) using 16S rRNA gene V3-V4 amplicon sequencing. None of the subjects received antimicrobial therapy within 2 weeks prior to sample collection. Both COVID-19 and non-COVID-19 hospitalized patients differed in the composition, alpha and beta diversity, and metabolic potential of the naso-oropharyngeal microbiota compared with local controls. However, the microbial communities in the two hospitalized patient groups did not differ significantly from each other. Differential abundance analysis revealed the enrichment of nine bacterial genera in the COVID-19 patients compared with local controls; however, six of them were also enriched in the non-COVID-19 patients. Bacterial genera uniquely enriched in the COVID-19 patients included Alloprevotella and Solobacterium. In contrast, Mogibacterium and Lactococcus were dramatically decreased in COVID-19 patients only. Association analysis revealed that Alloprevotella in COVID-19 patients was positively correlated with the level of the inflammation biomarker C-reactive protein. Our findings reveal a limited impact of SARS-CoV-2 on the naso-oropharyngeal microbiota in hospitalized patients and suggest that Alloprevotella and Solobacterium are more specific biomarkers for COVID-19 detection. IMPORTANCE Our results showed that while both COVID-19 and non-COVID-19 hospitalized patients differed in the composition, alpha and beta diversity, and metabolic potential of the naso-oropharyngeal microbiota compared with local controls, the microbial communities in the two hospitalized patient groups did not differ significantly from each other, indicating a limited impact of SARS-CoV-2 on the naso-oropharyngeal microbiota in hospitalized patients. Besides, we identified Alloprevotella and Solobacterium as bacterial genera uniquely enriched in COVID-19 patients, which may serve as more specific biomarkers for COVID-19 detection.},
}
@article {pmid36350082,
year = {2022},
author = {Simpson, AMR and De Souza, MJ and Damani, J and Rogers, C and Williams, NI and Weaver, C and Ferruzzi, MG and Chadwick-Corbin, S and Nakatsu, CH},
title = {Prune supplementation for 12 months alters the gut microbiome in postmenopausal women.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d2fo02273g},
pmid = {36350082},
issn = {2042-650X},
abstract = {Prunes have health benefits, particularly in postmenopausal women. It is likely that the gut microbiome mediates some of these effects, but its exact role remains to be elucidated. This study aims to characterize the effect of prune supplementation on the gut microbiome of postmenopausal women. The fecal microbiome of 143 postmenopausal women ages 55-75 who met the compliance criteria in a randomized controlled trial of a 12-month dietary intervention in one of three treatment groups - no prunes (n = 52), 50 g prunes per day (n = 54), or 100 g prunes per day (n = 37) - was characterized at baseline and at the 12-month endpoint using 16S rRNA gene sequencing and QIIME2. Additional outcomes included assessment of select urinary phenolic metabolites and inflammatory markers. After 12 months, microbiomes of women consuming 50 g prunes had decreased evenness in bacteria taxa (Pielou's Evenness, Kruskal-Wallis p = 0.026). Beta diversity comparisons indicated significant differences in microbiomes among prune treatments (Bray-Curtis PERMANOVA, p = 0.005), and the effect was different at each prune dose (p = 0.057). Prunes enriched some bacterial taxa such as the family Lachnospiraceae (LEfSe LDA = 4.5). Some taxa correlated with urinary phenolic metabolites and inflammatory markers. Blautia negatively correlated with total urinary phenolics (r = -0.25, p = 0.035) and Lachnospiraceae UCG-001 negatively correlated with plasma concentrations of IL-1β (r = -0.29, p = 0.002). Differing gut microbiomes and correlation of some taxa with select phenolic metabolites and inflammatory markers, particularly Lachnospiraceae, after prune consumption suggest a potential mechanism mediating health effects. The microbiome differences at each dose may have implications for the use of prunes as a non-pharmacological whole food intervention for gut health.},
}
@article {pmid36350044,
year = {2022},
author = {Leth, ML and Pichler, MJ and Abou Hachem, M},
title = {Butyrate-producing colonic clostridia: picky glycan utilization specialists.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20220125},
pmid = {36350044},
issn = {1744-1358},
abstract = {Butyrate-producing human gut microbiota members are recognized for their strong association with a healthy immune-homeostasis and protection from inflammatory disorders and colorectal cancer. These effects are attributed to butyrate, the terminal electron sink of glycan fermentation by prevalent and abundant colonic Firmicutes from the Lachnospiraceae and Oscillospiraceae families. Remarkably, our insight into the glycan utilization mechanisms and preferences of butyrogenic Firmicutes remains very limited as compared with other gut symbionts, especially from the Bacteroides, Bifidobacterium, and Lactobacillus genera. Here, we summarize recent findings on the strategies that colonic butyrate producers have evolved to harvest energy from major dietary fibres, especially plant structural and storage glycans, such as resistant starch, xylans, and mannans. Besides dietary fibre, we also present the unexpected discovery of a conserved protein apparatus that confers the growth of butyrate producers on human milk oligosaccharides (HMOs), which are unique to mother's milk. The dual dietary fibre/HMO utilization machinery attests the adaptation of this group to both the infant and adult guts. These finding are discussed in relation to the early colonization of butyrogenic bacteria and the maturation of the microbiota during the transition from mother's milk to solid food. To date, the described butyrogenic Firmicutes are glycan utilization specialists that target only a few glycans in a highly competitive manner relying on co-regulated glycan utilization loci. We describe the common pillars of this machinery, highlighting butyrate producers as a source for discovery of biochemically and structurally novel carbohydrate active enzymes.},
}
@article {pmid36349783,
year = {2022},
author = {Serrano, M and Srivastava, A and Buck, G and Zhu, B and Edupuganti, L and Adegbulugbe, E and Shankaranarayanan, D and Kopp, JB and Raj, DS},
title = {Dietary Protein and Fiber Affect Gut Microbiome and Treg/Th17 Commitment in Chronic Kidney Disease Mice.},
journal = {American journal of nephrology},
volume = {},
number = {},
pages = {1-6},
doi = {10.1159/000526957},
pmid = {36349783},
issn = {1421-9670},
abstract = {BACKGROUND: Patients with chronic kidney disease (CKD) have dysbiosis, dysmetabolism, and immune dysregulation. Gut microbiome plays an important role shaping the immune system which is an important modulator of CKD progression.<br><br>METHODS: We compared the effect of a diet low in protein and high in fiber (LP-HF; n = 7) to that of diet rich in protein, but low in fiber (HP-LF; n = 7) on gut microbiome and T-cell commitment in male CKD (Alb/TGF-β1) mice. The gut microbiomes of these mice were subjected to 16S rRNA taxonomic profiling at baseline, 6 weeks and 12 weeks of the study.<br><br>RESULTS: The LP-HF diet was associated with an increase in Butyricicoccus pullicaecorum BT, a taxon whose functions include those closely related to butyric acid synthesis (Kendall's W statistic = 180 in analysis of microbiome composition). HP-LF diet was associated with increased abundance of two predominantly proteolytic bacterial strains related to Parabacteroides distasonis (W statistic = 173), Mucispirillum schaedleri, and Bacteroides dorei (W statistic = 192). Pathway analysis suggested that the LP-HF diet induced carbohydrate, lipid, and butyrate metabolism. As compared with HP-LF mice, LP-HF mice had 1.7-fold increase in CD4+Foxp3+Treg cells in spleen and 2.4-fold increase of these cells in peripheral blood. There was an 87% decrease in percentage of CD4+ Th17 + cells in spleen and an 85% decrease in peripheral blood, respectively, in LP-HF mice compared to the HP-LF mice.<br><br>CONCLUSION: The LP-HF diet promotes the proliferation of saccharolytic bacteria and favors T-cell commitment toward Treg cells in a CKD mouse of model. Clinical significance of the finding needs to be further investigated.},
}
@article {pmid36349647,
year = {2022},
author = {Almeida, HM and Sardeli, AV and Conway, J and Duggal, NA and Cavaglieri, CR},
title = {Comparison between frail and non-frail older adults' gut microbiota: A systematic review and meta-analysis.},
journal = {Ageing research reviews},
volume = {82},
number = {},
pages = {101773},
doi = {10.1016/j.arr.2022.101773},
pmid = {36349647},
issn = {1872-9649},
abstract = {BACKGROUND: Emerging evidence suggests that the intestinal microbiota (IM) undergoes remodelling as we age, and this impacts the ageing trajectory and mortality in older adults. The aim was to investigate IM diversity differences between frail and non-frail older adults by meta-analysing previous studies.<br><br>METHODS: The protocol of this systematic review with meta-analysis was registered on PROSPERO (CRD42021276733). We searched for studies comparing IM diversity of frail and non-frail older adults indexed on PubMed, Embase, Cochrane, and Web of Science in November 2021.<br><br>RESULTS: We included 11 studies with 1239 participants, of which 340 were meta-analysed. Frailty was defined by a variety of criteria (i.e. Fried Scale, European Consensus on Sarcopenia). There were no differences in the meta-analyses between the frail and non-frail groups for species richness index (SMD = -0.147; 95% CI = -0.394, 0.100; p = 0.243) and species diversity index (SMD = -0.033; 95% CI = -0.315, 0.250; p = 0.820). However, we identified almost 50 differences between frail and non-frail within the relative abundance of bacteria phyla, families, genera, and species in the primary studies.<br><br>CONCLUSIONS: The evidence to prove that there are differences between frail and non-frail IM diversity by meta-analysis is still lacking. The present results suggest that further investigation into the role of specific bacteria, their function, and their influence on the physiopathology of frailty is needed.},
}
@article {pmid36349520,
year = {2022},
author = {Wang, H and Chen, K and Ning, M and Wang, X and Wang, Z and Yue, Y and Yuan, Y and Yue, T},
title = {Intake of Pro- and/or Prebiotics as a Promising Approach for Prevention and Treatment of Colorectal Cancer.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e2200474},
doi = {10.1002/mnfr.202200474},
pmid = {36349520},
issn = {1613-4133},
abstract = {BACKGROUND: Colorectal cancer (CRC) is the third most common type of cancer, posing a serious threat to human life. It is widely believed that dietary factors may be crucial modifiers of CRC risk, with pro-and/or prebiotics being especially promising.<br><br>SCOPE: In this review, we gave a synthesis of CRC prevention and treatment of strategies relying on usage of pro- and/or prebiotics supplements, as well as discuss mechanisms underlying the contribution of pro-and/or prebiotics to the suppression of colonic carcinogenesis. Furthermore, we suggest a framework for personalizing such supplements according to the composition of an individual's gut microbiome.<br><br>CONCLUSIONS: Various factors including diversity of one's intestinal microflora, integrity of their intestinal barrier, and the presence of mutagenic/carcinogenic/genotoxic and beneficial compounds are known to have a prominent influence on the development of CRC; thus, clarifying the role of pro- and/or prebiotics will yield valuable insight toward optimizing interventions for enhanced patient outcomes in the future. This article is protected by copyright. All rights reserved.},
}
@article {pmid36349306,
year = {2022},
author = {Li, H and Wang, S and Wang, S and Yu, H and Yu, W and Ma, X and He, X},
title = {Atorvastatin Inhibits High-Fat Diet-Induced Lipid Metabolism Disorders in Rats by Inhibiting Bacteroides Reduction and Improving Metabolism.},
journal = {Drug design, development and therapy},
volume = {16},
number = {},
pages = {3805-3816},
doi = {10.2147/DDDT.S379335},
pmid = {36349306},
issn = {1177-8881},
abstract = {Purpose: The prevalence of hyperlipidemia and related illnesses is on its rise, and atorvastatin is the frequently used hypolipidemic agent. However, there is still uncertainty about the mechanisms, especially the relationship between the lipid-lowering effect, intestinal microbiome, and metabolic profiles. We aim to intensively explain the mechanism of the hypolipidemic effect of atorvastatin through multi-omics perspective of intestinal microbiome and metabolomics.<br><br>Methods: Multi-omics methods play an increasingly important role in the analysis of intestinal triggers and evaluation of metabolic disorders such as obesity, hyperlipidemia, and diabetes. Therefore, we were prompted to explore intestinal triggers, underlying biomarkers, and potential intervention targets of atorvastatin in the treatment of dyslipidemia through multi-omics. To achieve this, SPF Wistar rats were fed a high-fat diet or normal diet for 8 weeks. Atorvastatin was then administered to high-fat diet-fed rats.<br><br>Results: By altering intestinal microbiome, a high-fat diet can affect feces and plasma metabolic profiles. Treatment with atorvastatin possibly increases the abundance of Bacteroides, thereby improving "propanoate metabolism" and "glycine, serine and threonine metabolism" in feces and plasma, and contributing to blood lipid reduction.<br><br>Conclusion: Our study elucidated the intestinal triggers and metabolites of high-fat diet-induced dyslipidemia from the perspective of intestinal microbiome and metabolomics. It equally identified potential intervention targets of atorvastatin. This further explains the mechanism of the hypolipidemic effect of atorvastatin from a multi-omics perspective.},
}
@article {pmid36348807,
year = {2022},
author = {Wang, B and Wu, C and Cui, L and Wang, H and Liu, Y and Cui, W},
title = {Dietary aluminium intake disrupts the overall structure of gut microbiota in Wistar rats.},
journal = {Food science &amp; nutrition},
volume = {10},
number = {11},
pages = {3574-3584},
doi = {10.1002/fsn3.2955},
pmid = {36348807},
issn = {2048-7177},
abstract = {Approximately, 40% of ingested dietary aluminium accumulates in the intestine, which has been considered a target organ for dietary aluminium exposure. The gut microbiota may be the first protective barrier against the toxic metal aluminium and a crucial mediator of the bioavailability of metal aluminium. We previously evaluated dietary aluminium intake and its health risks in a population from Jilin Province, China, and found that the average daily intake of aluminium in the diet of residents in Jilin Province was 0.163 mg/kg after the total diet survey. In the present study, the equivalent concentration of aluminium in rats was extrapolated by the average dietary aluminium intake in the population of Jilin Province based on body surface area. Furthermore, healthy adult Wistar rats were randomly divided into four groups (n = 15 for each group): a control group and three groups treated with aluminium solution (1, 10, and 100 mg/kg/day, intragastrically) for 28 days. Following treatment, necrosis of renal tubular epithelial cells, hyperplasia of bile ducts and hyperplasia of heart tissue, as well as fiber in the liver, kidney, and heart tissues of aluminium-treated rats were observed, although there were no significant changes in the spleen and brain. Subsequently, fecal samples were withdrawn for 16S rRNA gene sequence analysis. It was found that aluminium decreased the microbiota diversity and changed the overall community structure of the gut microbiota, including three phyla and four genera, together with the regulation of 12 signaling pathways. Collectively, treatment with aluminium markedly altered the structure of the gut microbiota, suggesting that the disorders of intestinal flora induced by aluminium may be an important mechanism for aluminium toxicity.},
}
@article {pmid36348794,
year = {2022},
author = {Zhang, J and Yi, C and Han, J and Ming, T and Zhou, J and Lu, C and Li, Y and Su, X},
title = {Gut microbiome and metabolome analyses reveal the protective effect of special high-docosahexaenoic acid tuna oil on d-galactose-induced aging in mice.},
journal = {Food science &amp; nutrition},
volume = {10},
number = {11},
pages = {3814-3827},
doi = {10.1002/fsn3.2978},
pmid = {36348794},
issn = {2048-7177},
abstract = {Aging is closely related to altered gut function and its microbiome composition. To elucidate the mechanisms involved in the preventive effect of special high-docosahexaenoic acid tuna oil (HDTO) on senescence, the effects of different doses of HDTO on the gut microbiome and metabolome of d-galactose-induced aging mice were studied. Deferribacteres and Tenericutes and uridine might be used as indicator bacteria and characteristic metabolites to identify aging, respectively. HDTO markedly improved the impaired memory and antioxidant abilities induced by d-galactose. At the phylum level, the abundance of Firmicutes and Tenericutes was significantly increased upon d-galactose induction, while that of Bacteroidetes, Proteobacteria, and Deferribacteres was significantly decreased. At the genus level, the variation mainly presented as an increase in the abundance of the Firmicutes genera Ligilactobacillus, Lactobacillus, and Erysipelothrix, the decrease in the abundance of the Bacteroidetes genera Bacteroides and Alistipes, the Firmicutes genus Dielma, and the Deferribacteres genus Mucispirillum. HDTO supplementation reversed the alterations in the intestinal flora by promoting the proliferation of beneficial flora during the aging process; the metabolic pathways, such as glycine-serine-threonine metabolism, valine-leucine-isoleucine biosynthesis, and some metabolic pathways involved in uridine, were also partially restored. Furthermore, the correlation analysis illustrated an obvious correlation between gut microbiota, its metabolites, and aging-related indices. Moreover, it is worth noting that the metabolic regulation by dietary intervention varied with different HDTO doses and did not present a simple additive effect; indeed, each dose showed a unique modulation mechanism.},
}
@article {pmid36348267,
year = {2022},
author = {Song, K and Zhou, YH},
title = {C3NA: correlation and consensus-based cross-taxonomy network analysis for compositional microbial data.},
journal = {BMC bioinformatics},
volume = {23},
number = {1},
pages = {468},
pmid = {36348267},
issn = {1471-2105},
support = {KNOWLE21XX0//Cystic Fibrosis Foundation/ ; 2133504//National Science Foundation/ ; },
abstract = {BACKGROUND: Studying the co-occurrence network structure of microbial samples is one of the critical approaches to understanding the perplexing and delicate relationship between the microbe, host, and diseases. It is also critical to develop a tool for investigating co-occurrence networks and differential abundance analyses to reveal the disease-related taxa-taxa relationship. In addition, it is also necessary to tighten the co-occurrence network into smaller modules to increase the ability for functional annotation and interpretability of these taxa-taxa relationships. Also, it is critical to retain the phylogenetic relationship among the taxa to identify differential abundance patterns, which can be used to resolve contradicting functions reported by different studies.<br><br>RESULTS: In this article, we present Correlation and Consensus-based Cross-taxonomy Network Analysis (C3NA), a user-friendly R package for investigating compositional microbial sequencing data to identify and compare co-occurrence patterns across different taxonomic levels. C3NA contains two interactive graphic user interfaces (Shiny applications), one of them dedicated to the comparison between two diagnoses, e.g., disease versus control. We used C3NA to analyze two well-studied diseases, colorectal cancer, and Crohn's disease. We discovered clusters of study and disease-dependent taxa that overlap with known functional taxa studied by other discovery studies and differential abundance analyses.<br><br>CONCLUSION: C3NA offers a new microbial data analyses pipeline for refined and enriched taxa-taxa co-occurrence network analyses, and the usability was further expanded via the built-in Shiny applications for interactive investigation.},
}
@article {pmid36348188,
year = {2022},
author = {Rasmussen, N},
title = {René Dubos, the Autochthonous Flora, and the Discovery of the Microbiome.},
journal = {Journal of the history of biology},
volume = {},
number = {},
pages = {},
pmid = {36348188},
issn = {1573-0387},
abstract = {Now characterised by high-throughput sequencing methods that enable the study of microbes without lab culture, the human "microbiome" (the microbial flora of the body) is said to have revolutionary implications for biology and medicine. According to many experts, we must now understand ourselves as "holobionts" like lichen or coral, multispecies superorganisms that consist of animal and symbiotic microbes in combination, because normal physiological function depends on them. Here I explore the 1960s research of biologist René Dubos, a forerunner figure mentioned in some historical accounts of the microbiome, and argue that he arrived at the superorganism concept 40 years before the Human Microbiome Project. This raises the question of why his contribution was not hailed as revolutionary at the time and why Dubos is not remembered for it.},
}
@article {pmid36347850,
year = {2022},
author = {Yang, Q and Van Haute, M and Korth, N and Sattler, SE and Toy, J and Rose, DJ and Schnable, JC and Benson, AK},
title = {Author Correction: Genetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {6743},
doi = {10.1038/s41467-022-34544-7},
pmid = {36347850},
issn = {2041-1723},
}
@article {pmid36347649,
year = {2022},
author = {Liu, C and Li, Z and Song, Z and Fan, X and Shao, H and Schönke, M and Boon, MR and Rensen, PCN and Wang, Y},
title = {Choline and butyrate beneficially modulate the gut microbiome without affecting atherosclerosis in APOE*3-Leiden.CETP mice.},
journal = {Atherosclerosis},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.atherosclerosis.2022.10.009},
pmid = {36347649},
issn = {1879-1484},
abstract = {BACKGROUND AND AIMS: Choline has been shown to exert atherogenic effects in Apoe-/- and Ldlr-/- mice, related to its conversion by gut bacteria into trimethylamine (TMA) that is converted by the liver into the proinflammatory metabolite trimethylamine-N-oxide (TMAO). Since butyrate beneficially modulates the gut microbiota and has anti-inflammatory and antiatherogenic properties, the aim of the present study was to investigate whether butyrate can alleviate choline-induced atherosclerosis. To this end, we used APOE*3-Leiden.CETP mice, a well-established atherosclerosis-prone model with human-like lipoprotein metabolism.<br><br>METHODS: Female APOE*3-Leiden.CETP mice were fed an atherogenic diet alone or supplemented with choline, butyrate or their combination for 16 weeks.<br><br>RESULTS: Interestingly, choline protected against fat mass gain, increased the abundance of anti-inflammatory gut microbes, and increased the expression of gut microbial genes involved in TMA and TMAO degradation. Butyrate similarly attenuated fat mass gain and beneficially modulated the gut microbiome, as shown by increased abundance of anti-inflammatory and short chain fatty acid-producing microbes, and inhibited expression of gut microbial genes involved in lipopolysaccharide synthesis. Both choline and butyrate upregulated hepatic expression of flavin-containing monooxygenases, and their combination resulted in highest circulating TMAO levels. Nonetheless, choline, butyrate and their combination did not influence atherosclerosis development, and TMAO levels were not associated with atherosclerotic lesion size.<br><br>CONCLUSIONS: While choline and butyrate have been reported to oppositely modulate atherosclerosis development in Apoe-/- and Ldlr-/- mice as related to changes in the gut microbiota, both dietary constituents did not affect atherosclerosis development while beneficially modulating the gut microbiome in APOE*3-Leiden.CETP mice.},
}
@article {pmid36347632,
year = {2022},
author = {Lv, H and Jia, H and Cai, W and Cao, R and Xue, C and Dong, N},
title = {Rehmannia glutinosa polysaccharides attenuates colitis via reshaping gut microbiota and short-chain fatty acid production.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.12326},
pmid = {36347632},
issn = {1097-0010},
abstract = {BACKGROUND: Ulcerative colitis is a gastrointestinal disease closely related to intestinal epithelial barrier damage and intestinal microbiome imbalance; however, effective treatment methods are currently limited. Rehmannia glutinosa polysaccharide (RGP) is an important active ingredient with a wide range of pharmacological activities, although its protective effect on colitis remains to be explored. Herein, this experiment verified the in vitro anti-inflammatory effect of RGP, and observed the ameliorating effect of RGP on DSS-induced colitis in mice.<br><br>RESULTS: The results showed that (1) RGP attenuated LPS-induced overexpression of inflammatory factors in RAW264.7 cells; (2) RGP improved the pathological damage caused by DSS, including weight loss, increased disease activity index and intestinal tissue ulcers; (3) RGP improves tight junction proteins to protects the tightness of the intestinal epithelium; (4) RGP inhibited the expression of inflammatory factors through the NF-κB pathway, and improved the of intestinal tissues inflammation; (5) RGP can maintain the species diversity of intestinal microbes, increase the content of short-chain fatty acids and then restore the imbalance of intestinal microecology.<br><br>CONCLUSION: RGP can improve the intestinal microbiota to strengthen the intestinal epithelial barrier and protect against DSS-induced colitis. This article is protected by copyright. All rights reserved.},
}
@article {pmid36347253,
year = {2022},
author = {Dumitrescu, DG and Gordon, EM and Kovalyova, Y and Seminara, AB and Duncan-Lowey, B and Forster, ER and Zhou, W and Booth, CJ and Shen, A and Kranzusch, PJ and Hatzios, SK},
title = {A microbial transporter of the dietary antioxidant ergothioneine.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2022.10.008},
pmid = {36347253},
issn = {1097-4172},
abstract = {Low-molecular-weight (LMW) thiols are small-molecule antioxidants required for the maintenance of intracellular redox homeostasis. However, many host-associated microbes, including the gastric pathogen Helicobacter pylori, unexpectedly lack LMW-thiol biosynthetic pathways. Using reactivity-guided metabolomics, we identified the unusual LMW thiol ergothioneine (EGT) in H. pylori. Dietary EGT accumulates to millimolar levels in human tissues and has been broadly implicated in mitigating disease risk. Although certain microorganisms synthesize EGT, we discovered that H. pylori acquires this LMW thiol from the host environment using a highly selective ATP-binding cassette transporter-EgtUV. EgtUV confers a competitive colonization advantage in vivo and is widely conserved in gastrointestinal microbes. Furthermore, we found that human fecal bacteria metabolize EGT, which may contribute to production of the disease-associated metabolite trimethylamine N-oxide. Collectively, our findings illustrate a previously unappreciated mechanism of microbial redox regulation in the gut and suggest that inter-kingdom competition for dietary EGT may broadly impact human health.},
}
@article {pmid36347213,
year = {2022},
author = {Brown, TL and Charity, OJ and Adriaenssens, EM},
title = {Ecological and functional roles of bacteriophages in contrasting environments: marine, terrestrial and human gut.},
journal = {Current opinion in microbiology},
volume = {70},
number = {},
pages = {102229},
doi = {10.1016/j.mib.2022.102229},
pmid = {36347213},
issn = {1879-0364},
abstract = {While they are the most abundant biological entities on the planet, the role of bacteriophages (phages) in the microbiome remains enigmatic and understudied. With a rise in the number of metagenomics studies and the publication of highly efficient phage mining programmes, we now have extensive data on the genomic and taxonomic diversity of (mainly) DNA bacteriophages in a wide range of environments. In addition, the higher throughput and quality of sequencing is allowing for strain-level reconstructions of phage genomes from metagenomes. These factors will ultimately help us to understand the role these phages play as part of specific microbial communities, enabling the tracking of individual virus genomes through space and time. Using lessons learned from the latest metagenomic studies, we focus on two explicit aspects of the role bacteriophages play within the microbiome, their ecological role in structuring bacterial populations, and their contribution to microbiome functioning by encoding auxiliary metabolism genes.},
}
@article {pmid36347161,
year = {2022},
author = {Gonzalez-Visiedo, M and Kulis, MD and Markusic, DM},
title = {Manipulating the microbiome to enhance oral tolerance in food allergy.},
journal = {Cellular immunology},
volume = {382},
number = {},
pages = {104633},
doi = {10.1016/j.cellimm.2022.104633},
pmid = {36347161},
issn = {1090-2163},
abstract = {Loss of oral tolerance (OT) to food antigens results in food allergies. One component of achieving OT is the symbiotic microorganisms living in the gut (microbiota). The composition of the microbiota can drive either pro-tolerogenic or pro-inflammatory responses against dietary antigens though interactions with the local immune cells within the gut. Products from bacterial fermentation, such as butyrate, are one of the main communication molecules involved in this interaction, however, this is released by a subset of bacterial species. Thus, strategies to specifically expand these bacteria with protolerogenic properties have been explored to complement oral immunotherapy in food allergy. These approaches either provide digestible biomolecules to induce beneficial bacteria species (prebiotics) or the direct administration of live bacteria species (probiotics). While this combined therapy has shown positive outcomes in clinical trials for cow's milk allergy, more research is needed to determine if this therapy can be extended to other food allergens.},
}
@article {pmid36347103,
year = {2022},
author = {Ghotaslou, R and Nabizadeh, E and Memar, MY and Law, WMH and Ozma, MA and Abdi, M and Yekani, M and Kadkhoda, H and Hosseinpour, R and Bafadam, S and Ghotaslou, A and Leylabadlo, HE and Nezhadi, J},
title = {The metabolic, protective, and immune functions of Akkermansia muciniphila.},
journal = {Microbiological research},
volume = {266},
number = {},
pages = {127245},
doi = {10.1016/j.micres.2022.127245},
pmid = {36347103},
issn = {1618-0623},
abstract = {Numerous studies have almost proven the beneficial effects of gut microbiota in various aspects of human health, and even the gut microbiota is known as a new and forgotten organ. Akkermansia muciniphila, as a member of the gut microbiota, is considered a bacterium with probiotic properties; consequently, it has a remarkable position in microbiome research. This bacterium accounts for about 1-4 % of the total fecal microbiota population and is also considered a health marker. The accumulated evidence has shown a significant association between A. muciniphila and several disorders and diseases, such as obesity, fatty liver disease, diabetes, and even behavioral disorders. On the other hand, the beneficial effects of A. muciniphila in different studies have shown, such as protective role against pathogenic agents, antitumor properties, tight junctions' improvement, reduction of inflammation, gut permeability, and boosting adaptive immune responses. In this review, based on the available evidence and the latest research, we comprehensively evaluated the impact of A. muciniphila on host health from three points of view: metabolic, protective, and immune functions, as well as the possible mechanisms of each process.},
}
@article {pmid36346820,
year = {2022},
author = {Oost, LJ and Tack, CJ and de Baaij, JHF},
title = {Hypomagnesemia and Cardiovascular Risk in Type 2 Diabetes.},
journal = {Endocrine reviews},
volume = {},
number = {},
pages = {},
doi = {10.1210/endrev/bnac028},
pmid = {36346820},
issn = {1945-7189},
abstract = {Hypomagnesemia is tenfold more common in individuals with type 2 diabetes (T2D), compared to the healthy population. Factors that are involved in this high prevalence are low Mg2+ intake, gut microbiome composition, medication use and presumably genetics. Hypomagnesemia is associated with insulin resistance, which subsequently increases the risk to develop T2D or deteriorates glycaemic control in existing diabetes. Mg2+ supplementation decreases T2D associated features like dyslipidaemia and inflammation; which are important risk factors for cardiovascular disease (CVD). Epidemiological studies have shown an inverse association between serum Mg2+ and the risk to develop heart failure (HF), atrial fibrillation (AF) and microvascular disease in T2D. The potential protective effect of Mg2+ on HF and AF may be explained by reduced oxidative stress, fibrosis and electrical remodeling in the heart. In microvascular disease, Mg2+ reduces the detrimental effects of hyperglycemia and improves endothelial dysfunction. Though, clinical studies assessing the effect of long-term Mg2+ supplementation on CVD incidents are lacking and gaps remain on how Mg2+ may reduce CVD risk in T2D. Despite the high prevalence of hypomagnesemia in people with T2D, routine screening of Mg2+ deficiency to provide Mg2+ supplementation when needed is not implemented in clinical care as sufficient clinical evidence is lacking. In conclusion, hypomagnesemia is common in people with T2D and is both involved as cause, probably through molecular mechanisms leading to insulin resistance, and consequence and is prospectively associated with development of HF, AF and microvascular complications. Whether long-term supplementation of Mg2+ is beneficial, however, remains to be determined.},
}
@article {pmid36346615,
year = {2022},
author = {Peterson, LS and Scheible, K},
title = {Leveraging Microbial Symbiosis to Modulate Bronchopulmonary Dysplasia.},
journal = {American journal of respiratory cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1165/rcmb.2022-0415ED},
pmid = {36346615},
issn = {1535-4989},
}
@article {pmid36346385,
year = {2022},
author = {Abdel-Haq, R and Schlachetzki, JCM and Boktor, JC and Cantu-Jungles, TM and Thron, T and Zhang, M and Bostick, JW and Khazaei, T and Chilakala, S and Morais, LH and Humphrey, G and Keshavarzian, A and Katz, JE and Thomson, M and Knight, R and Gradinaru, V and Haymaker, BR and Glass, CK and Mazmanian, SK},
title = {A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
doi = {10.7554/eLife.81453},
pmid = {36346385},
issn = {2050-084X},
support = {PD160030//U.S. Department of Defense/ ; HMRI-15-09-01//Heritage Medical Research Institute/ ; ASAP-000375//Aligning Science Across Parkinson's/ ; },
abstract = {Parkinson's disease (PD) is a movement disorder characterized by neuroinflammation, α-synuclein pathology, and neurodegeneration. Most cases of PD are non-hereditary, suggesting a strong role for environmental factors, and it has been speculated that disease may originate in peripheral tissues such as the gastrointestinal (GI) tract before affecting the brain. The gut microbiome is altered in PD and may impact motor and GI symptoms as indicated by animal studies, though mechanisms of gut-brain interactions remain incompletely defined. Intestinal bacteria ferment dietary fibers into short-chain fatty acids, with fecal levels of these molecules differing between PD and healthy controls and in mouse models. Among other effects, dietary microbial metabolites can modulate activation of microglia, brain-resident immune cells implicated in PD. We therefore investigated whether a fiber-rich diet influences microglial function in α-synuclein overexpressing (ASO) mice, a preclinical model with PD-like symptoms and pathology. Feeding a prebiotic high-fiber diet attenuates motor deficits and reduces α-synuclein aggregation in the substantia nigra of mice. Concomitantly, the gut microbiome of ASO mice adopts a profile correlated with health upon prebiotic treatment, which also reduces microglial activation. Single-cell RNA-seq analysis of microglia from the substantia nigra and striatum uncovers increased pro-inflammatory signaling and reduced homeostatic responses in ASO mice compared to wild-type counterparts on standard diets. However, prebiotic feeding reverses pathogenic microglial states in ASO mice and promotes expansion of protective disease-associated macrophage (DAM) subsets of microglia. Notably, depletion of microglia using a CSF1R inhibitor eliminates the beneficial effects of prebiotics by restoring motor deficits to ASO mice despite feeding a prebiotic diet. These studies uncover a novel microglia-dependent interaction between diet and motor symptoms in mice, findings that may have implications for neuroinflammation and PD.},
}
@article {pmid36346384,
year = {2022},
author = {Williams, RBH},
title = {Adapt or perish.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
doi = {10.7554/eLife.83617},
pmid = {36346384},
issn = {2050-084X},
abstract = {Microbial communities in wastewater treatment plants provide insights into the development and mechanisms of antimicrobial resistance.},
}
@article {pmid36346231,
year = {2022},
author = {Dahdouh, E and Fernández-Tomé, L and Cendejas, E and Ruiz-Carrascoso, G and Schüffelmann, C and Alós-Díez, M and Lázaro-Perona, F and Castro-Martínez, M and Escosa-García, L and Jiménez-Díaz, S and Hierro-Llanillo, L and Mingorance, J},
title = {Intestinal Dominance by Multidrug-Resistant Bacteria in Pediatric Liver Transplant Patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0284222},
doi = {10.1128/spectrum.02842-22},
pmid = {36346231},
issn = {2165-0497},
abstract = {Pediatric liver transplantation (PLTx) is commonly associated with extensive antibiotic treatments that can produce gut microbiome alterations and open the way to dominance by multidrug-resistant organisms (MDROs). In this study, the relationship between intestinal Relative Loads (RLs) of β-lactamase genes, antibiotic consumption, microbiome disruption, and the extraintestinal dissemination of MDROs among PLTx patients is investigated. 28 PLTx patients were included, from whom 169 rectal swabs were collected. Total DNA was extracted and blaCTX-M-1-Family, blaOXA-1, blaOXA-48, and blaVIM were quantified via quantitative polymerase chain reaction (qPCR) and normalized to the total bacterial load (16SrRNA) through LogΔΔCt to determine the RLs. 16SrRNA sequencing was performed for 18 samples, and metagenomic sequencing was performed for 2. Patients' clinical data were retrieved from the hospital's database. At least one of the genes tested were detected in all of the patients. The RLs for blaCTX-M-1-Family, blaOXA-1, blaOXA-48, and blaVIM were higher than 1% of the total bacterial population in 67 (80.73%), 56 (78.87%), 57 (77.03%) and 39 (61.9%) samples, respectively. High RLs for blaCTX-M-1-Family, blaOXA-1, and/or blaOXA-48, were positively associated with the consumption of carbapenems with trimethoprim-sulfamethoxazole and coincided with low diversity in the gut microbiome. Low RLs were associated with the consumption of noncarbapenem β-lactams with aminoglycosides (P < 0.05). Extraintestinal isolates harboring the same gene(s) as those detected intraintestinally were found in 18 samples, and the RLs of the respective swabs were high. We demonstrated a relationship between the consumption of carbapenems with trimethoprim-sulfamethoxazole, intestinal dominance by MDROs and extraintestinal spread of these organisms among PLTx patients. IMPORTANCE In this study, we track the relative intestinal loads of antibiotic resistance genes among pediatric liver transplant patients and determine the relationship between this load, antibiotic consumption, and infections caused by antibiotic-resistant organisms. We demonstrate that the consumption of broad spectrum antibiotics increase this load and decrease the gut microbial diversity among these patients. Moreover, the high loads of resistance genes were related to the extraintestinal spread of multidrug-resistant organisms. Together, our data show that the tracking of the relative intestinal loads of antibiotic resistance genes can be used as a biomarker that has the potential to stop the extraintestinal spread of antibiotic-resistant bacteria via the measurement of the intestinal dominance of these organisms, thereby allowing for the application of preventive measures.},
}
@article {pmid36346230,
year = {2022},
author = {Goggans, ML and Bilbrey, EA and Quiroz-Moreno, CD and Francis, DM and Jacobi, SK and Kovac, J and Cooperstone, JL},
title = {Short-Term Tomato Consumption Alters the Pig Gut Microbiome toward a More Favorable Profile.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0250622},
doi = {10.1128/spectrum.02506-22},
pmid = {36346230},
issn = {2165-0497},
abstract = {Diets rich in fruits and vegetables have been shown to exert positive effects on the gut microbiome. However, little is known about the specific effect of individual fruits or vegetables on gut microbe profiles. This study aims to elucidate the effects of tomato consumption on the gut microbiome, as tomatoes account for 22% of vegetable consumption in Western diets, and their consumption has been associated with positive health outcomes. Using piglets as a physiologically relevant model of human metabolism, 20 animals were assigned to either a control or a tomato powder-supplemented diet (both macronutrient matched and isocaloric) for 14 days. The microbiome was sampled rectally at three time points: day 0 (baseline), day 7 (midpoint), and day 14 (end of study). DNA was sequenced using shotgun metagenomics, and reads were annotated using MG-RAST. There were no differences in body weight or feed intake between our two treatment groups. There was a microbial shift which included a higher ratio of Bacteroidota to Bacillota (formerly known as Bacteroidetes and Firmicutes, respectively) and higher alpha-diversity in tomato-fed animals, indicating a shift to a more desirable phenotype. Analyses at both the phylum and genus levels showed global microbiome profile changes (permutational multivariate analysis of variance [PERMANOVA], P ≤ 0.05) over time but not with tomato consumption. These data suggest that short-term tomato consumption can beneficially influence the gut microbial profile, warranting further investigation in humans. IMPORTANCE The composition of the microorganisms in the gut is a contributor to overall health, prompting the development of strategies to alter the microbiome composition. Studies have investigated the role of the diet on the microbiome, as it is a major modifiable risk factor contributing to health; however, little is known about the causal effects of consumption of specific foods on the gut microbiota. A more complete understanding of how individual foods impact the microbiome will enable more evidence-based dietary recommendations for long-term health. Tomatoes are of interest as the most consumed nonstarchy vegetable and a common source of nutrients and phytochemicals across the world. This study aimed to elucidate the effect of short-term tomato consumption on the microbiome, using piglets as a physiologically relevant model to humans. We found that tomato consumption can positively affect the gut microbial profile, which warrants further investigation in humans.},
}
@article {pmid36345851,
year = {2022},
author = {Walker, H and Shanthikumar, S and Cole, T and Neeland, M and Hanna, D and Haeusler, GM},
title = {Novel approaches to the prediction and diagnosis of pulmonary complications in the paediatric haematopoietic stem cell transplant patient.},
journal = {Current opinion in infectious diseases},
volume = {35},
number = {6},
pages = {493-499},
doi = {10.1097/QCO.0000000000000883},
pmid = {36345851},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: Haematopoietic stem cell transplant (HSCT) remains the only curative treatment option for many children with relapsed leukaemia, primary immunodeficiencies and haemoglobinopathies. Unfortunately, infectious and noninfectious pulmonary complications following HSCT continue to cause significant morbidity and mortality. This review will focus on recent advances in the field that enhance clinically available diagnostic tools and the role of novel diagnostic techniques.<br><br>RECENT FINDINGS: Research continues to highlight the role of standard diagnostic modalities, including imaging using computed topography chest and Fluorodeoxyglucose-positron emission tomography (FDG-PET) in the diagnosis of posttransplant pulmonary infections. Similarly, bronchoalveolar lavage using bronchoscopy to obtain samples for microbiological analysis remains an important tool in the clinical and diagnostic algorithm for these children. The application of more novel diagnostic techniques such as metagenomic next-generation sequencing and the use of specific biomarkers remain potential future tools in children in whom the aetiology of posttransplant lung disease is unknown. The impact of the pulmonary microbiome on infectious and noninfectious pulmonary disease post HSCT is a future research direction.<br><br>SUMMARY: Pulmonary infectious complications post HSCT remain a devastating complication for children and their families. Despite improvements in standard and novel diagnostic modalities, the aetiology of pulmonary disease remains unknown for many patients. There is an urgent need for ongoing collaborative research to bridge this critical knowledge gap and lead to better patient outcomes.},
}
@article {pmid36345525,
year = {2022},
author = {Song, Y and Perlman, K and Gyarmati, P},
title = {Microbial and host factors contribute to bloodstream infection in a pediatric acute lymphocytic leukemia mouse model.},
journal = {Heliyon},
volume = {8},
number = {11},
pages = {e11340},
doi = {10.1016/j.heliyon.2022.e11340},
pmid = {36345525},
issn = {2405-8440},
abstract = {Background: Hematological malignancies are the most common cancers in the pediatric population, and T-cell acute lymphocytic leukemia (T-ALL) is the most common hematological malignancy in children. Bloodstream infection (BSI) is a commonly occurring complication in leukemia due to underlying conditions and therapy-induced neutropenia. Several studies identified the gut microbiome as a major source of BSI due to bacterial translocation. This study aimed to investigate changes in the intestinal and fecal microbiome, and their roles in the pathophysiology of BSI in a pediatric T-ALL mouse model using high-throughput shotgun metagenomics sequencing, and metabolomics.<br><br>Results: Our results show that BSI in ALL is characterized by an increase of a mucin degrading bacterium (Akkermansia muciniphila) and a decrease of butyrate producer Clostridia spp., along with a decrease in short-chain fatty acid (SCFA) concentrations and differential expression of tight junction proteins in the small intestine. Functional analysis of the small intestinal microbiome indicated a reduced capability of SCFA synthesis, while SCFA supplementation ameliorated the development of BSI in ALL.<br><br>Conclusions: Our data indicates that changes in the microbiome, and the resulting changes in levels of SCFAs contribute significantly to the pathogenesis of bloodstream infection in ALL. Our study provides tailored preventive or therapeutic approaches to reduce BSI-associated mortality in ALL.},
}
@article {pmid36345322,
year = {2022},
author = {Esposito, P and Gandelman, M and Rodriguez, C and Liang, J and Ismail, N},
title = {The acute effects of antimicrobials and lipopolysaccharide on the cellular mechanisms associated with neurodegeneration in pubertal male and female CD1 mice.},
journal = {Brain, behavior, &amp; immunity - health},
volume = {26},
number = {},
pages = {100543},
doi = {10.1016/j.bbih.2022.100543},
pmid = {36345322},
issn = {2666-3546},
abstract = {Exposure to stressors during puberty can cause enduring effects on brain functioning and behaviours related to neurodegeneration. However, the mechanisms underlying these effects remain unclear. The gut microbiome is a complex and dynamic system that could serve as a possible mechanism through which early life stress may increase the predisposition to neurodegeneration. Therefore, the current study was designed to examine the acute effects of pubertal antimicrobial and lipopolysaccharide (LPS) treatments on the cellular mechanisms associated with neurodegenerative disorders in male and female mice. At five weeks of age, male and female CD-1 mice received 200 μL of broad-spectrum antimicrobials or water, through oral gavage, twice daily for seven days. Mice received an intraperitoneal (i.p.) injection of either saline or LPS at 6 weeks of age (i.e., pubertal period). Sickness behaviours were recorded and mice were euthanized 8 h post-injection. Following euthanasia, brains and blood samples were collected. The results indicated that puberal antimicrobial and LPS treatment induced sex-dependent changes in biomarkers related to sickness behaviour, peripheral inflammation, intestinal permeability, and neurodegeneration. The findings suggest that pubertal LPS and antimicrobial treatment may increase susceptibility to neurodegenerative diseases later in life, particularly in males.},
}
@article {pmid36345145,
year = {2022},
author = {Molina, L and Rajchenberg, M and de Errasti, A and Vogel, B and Coetzee, MPA and Aime, MC and Pildain, MB},
title = {Sapwood mycobiome vary across host, plant compartment and environments in Nothofagus forests from Northern Patagonia.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16771},
pmid = {36345145},
issn = {1365-294X},
abstract = {Global forests are increasingly threatened by altered climatic conditions and increased attacks by pests and pathogens. The complex ecological interactions among pathogens, microbial communities, tree host, and environment are important drivers of forest dynamics. Little is known about the ecology of forest pathology and related microbial communities in temperate forests of the southern hemisphere. In this study, we used next-generation sequencing to characterize sapwood-inhabiting fungal communities in North Patagonian Nothofagus forests and assessed patterns of diversity of taxa and ecological guilds across climatic, site and host variables (health condition and compartment) as a contribution to Nothofagus autecology. The diversity patterns inferred through the metabarcoding analysis were similar to those obtained through culture-dependent approaches. However, we detected additional heterogeneity and greater richness with culture-free methods. Host species was the strongest driver of fungal community structure and composition, while the host health status was the weakest. The relative impact of site, season, plant compartment and health status were different for each tree species; these differences can be interpreted as a matter of water availability. For N. dombeyi, which is distributed across a wide range of climatic conditions, site was the strongest driver of community composition. Nothofagus pumilio's microbiome varied more with season and temperature, a relevant factor for forest conservation in the present climate change scenario. Both species carry a number of potential fungal pathogens in their sapwood, whether they exhibit symptoms or not. Our results provide an insight into the diversity of fungi associated with the complex pathobiome of the dominant Nothofagus species in southern south America.},
}
@article {pmid36345047,
year = {2022},
author = {Rao, BC and Zhang, GZ and Zou, YW and Ren, T and Ren, HY and Liu, C and Yu, ZJ and Ren, ZG},
title = {Alterations in the human oral microbiome in cholangiocarcinoma.},
journal = {Military Medical Research},
volume = {9},
number = {1},
pages = {62},
pmid = {36345047},
issn = {2054-9369},
support = {U2004121//National Natural Science Foundation of China/ ; 82070643//National Natural Science Foundation of China/ ; U1904164//National Natural Science Foundation of China/ ; JNL-2022015B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; JNL-2022001A//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; 2018YFC2000500//National Key Research and Development Program of China/ ; },
}
@article {pmid36344941,
year = {2022},
author = {Lincoln, A and Benton, S and Piggott, C and North, BV and Rigney, J and Young, C and Quirke, P and Sasieni, P and Monahan, KJ},
title = {Exploring the utility and acceptability of Faecal immunochemical testing (FIT) as a novel intervention for the improvement of colorectal Cancer (CRC) surveillance in individuals with lynch syndrome (FIT for lynch study): a single-arm, prospective, multi-centre, non-randomised study.},
journal = {BMC cancer},
volume = {22},
number = {1},
pages = {1144},
pmid = {36344941},
issn = {1471-2407},
abstract = {BACKGROUND: Lynch Syndrome (LS) is an inherited cancer predisposition syndrome defined by pathogenic variants in the mismatch repair (MMR) or EPCAM genes. In the United Kingdom, people with LS are advised to undergo biennial colonoscopy from as early as 25 until 75 years of age to mitigate a high lifetime colorectal cancer (CRC) risk, though the consideration of additional surveillance intervention(s) through the application of non-invasive diagnostic devices has yet to be longitudinally observed in LS patients. In this study, we will examine the role of annual faecal immunochemical testing (FIT) alongside biennial colonoscopy for CRC surveillance in people with LS.<br><br>METHODS/DESIGN: In this single-arm, prospective, non-randomised study, 400 LS patients will be recruited across 11 National Health Service (NHS) Trusts throughout the United Kingdom. Study inclusion requires a LS diagnosis, between 25 and 73 years old, and a routine surveillance colonoscopy scheduled during the recruitment period. Eligible patients will receive a baseline OC-Sensor™ FIT kit ahead of their colonoscopy, and annually for 3 years thereafter. A pre-paid envelope addressed to the central lab will be included within all patient mailings for the return of FIT kits and relevant study documents. A questionnaire assessing attitudes and perception of FIT will also be included at baseline. All study samples received by the central lab will be assayed on an OC-Sensor™ PLEDIA Analyser. Patients with FIT results of ≥6 μg of Haemoglobin per gram of faeces (f-Hb) at Years 1 and/or 3 will be referred for colonoscopy via an urgent colonoscopy triage pathway. 16S rRNA gene V4 amplicon sequencing will be carried out on residual faecal DNA of eligible archived FIT samples to characterise the faecal microbiome.<br><br>DISCUSSION: FIT may have clinical utility alongside colonoscopic surveillance in people with LS. We have designed a longitudinal study to examine the efficacy of FIT as a non-invasive modality. Potential limitations of this method will be assessed, including false negative or false positive FIT results related to specific morphological features of LS neoplasia or the presence of post-resection anastomotic inflammation. The potential for additional colonoscopies in a subset of participants may also impact on colonoscopic resources and patient acceptability.<br><br>TRIAL REGISTRATION: Trial Registration: ISRCTN, ISRCTN15740250 . Registered 13 July 2021.},
}
@article {pmid36344828,
year = {2022},
author = {Bringhurst, B and Allert, M and Greenwold, M and Kellner, K and Seal, JN},
title = {Environments and Hosts Structure the Bacterial Microbiomes of Fungus-Gardening Ants and their Symbiotic Fungus Gardens.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36344828},
issn = {1432-184X},
support = {IOS-1552822//Directorate for Biological Sciences/ ; DEB-1354629//Directorate for Biological Sciences/ ; },
abstract = {The fungus gardening-ant system is considered a complex, multi-tiered symbiosis, as it is composed of ants, their fungus, and microorganisms associated with either ants or fungus. We examine the bacterial microbiome of Trachymyrmex septentrionalis and Mycetomoellerius turrifex ants and their symbiotic fungus gardens, using 16S rRNA Illumina sequencing, over a region spanning approximately 350 km (east and central Texas). Typically, microorganisms can be acquired from a parent colony (vertical transmission) or from the environment (horizontal transmission). Because the symbiosis is characterized by co-dispersal of the ants and fungus, elements of both ant and fungus garden microbiome could be characterized by vertical transmission. The goals of this study were to explore how both the ant and fungus garden bacterial microbiome are acquired. The main findings were that different mechanisms appear to explain the structure the microbiomes of ants and their symbiotic fungus gardens. Ant associated microbiomes had a strong host ant signature, which could be indicative of vertical inheritance of the ant associated bacterial microbiome or an unknown mechanism of active uptake or screening. On the other hand, the bacterial microbiome of the fungus garden was more complex in that some bacterial taxa appear to be structured by the ant host species, whereas others by fungal lineage or the environment (geographic region). Thus bacteria in fungus gardens appear to be acquired both horizontally and vertically.},
}
@article {pmid36344781,
year = {2022},
author = {Basha, OM and Hafez, RA and Salem, SM and Anis, RH and Hanafy, AS},
title = {Impact of gut Microbiome alteration in Ulcerative Colitis patients on disease severity and outcome.},
journal = {Clinical and experimental medicine},
volume = {},
number = {},
pages = {},
pmid = {36344781},
issn = {1591-9528},
abstract = {BACKGROUND: Ulcerative colitis is a heterogeneous disease in terms of disease course, location, and therapeutic response. The current study was done to assess the alteration of the gut microbiome in UC patients and its relationship to severity, response to therapy, and outcome.<br><br>PATIENTS AND METHODS: The study included 96 participants who were divided into a case group (n = 48, recent onset, treatment naive ulcerative colitis patients who were subdivided into mild, moderate, and severe subgroups based on Truelove-Witts and endoscopic severity) and a healthy control group (n = 48). All were subjected to a thorough history, clinical examination, colonoscopy, routine laboratory tests, and quantitative real-time PCR to quantify Bacteroides, Lactobacilli, Faecalibacterium prausnitzii, Veillonella, and Hemophilus in fecal samples at baseline and 6 months after treatment.<br><br>RESULTS: Bacterial 16S rRNA gene sequencing revealed a significant reduction in the phylum Firmicutes in UC patients, with a significant predominance of the phylum Bacteriodetes. F. prausnitzii and lactobacilli were inversely proportional to disease severity, whereas Bacteroides, Hemophilus, and Veillonella were directly proportional to it. Six months after therapy, a statistically significant increase in F. prausnitzii and lactobacilli was observed, with a decrease in the levels of other bacteria. Lower baseline F. praustinizii (< 8.5) increased the risk of relapse; however, lower ESR (< 10), lower post-treatment CRP (< 6), lower Bacteroides (< 10.6) indefinitely protect against relapse.<br><br>CONCLUSION: The gut microbiome of recently diagnosed UC showed lower levels of Lactobacilli, Faecalibacterium, and higher levels of Bacteroides and Veillonella, and the change in their levels can be used to predict response to therapy.},
}
@article {pmid36344551,
year = {2022},
author = {Zakavi, M and Askari, H and Shahrooei, M},
title = {Characterization of bacterial diversity between two coastal regions with heterogeneous soil texture.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {18901},
pmid = {36344551},
issn = {2045-2322},
abstract = {Studying microbial diversity and the effects of external factors on the microbiome could expand our understanding of environmental alterations. Silt and sand are mineral particles that form soil texture and even though most of the soils on earth contain a fraction of them and some other soils form almost by them, their effects on the microbiome remained to elucidate. In this study, the bacterial biodiversity of sand and silt clay soils was investigated. Furthermore, their effects on plant growth have been determined. Our data showed that biodiversity and biomass of microbiome are higher in silt-based soil. It is interesting that the pseudomonas genera only exist in silt-based soil while it is in the absence of sand-based soil. In contrast, B. thuringiensis could be found in sand-based soil while it is not found in silt texture. Our data also demonstrated that there are no significant changes in stress response between the two groups however, differential physiological changes in plants inoculated with silt and sand based bacterial isolates have been observed. This data could indicate that smaller size particles could contain more bacteria with higher biodiversity due to providing more surfaces for bacteria to grow.},
}
@article {pmid36344337,
year = {2022},
author = {Kunimitsu, M and Nakagami, G and Kitamura, A and Minematsu, T and Koudounas, S and Ogai, K and Sugama, J and Takada, C and Yeo, S and Sanada, H},
title = {Relationship between healing status and microbial dissimilarity in wound and peri-wound skin in pressure injuries.},
journal = {Journal of tissue viability},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtv.2022.10.006},
pmid = {36344337},
issn = {0965-206X},
abstract = {AIM: Wound infection is the most serious cause of delayed healing for patients with pressure injuries. The wound microbiota, which plays a crucial role in delayed healing, forms by bacterial dissemination from the peri-wound skin. To manage the bioburden, wound and peri-wound skin care has been implemented; however, how the microbiota at these sites contribute to delayed healing is unclear. Therefore, we investigated the relationship between healing status and microbial dissimilarity in wound and peri-wound skin.<br><br>METHODS: A prospective cohort study was conducted at a long-term care hospital. The outcome was healing status assessed using the DESIGN-R® tool, a wound assessment tool to monitor the wound healing process. Bacterial DNA was extracted from the wound and peri-wound swabs, and microbiota composition was analyzed using 16S rRNA gene analysis. To evaluate microbial similarity, the weighted UniFrac dissimilarity index between wound and peri-wound microbiota was calculated.<br><br>RESULTS: Twenty-two pressure injuries (7 deep and 15 superficial wounds) were included in the study. For deep wounds, the predominant bacteria in wound and peri-wound skin were the same in the healing wounds, whereas they were different in all cases of hard-to-heal wounds. Analysis based on the weighted UniFrac dissimilarity index, there was no significant difference for healing wounds (p = 0.639), while a significant difference was found for hard-to-heal wounds (p = 0.047).<br><br>CONCLUSIONS: Delayed healing is possibly associated with formation of wound microbiota that is different in composition from that of the skin commensal microbiota. This study provides a new perspective for assessing wound bioburden.},
}
@article {pmid36343977,
year = {2022},
author = {Boesch, M and Horvath, L and Baty, F and Pircher, A and Wolf, D and Spahn, S and Straussman, R and Tilg, H and Brutsche, MH},
title = {Compartmentalization of the host microbiome: how tumor microbiota shapes checkpoint immunotherapy outcome and offers therapeutic prospects.},
journal = {Journal for immunotherapy of cancer},
volume = {10},
number = {11},
pages = {},
doi = {10.1136/jitc-2022-005401},
pmid = {36343977},
issn = {2051-1426},
abstract = {The host microbiome is polymorphic, compartmentalized, and composed of distinctive tissue microbiomes. While research in the field of cancer immunotherapy has provided an improved understanding of the interaction with the gastrointestinal microbiome, the significance of the tumor-associated microbiome has only recently been grasped. This article provides a state-of-the-art review about the tumor-associated microbiome and sheds light on how local tumor microbiota shapes anticancer immunity and influences checkpoint immunotherapy outcome. The direct route of interaction between cancer cells, immune cells, and microbiota in the tumor microenvironment is emphasized and advocates a focus on the tumor-associated microbiome in addition to the spatially separated gut compartment. Since the mechanisms underlying checkpoint immunotherapy modulation by tumor-associated microbiota remain largely elusive, future research should dissect the pathways involved and outline strategies to therapeutically modulate microbes and their products within the tumor microenvironment. A more detailed knowledge about the mechanisms governing the composition and functional quality of the tumor microbiome will improve cancer immunotherapy and advance precision medicine for solid tumors.},
}
@article {pmid36343820,
year = {2022},
author = {Li, H and Xia, W and Liu, X and Wang, X and Liu, G and Chen, H and Zhu, L and Li, D},
title = {Food provisioning results in functional, but not compositional, convergence of the gut microbiomes of two wild Rhinopithecus species: Evidence of functional redundancy in the gut microbiome.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {159957},
doi = {10.1016/j.scitotenv.2022.159957},
pmid = {36343820},
issn = {1879-1026},
abstract = {The consumption of similar diets has led to the convergence of gut microbial compositions and functions across phylogenetically distinct animals. However, given the functional redundancy in gut microbiomes, it remains unclear whether synchrony occurs in their functions only and not in their composition, even within phylogenetically close animals consuming a similar diet. In this study, we collected fresh fecal samples from a Rhinopithecus roxellana population in April 2021 (before food provisioning) and June and December 2021 (after food provisioning) and used high-throughput sequencing methods (full-length 16S rRNA gene sequencing and metagenomes) to investigate changes in the gut microbiome due to food provisioning. Combining the results from our previous studies on a wild Rhinopithecus bieti population, we found that the artificial food provisions (e.g., apples, carrots, and peanuts) affected the gut microbiome, and synchrony occurred only in its functions and antibiotic resistance gene community in both Rhinopithecus species, reflecting its ecological functional redundancy. Given the current findings (e.g., depletion in probiotic microbes, dysbiosis in the gut microbial community, and changes in the antibiotic resistance gene profile), anthropogenic disturbances (e.g., food provisioning) would have potential negative effects on host health. Therefore, human activity in animal conservation should be rethought from the standpoint of gut microbial diversity.},
}
@article {pmid36343797,
year = {2022},
author = {Huang, HS and Lin, YE and Panyod, S and Chen, RA and Lin, YC and Chai, LMX and Hsu, CC and Wu, WK and Lu, KH and Huang, YJ and Sheen, LY},
title = {Anti-depressive-like and cognitive impairment alleviation effects of Gastrodia elata Blume water extract is related to gut microbiome remodeling in ApoE-/- mice exposed to unpredictable chronic mild stress.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {115872},
doi = {10.1016/j.jep.2022.115872},
pmid = {36343797},
issn = {1872-7573},
abstract = {ETHNOPHARMACOLOGY RELEVANCE: Gastrodia elata Blume (GE) is a traditional Chinese dietary therapy used to treat neurological disorders. Gastrodia elata Blume water extract (WGE) has been shown to ameliorate inflammation and improve social frustration in mice in a chronic social defeat model. However, studies on the anti-depressive-like effects and cognitive impairment alleviation related to the impact of WGE on the gut microbiome of ApoE-/- mice remain elusive.<br><br>AIM OF THE STUDY: The present study aimed to investigate the anti-depressive-like effect and cognitive impairment alleviation and mechanisms of WGE in ApoE-/- mice subjected to unpredictable chronic mild stress (UCMS), as well as its impact on the gut microbiome of the mice.<br><br>MATERIALS AND METHODS: Sixty ApoE-/- mice (6 months old) were randomly grouped into six groups: control, UCMS, WGE groups [5, 10, 20 mL WGE/kg body weight (bw) + UCMS], and a positive group (fluoxetine 20 mg/kg bw + UCMS). After four weeks of the UCMS paradigm, the sucrose preference, novel object recognition, and open field tests were conducted. The neurotransmitters serotonin (5-HT) and dopamine (DA) and their metabolites were measured in the prefrontal cortex. Serum was collected to measure corticosterone and amyloid-42 (Aβ-42) levels. Feces were collected, and the gut microbiome was analyzed.<br><br>RESULTS: WGE restored sucrose preference, exploratory behavior and recognition ability, and decreased the levels of serum corticosterone and Aβ-42 in ApoE-/- mice to alleviate depressive-like behavior and cognitive impairment. Furthermore, WGE regulated the monoamine neurotransmitter via reduced the 5-HT and DA turnover rates in the prefrontal cortex. Moreover, WGE elevated the levels of potentially beneficial bacteria such as Bifidobacterium, Akkermansia, Alloprevotella, Defluviitaleaceae_UCG-011, and Bifidobacterium pseudolongum as well as balanced fecal short-chain fatty acids (SCFAs).<br><br>CONCLUSION: WGE demonstrates anti-depressive-like effects, cognitive impairment alleviation, and gut microbiome and metabolite regulation in ApoE-/- mice. Our results support the possibility of developing a functional and complementary medicine to prevent or alleviate depression and cognitive decline using WGE in CVDs patients.},
}
@article {pmid36343772,
year = {2022},
author = {Perez-Garcia, J and González-Carracedo, M and Espuela-Ortiz, A and Hernández-Pérez, JM and González-Pérez, R and Sardón-Prado, O and Martin-Gonzalez, E and Mederos-Luis, E and Poza-Guedes, P and Corcuera-Elosegui, P and Callero, A and Sánchez-Machín, I and Korta-Murua, J and Pérez-Pérez, JA and Villar, J and Pino-Yanes, M and Lorenzo-Diaz, F},
title = {The Upper-Airway Microbiome as a Biomarker of Asthma Exacerbations despite Inhaled Corticosteroid Treatment.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2022.09.041},
pmid = {36343772},
issn = {1097-6825},
abstract = {BACKGROUND: The response to inhaled corticosteroids (ICS) in asthma is affected by the interplay of several factors. Among these, the role of the upper-airway microbiome has been scarcely investigated. We aimed to evaluate the association between the salivary, pharyngeal, and nasal microbiome with asthma exacerbations despite ICS use.<br><br>METHODS: Samples from 250 asthma patients from the Genomics and Metagenomics of Asthma Severity (GEMAS) study treated with ICS were analyzed. Controls/cases were defined by the absence/presence of asthma exacerbations in the past six months despite being treated with ICS. The bacterial microbiota was profiled by sequencing the V3-V4 region of the 16S rRNA gene. Differences between groups were assessed by PERMANOVA and regression models adjusted for potential confounders. A false discovery rate (FDR) of 5% was used to correct for multiple comparisons. Classification models of asthma exacerbations despite ICS treatment were built with machine learning approaches based on clinical, genetic, and microbiome data.<br><br>RESULTS: In nasal and saliva samples, cases had lower bacterial diversity (Richness, Shannon, and Faith indexes) than controls (0.007≤p≤0.037). Asthma exacerbations accounted for 8-9% of the interindividual variation of the salivary and nasal microbiomes (0.003≤p≤0.046). Three, four, and eleven bacterial genera from the salivary, pharyngeal, and nasal microbiomes were differentially abundant between groups (4.09x10-12≤FDR≤0.047). Integrating clinical, genetic, and microbiome data showed good discrimination for the development of asthma exacerbations despite ICS use (AUCtraining:0.82 and AUCvalidation:0.77).<br><br>CONCLUSION: The diversity and composition of the upper-airway microbiome are associated with asthma exacerbations despite ICS treatment. The salivary microbiome has a potential application as a biomarker of asthma exacerbations despite ICS use.},
}
@article {pmid36343710,
year = {2022},
author = {Victor Mercado, J and Koyama, M and Nakasaki, K},
title = {Complexity of acclimatization substrate affects anaerobic digester microbial community response to organic load shocks.},
journal = {Environmental research},
volume = {},
number = {},
pages = {114722},
doi = {10.1016/j.envres.2022.114722},
pmid = {36343710},
issn = {1096-0953},
abstract = {This study elucidated the changes in the short-term response to organic load shocks of the anaerobic digestion (AD) microbiome acclimatized to a simple substrate and a complex substrate. Batch vial reactors were inoculated with AD sludge acclimatized to either a simple (starch and hipolypeptone) or a complex (dog food and starch) substrate, both with carbon-to-nitrogen ratio of 25. Organic loads in the form of an easily degradable substrate mix (starch and hipolypeptone) with concentrations varying from 0 to 5 g VS/L were applied to the reactors. Runs utilizing the inoculum acclimatized to a complex substrate sustained its methane productivity despite the high organic load shocks which the inoculum acclimatized to a simple substrate was unable to handle efficiently. The alpha-diversity of the microbiome decreased with increase in organic load for inoculum acclimatized with a simple substrate but was unaffected for the case of the inoculum acclimatized with a complex substrate. Lactobacillales and Cloacimonadales were inferred to be major players in starch degradation pathways for the inoculum acclimatized using a simple substrate as predicted by the bioinformatics package PICRUSt2. However, acclimatizing using a complex substrate did not support their growth and were replaced by Coriobacteriales which provided higher flexibility in terms of the predicted regulated metabolic functions. The predicted functional regulation of Synergistales and Syntrophales increased with acclimatization using a complex substrate which also showed increase in the flexibility of the microbiome towards handling organic load shocks. Acetoclastic pathway was upregulated with increase in organic load regardless of the acclimatization substrate while the hydrogenotrophic pathway was downregulated. Overall, acclimatization using a complex substrate increased the robustness and flexibility of the microbiome towards organic load shocks.},
}
@article {pmid36343662,
year = {2022},
author = {Lee, JW and Cowley, ES and Wolf, PG and Doden, HL and Murai, T and Caicedo, KYO and Ly, LK and Sun, F and Takei, H and Nittono, H and Daniel, SL and Cann, I and Gaskins, HR and Anantharaman, K and Alves, JMP and Ridlon, JM},
title = {Formation of secondary allo-bile acids by novel enzymes from gut Firmicutes.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2132903},
doi = {10.1080/19490976.2022.2132903},
pmid = {36343662},
issn = {1949-0984},
abstract = {The gut microbiome of vertebrates is capable of numerous biotransformations of bile acids, which are responsible for intestinal lipid digestion and function as key nutrient-signaling molecules. The human liver produces bile acids from cholesterol predominantly in the A/B-cis orientation in which the sterol rings are "kinked", as well as small quantities of A/B-trans oriented "flat" stereoisomers known as "primary allo-bile acids". While the complex multi-step bile acid 7α-dehydroxylation pathway has been well-studied for conversion of "kinked" primary bile acids such as cholic acid (CA) and chenodeoxycholic acid (CDCA) to deoxycholic acid (DCA) and lithocholic acid (LCA), respectively, the enzymatic basis for the formation of "flat" stereoisomers allo-deoxycholic acid (allo-DCA) and allo-lithocholic acid (allo-LCA) by Firmicutes has remained unsolved for three decades. Here, we present a novel mechanism by which Firmicutes generate the "flat" bile acids allo-DCA and allo-LCA. The BaiA1 was shown to catalyze the final reduction from 3-oxo-allo-DCA to allo-DCA and 3-oxo-allo-LCA to allo-LCA. Phylogenetic and metagenomic analyses of human stool samples indicate that BaiP and BaiJ are encoded only in Firmicutes and differ from membrane-associated bile acid 5α-reductases recently reported in Bacteroidetes that indirectly generate allo-LCA from 3-oxo-Δ4-LCA. We further map the distribution of baiP and baiJ among Firmicutes in human metagenomes, demonstrating an increased abundance of the two genes in colorectal cancer (CRC) patients relative to healthy individuals.},
}
@article {pmid36343601,
year = {2022},
author = {Wu, JY and Hua, ZL and Liang, ZY and Gu, L},
title = {Impacts of iron amendments and per-fluoroalkyl substances' bio-availability to the soil microbiome in wheat ecosystem.},
journal = {Chemosphere},
volume = {311},
number = {Pt 2},
pages = {137140},
doi = {10.1016/j.chemosphere.2022.137140},
pmid = {36343601},
issn = {1879-1298},
abstract = {Per-fluoroalkyl substances (PFASs) have become ubiquitous in farmland ecosystems and pose risks to agricultural safety, and iron is often applied to farmland soils to reduce the availability of pollutants. However, the effects of iron amendment on the availability of PFASs in the soil and on the soil microbiome are not well understood. Here, we investigated the responses of wheat soil containing PFASs to iron addition using a 21-day experiment. Our results showed that iron amendment enhanced PFAS availability (p < 0.05) and stimulated superoxide dismutase (SOD) activity in the wheat soil (p < 0.05), but iron amendment decreased the activities of soil catalase (CAT) and peroxidase (POD) (p < 0.05). Soil bacterial community was more structurally stable than fungal community in response to iron addition, while species' pools were more stable in fungi than in bacteria (p < 0.05). Finally, PFPeA's availability in the wheat soil was the most important abiotic factors driving community succession of iron-cycling bacteria (p < 0.05). These results highlighted the potential interactions among PFASs' availability and microbial iron cycling in wheat farmland soil ecosystems and provided guidance in farmland environmental conservation and management.},
}
@article {pmid36343402,
year = {2022},
author = {Liao, H and Li, C and Ai, S and Li, X and Ai, X and Ai, Y},
title = {A simulated ecological restoration of bare cut slope reveals the dosage and temporal effects of cement on ecosystem multifunctionality in a mountain ecosystem.},
journal = {Journal of environmental management},
volume = {325},
number = {Pt B},
pages = {116672},
doi = {10.1016/j.jenvman.2022.116672},
pmid = {36343402},
issn = {1095-8630},
abstract = {Cement is a critical building material used in the restorations of bare cut slopes. Yet, how cement affects ecosystem's functions and their undertakers remains elusive. Here, we revealed the dosage and temporal effects of cement on plant and soil traits, extracellular enzymes, greenhouse gas fluxes and microbiome using simulation experiments. The results showed that soil pH increased with the cement content at 1st day but relatively constant values around 7 to 7.5 were detected in the flowing days. The β-1,4-glucosidase, phenol oxidase, leucine aminopeptidase and acid phosphatase showed high activities under high cement content, and they generally increased with the cultivations except for acid phosphatase. CH4 fluxes at 16th day were less than zero, and they increased to peak around at 37th to 44th days followed by decreasing until reaching to relatively stable fluctuations around 0. Despite of decrease patterns, N2O fluxes stayed around zero across the temporal gradient except for the maximum around at 30th day in 2%, 5% and 8% cement treatment. Microbial diversity decreased with the cement content, in which there were a recovery trend for bacteria. By integrating above- and belowground ecosystem traits into a multifunctionality index, we identified a potential optimum cement content (11%). PLSPM showed that multifunctionality was affected by the shifts in soil bacterial community, enzyme activity and greenhouse gases while these components were effected by other environmental changes resulted from cement. Our results demonstrate that cement determines multifunctionality through mediating microbial community and activity, providing new insights for designing in situ experiments and ecological restoration strategies for bare cut slopes.},
}
@article {pmid36343281,
year = {2022},
author = {Moutsoglou, DM and Tatah, J and Prisco, SZ and Prins, KW and Staley, C and Lopez, S and Blake, M and Teigen, L and Kazmirczak, F and Weir, EK and Kabage, AJ and Guan, W and Khoruts, A and Thenappan, T},
title = {Pulmonary Arterial Hypertension Patients Have a Proinflammatory Gut Microbiome and Altered Circulating Microbial Metabolites.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202203-0490OC},
pmid = {36343281},
issn = {1535-4970},
abstract = {RATIONALE: Inflammation drives pulmonary arterial hypertension (PAH). Gut dysbiosis causes immune dysregulation and systemic inflammation by altering circulating microbial metabolites; however, little is known about gut dysbiosis and microbial metabolites in PAH.<br><br>OBJECTIVES: To characterize the gut microbiome and microbial metabolites in PAH patients.<br><br>METHODS: We performed 16S ribosomal ribonucleic acid gene and shotgun metagenomics sequencing on stool from PAH patients, family controls, and healthy controls. We measured markers of inflammation, gut permeability, and microbial metabolites in plasma from PAH patients, family controls, and healthy controls.<br><br>MAIN RESULTS: The gut microbiome was less diverse in PAH patients. Shannon diversity index correlated with measures of pulmonary vascular disease but not with right ventricular function. PAH patients had a distinct gut microbial signature at the phylogenetic level with lower copies of gut microbial genes that produce anti-inflammatory short-chain fatty acids (SCFAs) and secondary bile acids and lower relative abundances of species encoding these genes. Consistent with the gut microbial changes, PAH patients had relatively lower plasma levels of SCFAs and secondary bile acids. PAH patients also had enrichment of species with the microbial genes that encoded the proinflammatory microbial metabolite trimethylamine. The changes in the gut microbiome and circulating microbial metabolites between PAH patients and family controls were not as substantial as the differences between PAH patients and healthy controls.<br><br>CONCLUSIONS: PAH patients have proinflammatory gut dysbiosis in which lower circulating SCFAs and secondary bile acids may facilitate pulmonary vascular disease. These findings support investigating modulation of the gut microbiome as a potential treatment for PAH.},
}
@article {pmid36343261,
year = {2022},
author = {Nethery, MA and Hidalgo-Cantabrana, C and Roberts, A and Barrangou, R},
title = {CRISPR-based engineering of phages for in situ bacterial base editing.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {46},
pages = {e2206744119},
doi = {10.1073/pnas.2206744119},
pmid = {36343261},
issn = {1091-6490},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
abstract = {Investigation of microbial gene function is essential to the elucidation of ecological roles and complex genetic interactions that take place in microbial communities. While microbiome studies have increased in prevalence, the lack of viable in situ editing strategies impedes experimental progress, rendering genetic knowledge and manipulation of microbial communities largely inaccessible. Here, we demonstrate the utility of phage-delivered CRISPR-Cas payloads to perform targeted genetic manipulation within a community context, deploying a fabricated ecosystem (EcoFAB) as an analog for the soil microbiome. First, we detail the engineering of two classical phages for community editing using recombination to replace nonessential genes through Cas9-based selection. We show efficient engineering of T7, then demonstrate the expression of antibiotic resistance and fluorescent genes from an engineered λ prophage within an Escherichia coli host. Next, we modify λ to express an APOBEC-1-based cytosine base editor (CBE), which we leverage to perform C-to-T point mutations guided by a modified Cas9 containing only a single active nucleolytic domain (nCas9). We strategically introduce these base substitutions to create premature stop codons in-frame, inactivating both chromosomal (lacZ) and plasmid-encoded genes (mCherry and ampicillin resistance) without perturbation of the surrounding genomic regions. Furthermore, using a multigenera synthetic soil community, we employ phage-assisted base editing to induce host-specific phenotypic alterations in a community context both in vitro and within the EcoFAB, observing editing efficiencies from 10 to 28% across the bacterial population. The concurrent use of a synthetic microbial community, soil matrix, and EcoFAB device provides a controlled and reproducible model to more closely approximate in situ editing of the soil microbiome.},
}
@article {pmid36342653,
year = {2022},
author = {Orenstein, R},
title = {The Role of Microbiome-Based Therapeutics in Clostridioides difficile Infection: Durable, Long-Term Results of RBX2660.},
journal = {Infectious diseases and therapy},
volume = {},
number = {},
pages = {},
pmid = {36342653},
issn = {2193-8229},
abstract = {A recently published manuscript described findings from a phase 2 open label study of the microbiota-based live biotherapeutic product RBX2660 in patients with two or more previous recurrent Clostridioides difficile infection (rCDI) episodes, and described long-term safety and sustained treatment success through 24 months. As previous studies have typically focused on short-term clinical outcomes, these new data provide insight into the tolerability, safety, and efficacy of RBX2660 over the long term. When microbiota-based products were first evaluated, the long-term efficacy and safety were principal concerns of the United States Food and Drug Administration. Microbiota-based live biotherapeutic products (LBPs) represent an emerging approach to the management of CDI and perhaps other gastrointestinal and medical conditions whose pathogenesis is defined by microbial dysbiosis. RBX2660 is a human-derived, broad consortium microbiota-based LBP that consists of a population of microbes obtained from healthy stool donors and may reflect the symbiotic nature of a healthy colonic microbiome. RBX2660 is rectally administered and does not require sedation or special preparation of the recipient. Potential advantages of the rectal administration of RBX2660 include the ease of administration and lack of need for any bowel preparation, which may benefit those who are frail, have swallowing issues, or cannot take bowel laxative preparations. In this multicenter prospective trial of rCDI, patients who achieved treatment success 8 weeks after receiving RBX2660 continued to have a sustained clinical response over the course of long-term follow-up, with more than 90% of treatment responders remaining CDI-free at 6, 12, and 24 months. Following receipt of RBX2660, the gut microbiota of those with treatment success were restored from a dysbiotic state to become more diverse and similar to RBX2660 composition. The restoration of the microbiota occurred as early as 7 days after RBX2660 administration and remained stable through the 24-month analysis. No new adverse outcomes were observed during the prospective assessment, and the safety profile of RBX2660 was consistent with previous studies. Based on the clinical studies, RBX2660 will most likely benefit those with ≥ 1 rCDI episode or those who are at a high risk of subsequent rCDI, such as patients who have comorbid conditions including renal disease, heart disease, or inflammatory bowel disease, or who are immunosuppressed. The role of microbiome-based therapeutics in 47 Clostridioides difficile infection: Durable, long-term results of RBX2660 (MP4 511833 KB).},
}
@article {pmid36342297,
year = {2022},
author = {Mirabelli, C and Santos-Ferreira, N and Gillilland, MG and Cieza, RJ and Colacino, JA and Sexton, JZ and Neyts, J and Taube, S and Rocha-Pereira, J and Wobus, CE},
title = {Human Norovirus Efficiently Replicates in Differentiated 3D-Human Intestinal Enteroids.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0085522},
doi = {10.1128/jvi.00855-22},
pmid = {36342297},
issn = {1098-5514},
abstract = {Human norovirus (HNoV) accounts for one-fifth of all acute viral gastroenteritis worldwide and an economic burden of ~$60 billion globally. The lack of treatment options against HNoV is in part due to the lack of cultivation systems. Recently, a model of infection in biopsy-derived human intestinal enteroids (HIE) has been described: 3D-HIE are first dispersed in 2D-monolayers and differentiated prior to infection, resulting in a labor-intensive, time-consuming procedure. Here, we present an alternative protocol for HNoV infection of 3D-HIE. We found that 3D-HIE differentiated as efficiently as 2D-monolayers. In addition, immunofluorescence-based quantification of UEA-1, a lectin that stains the villus brush border, revealed that ~80% of differentiated 3D-HIE spontaneously undergo polarity inversion, allowing for viral infection without the need for microinjection. Infection with HNoV GII.4-positive stool samples attained a fold-increase over inoculum of ~2 Log10 at 2 days postinfection or up to 3.5 Log10 when ruxolitinib, a JAK1/2-inhibitor, was added. Treatment of GII.4-infected 3D-HIE with the polymerase inhibitor 2'-C-Methylcytidine (2CMC) and other antivirals showed a reduction in viral infection, suggesting that 3D-HIE are an excellent platform to test anti-infectives. The transcriptional host response to HNoV was then investigated by RNA sequencing in infected versus uninfected 3D-HIE in the presence of ruxolitinib to focus on virus-associated signatures while limiting interferon-stimulated gene signatures. The analysis revealed upregulated hormone and neurotransmitter signal transduction pathways and downregulated glycolysis and hypoxia-response pathways upon HNoV infection. Overall, 3D-HIE have proven to be a highly robust model to study HNoV infection, screen antivirals, and to investigate the host response to HNoV infection. IMPORTANCE The human norovirus (HNoV) clinical and socio-economic impact calls for immediate action in the development of anti-infectives. Physiologically relevant in vitro models are hence needed to study HNoV biology, tropism, and mechanisms of viral-associated disease, and also as a platform to identify antiviral agents. Biopsy-derived human intestinal enteroids are a biomimetic of the intestinal epithelium and were recently described as a model that supports HNoV infection. However, the established protocol is time-consuming and labor-intensive. Therefore, we sought to develop a simplified and robust alternative model of infection in 3D enteroids that undergoes differentiation and spontaneous polarity inversion. Advantages of this model are the shorter experimental time, better infection yield, and spatial integrity of the intestinal epithelium. This model is potentially suitable for the study of other pathogens that infect intestinal cells from the apical surface but also for unraveling the interactions between intestinal epithelium and indigenous bacteria of the human microbiome.},
}
@article {pmid36342282,
year = {2022},
author = {Bergen, N and Krämer, P and Romberg, J and Wichels, A and Gerlach, G and Brinkhoff, T},
title = {Shell Disease Syndrome Is Associated with Reduced and Shifted Epibacterial Diversity on the Carapace of the Crustacean Cancer pagurus.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0341922},
doi = {10.1128/spectrum.03419-22},
pmid = {36342282},
issn = {2165-0497},
abstract = {Cancer pagurus is highly susceptible to shell disease syndrome. However, little is known about concomitant changes in the epibacterial community. We compared the bacterial communities of black spot affected and nonaffected areas of the carapace by amplicon sequencing of 16S rRNA genes and 16S rRNA. Within each spot, bacterial communities of affected areas were less diverse compared to communities from nonaffected areas. Communities of different affected spots were, however, more divergent from each other, compared to those of different nonaffected areas. This indicates a reduced and shifted microbial community composition caused by the black spot disease. Different communities found in black spots likely indicate different stages of the disease. In affected areas, Flavobacteriaceae rose to one of the most abundant and active families due to the increase of Aquimarina spp., suggesting a significant role in shell disease syndrome. We isolated 75 bacterial strains from diseased and healthy areas, which are primarily affiliated with Proteobacteria and Bacteroidetes, reflecting the dominant phyla detected by amplicon sequencing. The ability to degrade chitin was mainly found for Gammaproteobacteria and Aquimarina spp. within the Flavobacteriia, while the ability to use N-acetylglucosamine, the monomer of the polysaccharide chitin, was observed for most isolates, including many Alphaproteobacteria. One-third of the isolates, including most Aquimarina spp., showed antagonistic properties, indicating a high potential for interactions between the bacterial populations. The combination of bacterial community analysis and the physiological properties of the isolates provided insights into a functional complex epibacterial community on the carapace of C. pagurus. IMPORTANCE In recent years, shell disease syndrome has been detected for several ecologically and economically important crustacean species. Large proportions of populations are affected, e.g., >60% of the widely distributed species Cancer pagurus in different North Sea areas. Bacteria play a significant role in the development of different forms of shell disease, all characterized by microbial chitinolytic degradation of the outer shell. By comparing the bacterial communities of healthy and diseased areas of the shell of C. pagurus, we demonstrated that the disease causes a reduced bacterial diversity within affected areas, a phenomenon co-occurring also with many other diseases. Furthermore, the community composition dramatically changed with some taxa rising to high relative abundances and showing increased activity, indicating strong participation in shell disease. Characterization of bacterial isolates obtained from affected and nonaffected spots provided deeper insights into their physiological properties and thus the possible role within the microbiome.},
}
@article {pmid36342150,
year = {2022},
author = {Mackenzie, CL and Pearce, CM and Leduc, S and Roth, D and Kellogg, CTE and Clemente-Carvalho, RBG and Green, TJ},
title = {Impacts of Seawater pH Buffering on the Larval Microbiome and Carry-Over Effects on Later-Life Disease Susceptibility in Pacific Oysters.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0165422},
doi = {10.1128/aem.01654-22},
pmid = {36342150},
issn = {1098-5336},
abstract = {Ocean acidification upwelling events and the resulting lowered aragonite saturation state of seawater have been linked to high mortality of marine bivalve larvae in hatcheries. Major oyster seed producers along North America's west coast have mitigated impacts via seawater pH buffering (e.g., addition of soda ash). However, little consideration has been given to whether such practice may impact the larval microbiome, with potential carry-over effects on immune competency and disease susceptibility in later-life stages. To investigate possible impacts, Pacific oysters (Crassostrea gigas) were reared under soda ash pH buffered or ambient pH seawater conditions for the first 24 h of development. Both treatment groups were then reared under ambient pH conditions for the remainder of the developmental period. Larval microbiome, immune status (via gene expression), growth, and survival were assessed throughout the developmental period. Juveniles and adults arising from the larval run were then subjected to laboratory-based disease challenges to investigate carry-over effects. Larvae reared under buffered conditions showed an altered microbiome, which was still evident in juvenile animals. Moreover, reduced survival was observed in both juveniles and adults of the buffered group under a simulated marine heatwave and Vibrio exposure compared with those reared under ambient conditions. Results suggest that soda ash pH buffering during early development may compromise later-life stages under stressor conditions, and illustrate the importance of a long-view approach with regard to hatchery husbandry practices and climate change mitigation. IMPORTANCE Shellfish industries are threatened worldwide by recurrent summer mortality events. Such incidences are often associated with Vibrio disease outbreaks, and thus, it is critical that animals are able to mount sufficient immune responses. The oyster immune system is linked to the microbiome which is laid down during early developmental stages. Consequently, shellfish hatcheries play a key role with regard to shaping the immune competency of later-life stages. This study represents the first in-depth examination of whether the adoption of seawater pH buffering practice by hatcheries for mitigation of ocean acidification may alter the larval microbiome, and thus, have repercussions for adult susceptibility to summer mortality events. Findings demonstrate that even minimal buffering results in a changed microbiome which is paralleled by increased mortality of later-life stages under Vibrio and temperature stressors, highlighting the importance of the hatchery environment with regard to shaping resilience to summer mortality events.},
}
@article {pmid36342141,
year = {2022},
author = {Begley, LA and Opron, K and Bian, G and Kozik, AJ and Liu, C and Felton, J and Wen, B and Sun, D and Huang, YJ},
title = {Effects of Fluticasone Propionate on Klebsiella pneumoniae and Gram-Negative Bacteria Associated with Chronic Airway Disease.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0037722},
doi = {10.1128/msphere.00377-22},
pmid = {36342141},
issn = {2379-5042},
abstract = {Inhaled corticosteroids (ICS) are commonly prescribed first-line treatments for asthma and chronic obstructive pulmonary disease (COPD). Recent evidence has shown that ICS use is associated with changes in the airway microbiome, which may impact clinical outcomes such as potential increased risk for pneumonia in COPD. Although the immunomodulatory effects of corticosteroids are well appreciated, whether ICS could directly influence the behavior of respiratory tract bacteria has been unknown. In this pilot study we explored the effects of fluticasone proprionate, a commonly prescribed inhaled corticosteroid, on respiratory bacteria with an expanded focus on Klebsiella pneumoniae, a species previously implicated in fluticasone-associated pneumonia in COPD. We observed significant effects of fluticasone proprionate on growth responses of K. pneumoniae, as well as other bacterial species isolated from asthmatic patients. Fluticasone-exposed K. pneumoniae displayed altered expression of several bacterial genes and reduced the metabolic activity of bronchial epithelial cells and their expression of human β-defensin 2. Targeted assays identified a fluticasone metabolite from fluticasone-exposed K. pneumoniae cells, suggesting this species may be capable of metabolizing fluticasone proprionate. Collectively, these observations support the hypothesis that specific members of the airway microbiota possess the functional repertoire to respond to or potentially utilize corticosteroids in their microenvironment. These findings lay a foundation for novel research directions into the potential direct effects of ICS, often prescribed long term to patients, on the broader airway microbial community and on the behavior of specific microbial species implicated in asthma and COPD outcomes. IMPORTANCE Inhaled corticosteroids are widely prescribed for many respiratory diseases, including asthma and COPD. While they benefit many patients, corticosteroids can also have negative effects. Some patients do not improve with treatment and even experience adverse side effects. Recent studies have shown that inhaled corticosteroids can change the make-up of bacteria in the human respiratory tract. However, whether these medications can directly impact the behavior of such bacteria has been unknown. Here, we explored the effects of fluticasone propionate, a commonly prescribed inhaled corticosteroid, on Klebsiella pneumoniae and other airway bacteria of interest, including primary species isolated from adult asthma patients. We provide evidence of growth responses to direct fluticasone exposure in culture and further examined fluticasone's effects on K. pneumoniae, including gene expression changes and effects of fluticasone-exposed bacteria on airway cells. These findings indicate that members of the human airway bacterial community possess the functional ability to respond to corticosteroids, which may have implications for the heterogeneity of treatment response observed clinically.},
}
@article {pmid36342051,
year = {2022},
author = {Jiang, H and Cao, HW and Chai, ZX and Chen, XY and Zhang, CF and Zhu, Y and Xin, JW},
title = {Dynamic alterations in yak (Bos grunniens) rumen microbiome in response to seasonal variations in diet.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00112.2022},
pmid = {36342051},
issn = {1531-2267},
support = {XZ202001ZY0016N//Key Research and Development Projects in Tibet: Preservation of Characteristic Biological Germplasm Resources and Utilization of Gene Technology in Tibet/ ; 2019QZKK0501//Second Tibetan Plateau Scientific Expedition and Research Program/ ; CARS-37//Program National Beef Cattle and Yak Industrial Technology System/ ; },
abstract = {Rumen microorganisms play important roles in the healthy growth of yaks. This study investigated changes of yak rumen microbiome during natural grazing at the warm seasons and supplementary feeding at cold seasons. High-throughput sequencing of 16S rRNA and metagenome analysis were conducted to investigate the structures and functions of yak rumen microbial communities. The results indicated that Bacteroidetes and Firmicutes were the most abundant phyla. In addition, Bacteroidetes might play a more important role than Firmicutes during the supplementary feeding stage (spring and winter), but less during natural grazing stage (summer and autumn). KEGG analysis showed that the amino sugar and nucleotide sugar metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, starch and sucrose metabolism, and fructose and mannose metabolism were the main pathways in the microbial community, which were significantly different between seasons. The carbohydrate-active enzymes (CAZyme) annotation revealed that cellulose was an important carbon source for microorganisms in yak rumen. Glycoside hydrolases (GHs) were the most abundant class of CAZymes, followed by glycosyl transferases (GTs), which were important to digestion of oil, cellulose, and hemicellulose in food. These results contribute to the understanding of microbial component and functions in yak rumen.},
}
@article {pmid36341539,
year = {2022},
author = {Chen, X and Zhang, D and Li, Y and Li, H and Lou, J and Li, X and Wei, M},
title = {Changes in rhizospheric microbiome structure and soil metabolic function in response to continuous cucumber cultivation.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiac129},
pmid = {36341539},
issn = {1574-6941},
abstract = {With the increasing reliance on intensive arable agriculture, analysis of the problems associated with continuous cropping has become a global research focus. Here, high-throughput sequencing and non-targeted metabolomics were used to evaluate the responses of soil microbial community structure and soil metabolic function to continuous cucumber cultivation (from one to 18 years of continuous cultivation) in greenhouses. Continuous cucumber cropping resulted in increased soil nutrient concentrations but decreased concentrations of available nutrients. The abundance of several bacterial genera associated with nutrient cycling, such as Bacillus and Sphingomonas, was reduced by continuous cucumber cultivation. The abundance of several beneficial fungal genera, including pathogen antagonists (e.g. Chaetomium, Mortierella, Aspergillus, and Penicillium), were found to gradually decrease in response to the increased duration of continuous cropping. 3-amino-2-naphthoic acid and L-valine increased initially and then decreased as the cropping continued, which were related to fatty acid metabolism and amino acid biosynthesis. We also confirmed a close association between microbial community structure and soil metabolites. This study linked the changes in microbial community structure and metabolites in the rhizosphere soil and provided new insights into soil-microbial interactions in continuous cucumber culture systems.},
}
@article {pmid36341518,
year = {2022},
author = {Kessler, C and Hou, J and Neo, O and Buckner, MMC},
title = {In situ, in vivo and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuac044},
pmid = {36341518},
issn = {1574-6976},
abstract = {Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence and manipulability of horizontal gene transfer in the gut microbiome.},
}
@article {pmid36341495,
year = {2022},
author = {Xu, J and Xu, J and Shi, T and Zhang, Y and Chen, F and Yang, C and Guo, X and Liu, G and Shao, D and Leong, KW and Nie, G},
title = {Probiotic-inspired nanomedicine restores intestinal homeostasis in colitis by regulating redox balance, immune responses, and the gut microbiome.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e2207890},
doi = {10.1002/adma.202207890},
pmid = {36341495},
issn = {1521-4095},
abstract = {Microbiota-based therapeutics offer innovative strategies to treat inflammatory bowel diseases (IBDs). However, the poor clinical outcome so far and the limited flexibility of the bacterial approach call for improvement. Inspired by the health benefits of probiotics in alleviating symptoms of bowel diseases, we designed bioartificial probiotics to restore the intestinal microenvironment in colitis by regulating redox balance, immune responses, and the gut microbiome. The bioartificial probiotic comprises two components: an E. coli Nissle 1917-derived membrane (EM) as the surface and the biodegradable diselenide-bridged mesoporous silica nanoparticles (SeM) as the core. When orally administered, the probiotic-inspired nanomedicine (SeM@EM) adhered strongly to the mucus layer and restored intestinal redox balance and immune regulation homeostasis in a murine model of acute colitis induced by dextran sodium sulfate. In addition, the respective properties of the EM and SeM synergistically altered the gut microbiome to a favorable state by increasing the bacterial diversity and shifting the microbiome profile to an anti-inflammatory phenotype. This work suggests a safe and effective nanomedicine that can restore intestinal homeostasis for IBDs therapy. This article is protected by copyright. All rights reserved.},
}
@article {pmid36341463,
year = {2022},
author = {Mousa, WK and Chehadeh, F and Husband, S},
title = {Microbial dysbiosis in the gut drives systemic autoimmune diseases.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {906258},
pmid = {36341463},
issn = {1664-3224},
mesh = {Humans ; Dysbiosis ; *Gastrointestinal Microbiome ; *Microbiota ; *Autoimmune Diseases ; *Probiotics/therapeutic use ; },
abstract = {Trillions of microbes survive and thrive inside the human body. These tiny creatures are crucial to the development and maturation of our immune system and to maintain gut immune homeostasis. Microbial dysbiosis is the main driver of local inflammatory and autoimmune diseases such as colitis and inflammatory bowel diseases. Dysbiosis in the gut can also drive systemic autoimmune diseases such as type 1 diabetes, rheumatic arthritis, and multiple sclerosis. Gut microbes directly interact with the immune system by multiple mechanisms including modulation of the host microRNAs affecting gene expression at the post-transcriptional level or production of microbial metabolites that interact with cellular receptors such as TLRs and GPCRs. This interaction modulates crucial immune functions such as differentiation of lymphocytes, production of interleukins, or controlling the leakage of inflammatory molecules from the gut to the systemic circulation. In this review, we compile and analyze data to gain insights into the underpinning mechanisms mediating systemic autoimmune diseases. Understanding how gut microbes can trigger or protect from systemic autoimmune diseases is crucial to (1) tackle these diseases through diet or lifestyle modification, (2) develop new microbiome-based therapeutics such as prebiotics or probiotics, (3) identify diagnostic biomarkers to predict disease risk, and (4) observe and intervene with microbial population change with the flare-up of autoimmune responses. Considering the microbiome signature as a crucial player in systemic autoimmune diseases might hold a promise to turn these untreatable diseases into manageable or preventable ones.},
}
@article {pmid36341422,
year = {2022},
author = {Mukanova, S and Borissenko, A and Kim, A and Bolatbek, A and Abdrakhmanova, A and Vangelista, L and Sonnenberg-Riethmacher, E and Riethmacher, D},
title = {Role of periostin in inflammatory bowel disease development and synergistic effects mediated by the CCL5-CCR5 axis.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {956691},
pmid = {36341422},
issn = {1664-3224},
mesh = {Humans ; Mice ; Animals ; *Receptors, Chemokine ; *Inflammatory Bowel Diseases ; Chemokine CCL3 ; Chemokine CCL4 ; Inflammation ; Chemokine CCL5 ; Receptors, CCR5/metabolism ; },
abstract = {Inflammatory bowel disease (IBD), comprising mainly Crohn's disease (CD) and ulcerative colitis (UC), is a chronic inflammatory disease of the gastrointestinal tract. In recent years, a wealth of data has been accumulated demonstrating the complex interplay of many different factors in the pathogenesis of IBD. Among these are factors impacting the epithelial barrier function, including vessel and extracellular matrix (ECM) formation, the gut microbiome (e.g., bacterial antigens), and, most importantly, the production of cytokines (pro- and anti-inflammatory) directly shaping the immune response. Patients failing to resolve the acute intestinal inflammation develop chronic inflammation. It has been shown that the expression of the matricellular protein periostin is enhanced during IBD and is one of the drivers of this disease. The C-C chemokine receptor 5 (CCR5) is engaged by the chemotactic mediators CCL3/MIP-1α, CCL4/MIP-1β, and CCL5/RANTES. CCR5 blockade has been reported to ameliorate inflammation in a murine IBD model. Thus, both periostin and CCR5 are involved in the development of IBD. In this study, we investigated the potential crosstalk between the two signaling systems and tested a highly potent CCL5 derivative acting as a CCR5 antagonist in a murine model of IBD. We observed that the absence of periostin influences the CCR5-expressing cell population of the gut. Our data further support the notion that targeted modulation of the periostin and CCR5 signaling systems bears therapeutic potential for IBD.},
}
@article {pmid36341414,
year = {2022},
author = {Ackerley, CG and Smith, SA and Murray, PM and Amancha, PK and Arthur, RA and Zhu, Z and Chahroudi, A and Amara, RR and Hu, YJ and Kelley, CF},
title = {The rectal mucosal immune environment and HIV susceptibility among young men who have sex with men.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {972170},
pmid = {36341414},
issn = {1664-3224},
mesh = {Adult ; Male ; Humans ; Homosexuality, Male ; *HIV Infections ; *Sexual and Gender Minorities ; Sexual Behavior ; Mucous Membrane ; },
abstract = {Young men who have sex with men (YMSM) represent a particularly high-risk group for HIV acquisition in the US, despite similarly reported rates of sexual activity as older, adult MSM (AMSM). Increased rates of HIV infection among YMSM compared to AMSM could be partially attributable to differences within the rectal mucosal (RM) immune environment associated with earlier sexual debut and less lifetime exposure to receptive anal intercourse. Using an ex vivo explant HIV challenge model, we found that rectal tissues from YMSM supported higher levels of p24 at peak viral replication timepoints compared to AMSM. Among YMSM, the RM was characterized by increased CD4+ T cell proliferation, as well as lower frequencies of tissue resident CD8+ T cells and pro-inflammatory cytokine producing CD4+ and CD8+ T cells. In addition, the microbiome composition of YMSM was enriched for anaerobic taxa that have previously been associated with HIV acquisition risk, including Prevotella, Peptostreptococcus, and Peptoniphilus. These distinct immunologic and microbiome characteristics were found to be associated with higher HIV replication following ex vivo challenge of rectal explants, suggesting the RM microenvironment of YMSM may be uniquely conducive to HIV infection.},
}
@article {pmid36341334,
year = {2022},
author = {Liu, Z and Xiang, Y and Zheng, Y and Kang, X},
title = {Advancing immune checkpoint blockade in colorectal cancer therapy with nanotechnology.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {1027124},
pmid = {36341334},
issn = {1664-3224},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; Immunotherapy ; Tumor Microenvironment ; Nanotechnology ; *Colorectal Neoplasms/drug therapy/pathology ; },
abstract = {Immune checkpoint blockade (ICB) has gained unparalleled success in the treatment of colorectal cancer (CRC). However, undesired side effects, unsatisfactory response rates, tumor metastasis, and drug resistance still hinder the further application of ICB therapy against CRC. Advancing ICB with nanotechnology can be game-changing. With the development of immuno-oncology and nanomaterials, various nanoplatforms have been fabricated to enhance the efficacy of ICB in CRC treatment. Herein, this review systematically summarizes these recent nano-strategies according to their mechanisms. Despite their diverse and complex designs, these nanoplatforms have four main mechanisms in enhancing ICB: 1) targeting immune checkpoint inhibitors (ICIs) to tumor foci, 2) increasing tumor immunogenicity, 3) remodeling tumor microenvironment, and 4) pre-sensitizing immune systems. Importantly, advantages of nanotechnology in CRC, such as innovating the mode-of-actions of ICB, modulating intestinal microbiome, and integrating the whole process of antigen presentation, are highlighted in this review. In general, this review describes the latest applications of nanotechnology for CRC immunotherapy, and may shed light on the future design of ICB platforms.},
}
@article {pmid36340583,
year = {2022},
author = {Yin, L and Li, X and Hou, J},
title = {Macrophages in periodontitis: A dynamic shift between tissue destruction and repair.},
journal = {The Japanese dental science review},
volume = {58},
number = {},
pages = {336-347},
pmid = {36340583},
issn = {1882-7616},
abstract = {Periodontitis is a chronic inflammatory disease associated with a dysbiotic bacterial biofilm in the subgingival environment that may disturb the balance between the oral microbiome and its host. The inability of the immune system to eliminate inflammation may result in the progressive destruction of tooth-support tissues. Macrophages are crucial cellular components of the innate immune system and play important roles in diverse physiological and pathological processes. In response to periodontitis-associated bacterial communities, macrophages contribute to inflammation and restoration of tissue homeostasis through pattern recognition receptor-induced signaling cascades; therefore, targeting macrophages can be a feasible strategy to treat patients with periodontitis. Although recent studies indicate that macrophages have a spectrum of activation states, ranging from pro-inflammatory to anti-inflammatory, the regulatory mechanism of the macrophage response to dysbiosis in a tissue-specific manner remains largely unclear. Herein, we attempt to summarize the potential role of macrophage activation in the progression of periodontitis, as well as its relevance to future approaches in the treatment of periodontitis.},
}
@article {pmid36340378,
year = {2022},
author = {Lin, Q and Wang, Y and Li, M and Xu, Z and Li, L},
title = {Ecological niche selection shapes the assembly and diversity of microbial communities in Casuarina equisetifolia L.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {988485},
pmid = {36340378},
issn = {1664-462X},
abstract = {The plant microbiome profoundly affects many aspects of host performance; however, the ecological processes by which plant hosts govern microbiome assembly, function, and dispersal remain largely unknown. Here, we investigated the bacterial and fungal communities in multiple compartment niches (bulk soil, rhizosphere soil, root endosphere, phylloplane, and leaf endosphere) of Casuarina equisetifolia L. at three developmental stages in Hainan Province, China. We found that microbiome assemblages along the soil-plant continuum were shaped by the compartment niches. Bacterial diversity and richness decreased from the soils to roots to leaves, with the highest network complexity found in the roots and the lowest found in the phylloplane. However, fungal diversity gradually increased from the soils to roots to phyllosphere, whereas fungal richness decreased from the soils to roots but increased from the roots to phyllosphere; the greatest network complexity was found in bulk soils and the lowest was found in the roots. Different biomarker taxa occurred in the different ecological niches. Bacterial and fungal communities exhibited distinct ecological functions; the former played important roles in maintaining plant growth and providing nutrients, whereas the latter predominantly decomposed organic matter. The bacterial community of C. equisetifolia mostly originated from bulk soil, whereas the fungal community was mainly derived from rhizosphere soil and air. Leaf endophytes were positively correlated with organic carbon, and root and soil microorganisms were positively correlated with total nitrogen, total phosphorus, and total potassium. Our findings provide empirical evidence for plant-microbiome interactions and contribute to future research on non-crop management and the manipulation of non-crop microbiomes.},
}
@article {pmid36340191,
year = {2022},
author = {Liu, W and Qiu, K and Xie, Y and Wang, R and Li, H and Meng, W and Yang, Y and Huang, Y and Li, Y and He, Y},
title = {Years of sand fixation with Caragana korshinskii drive the enrichment of its rhizosphere functional microbes by accumulating soil N.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e14271},
pmid = {36340191},
issn = {2167-8359},
abstract = {C. korshinskii is one of the most widely-planted sand-fixing legumes in northwest China and exploring its rhizosphere microbiome is of great ecological importance. However, the effect of long-term sand fixation on the composition, diversity, and underlying functions of microbes in the C. korshinskii rhizosphere in dryland ecosystems remain unclear. Here, we performed high-throughput sequencing using a 16S rRNA (absolute quantification) and bacterial functional annotation of prokaryotic taxa (FAPROTAX) analysis and an ITS (relative quantification) and fungal functional guild (FUNGuild) analysis to investigate the C. korshinskii rhizosphere microbiome and metabolic functional groups at different sand-fixing ages (six years, CK6; twelve years, CK12; and eighteen years, CK18) and determined the physicochemical properties of the rhizosphere soil. Results showed that the key bacterial taxa of the rhizosphere were significantly more abundant in CK18 than in CK12 and CK6 at the phylum-class-genus level, and that fungal Glomeromycota was also significantly more abundant in the CK18 rhizosphere compared to CK12 and CK6. Among these bacterial taxa, the enrichment effect of key, functional, genus-level species of bacteria was the most obvious, including Rhizobium, Ensifer, Neorhizobium, Mesorhizobium, Streptomyces, Sphingomonas, and Flavobacterium, which are N-fixing and/or phosphate-solubilizing groups. The significant improvement seen in the physicochemical properties of the CK18 rhizosphere soil, including the higher total nitrogen (TN), available nitrogen (AN), pH, electrical conductivity (EC), higher N:P ratio, and lower C:N ratio, all demonstrated the relationship between the rhizosphere microbes and soil carbon (C) and nitrogen (N) cycling. A redundancy analysis (RDA) of different taxonomic levels indicated a close positive relationship between rhizosphere microbes and AN. In addition, the functional groups of the C. korshinskii rhizosphere bacteria were closely related to soil AN and were mainly composed of chemoheterotrophy and aerobic chemoheterotrophy. A Spearman correlation analysis revealed that these functional groups were mainly identified from bacterial Actinobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, and fungal Glomeromycota. Our study provides evidence that the rhizosphere microbes of C. korshinskii are closely related to the accumulation of N in the restoration of desert ecosystems, and that the ecological functional processes they are involved in mainly involve C and N cycles, which play an important role in desertification reversal.},
}
@article {pmid36339429,
year = {2022},
author = {Han, S and Chen, M and Cheng, P and Zhang, Z and Lu, Y and Xu, Y and Wang, Y},
title = {A systematic review and meta-analysis of gut microbiota in diabetic kidney disease: Comparisons with diabetes mellitus, non-diabetic kidney disease, and healthy individuals.},
journal = {Frontiers in endocrinology},
volume = {13},
number = {},
pages = {1018093},
pmid = {36339429},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetic Nephropathies ; Glomerular Filtration Rate ; Bacteria ; Health Status ; *Diabetes Mellitus ; },
abstract = {Background: Gut microbiota has been reported to play an important role in diabetic kidney disease (DKD), however, the alterations of gut bacteria have not been determined.<br><br>Methods: Studies comparing the differences of gut microbiome between patients with DKD and non-DKD individuals using high-throughput sequencing technology, were systematically searched and reviewed. Outcomes were set as gut bacterial diversity, microbial composition, and correlation with clinical parameters of DKD. Qualitative data were summarized and compared through a funnel R script, and quantitative data were estimated by meta-analysis.<br><br>Results: A total of 15 studies and 1640 participants were included, the comparisons were conducted between DKD, diabetes mellitus (DM), non-diabetic kidney disease (NDKD), and healthy controls. There were no significant differences of α-diversity between DKD and DM, and between DKD and NDKD, however, significant lower microbial richness was found in DKD compared to healthy controls. Different bacterial compositions were found between DKD and non-DKD subjects. The phylum Actinobacteria were found to be enriched in DKD compared to healthy controls. At the genus level, we found the enrichment of Hungatella, Bilophila, and Escherichia in DKD compared to DM, patients with DKD showed lower abundances of Faecalibacterium compared to those with NDKD. The genera Butyricicoccus, Faecalibacterium, and Lachnospira were depleted in DKD compared to healthy controls, whereas Hungatella, Escherichia, and lactobacillus were significantly enriched. The genus Ruminococcus torques group was demonstrated to be inversely correlated with estimated glomerular filtration rate of DKD.<br><br>Conclusions: Gut bacterial alterations was demonstrated in DKD, characterized by the enrichment of the genera Hungatella and Escherichia, and the depletion of butyrate-producing bacteria, which might be associated with the occurrence and development of DKD. Further studies are still needed to validate these findings, due to substantial heterogeneity.<br><br>https://www.crd.york.ac.uk/prospero/, identifier CRD42022340870.},
}
@article {pmid36339428,
year = {2022},
author = {Calcaterra, V and Rossi, V and Massini, G and Regalbuto, C and Hruby, C and Panelli, S and Bandi, C and Zuccotti, G},
title = {Precocious puberty and microbiota: The role of the sex hormone-gut microbiome axis.},
journal = {Frontiers in endocrinology},
volume = {13},
number = {},
pages = {1000919},
pmid = {36339428},
issn = {1664-2392},
mesh = {Female ; Humans ; Child ; *Puberty, Precocious ; *Gastrointestinal Microbiome ; Gonadal Steroid Hormones ; Puberty ; *Microbiota ; },
abstract = {Puberty is a critical phase of life associated with physiological changes related to sexual maturation, and represents a complex process regulated by multiple endocrine and genetic controls. Puberty is driven by hormones, and it can impact the gut microbiome (GM). GM differences between sex emerge at puberty onset, confirming a relationship between microbiota and sex hormones. In this narrative review, we present an overview of precocious pubertal development and the changes in the GM in precocious puberty (PP) in order to consider the role of the sex hormone-gut microbiome axis from the perspective of pediatric endocrinology. Bidirectional interactions between the GM and sex hormones have been proposed in different studies. Although the evidence on the interaction between microbiota and sex hormones remains limited in pediatric patients, the evidence that GM alterations may occur in girls with central precocious puberty (CPP) represents an interesting finding for the prediction and prevention of PP. Deepening the understanding of the connection between the sex hormones and the role of microbiota changes can lead to the implementation of microbiota-targeted therapies in pubertal disorders by offering a pediatric endocrinology perspective.},
}
@article {pmid36339342,
year = {2022},
author = {Papp-Wallace, KM and Manning, SD and Craney, A and Kuboniwa, M and Vourli, S},
title = {Editorial: Women and clinical microbiology 2021.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {999967},
doi = {10.3389/fcimb.2022.999967},
pmid = {36339342},
issn = {2235-2988},
mesh = {Female ; Humans ; *Candidiasis, Vulvovaginal ; },
}
@article {pmid36339339,
year = {2022},
author = {Zhu, M and Liu, S and Zhao, C and Shi, J and Li, C and Ling, S and Cheng, J and Dong, W and Xu, J},
title = {Alterations in the gut microbiota of AIDS patients with pneumocystis pneumonia and correlations with the lung microbiota.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1033427},
pmid = {36339339},
issn = {2235-2988},
mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/microbiology ; *Gastrointestinal Microbiome ; *Acquired Immunodeficiency Syndrome/complications ; *HIV Infections/complications ; RNA, Ribosomal, 16S/genetics ; Lung/microbiology ; *Microbiota ; },
abstract = {Background: Due to the inability to be cultured in vitro, the biological characteristics and pathogenicity of Pneumocystis jirovecii remain unclear. Intestinal microflora disorder is related to the occurrence and development of various pulmonary diseases. This work explores the pathogenesis of pneumocystis pneumonia (PCP) in acquired immune deficiency syndrome (AIDS) patients from a microbiome perspective, to provide better strategies for the diagnosis, treatment, and prevention of PCP.<br><br>Methods: Subjects were divided into three groups: human immunodeficiency virus (HIV)-infected patients combined with PCP, HIV-infected patients without PCP, and HIV-negative. Stool and bronchoalveolar lavage fluid (BALF) samples were collected, total DNA was extracted, and 16S rRNA high-throughput sequencing was performed using an Illumina MiSeq platform. PICRUSt and BugBase were used to predict microflora functions, and correlation analysis of intestinal and lung bacterial flora was conducted.<br><br>Results: Compared with the HIV- group, prevotella and another 21 genera in the intestinal microbiome were statistically different in the HIV+ group; 25 genera including Escherichia-Shigella from HIV+PCP+ group were statistically different from HIV+PCP- group. The abundance of Genera such as Porphyromonas was positively or negatively correlated with CD16/CD56+ (μL). Compared with the HIV- group, identification efficiency based on area under the curve (AUC) >0.7 for the HIV+ group identified seven genera in the gut microbiota, including Enterococcus (total AUC = 0.9519). Compared with the HIV+PCP- group, there were no bacteria with AUC >0.7 in the lung or intestine of the HIV+PCP+ group. The number of shared bacteria between BALF and fecal samples was eight species in the HIV- group, 109 species in PCP- patients, and 228 species in PCP+ patients, according to Venn diagram analysis. Changes in various clinical indicators and blood parameters were also closely related to the increase or decrease in the abundance of intestinal and pulmonary bacteria, respectively.<br><br>Conclusions: HIV infection and PCP significantly altered the species composition of lung and intestinal microbiomes, HIV infection also significantly affected intestinal microbiome gene functions, and PCP exacerbated the changes. The classification model can be used to distinguish HIV+ from HIV- patients, but the efficiency of bacterial classification was poor between PCP+ and PCP- groups. The microbiomes in the lung and gut were correlated to some extent, providing evidence for the existence of a lung-gut axis, revealing a potential therapeutic target in patients with HIV and PCP.},
}
@article {pmid36339338,
year = {2022},
author = {Zhang, Y and Shang, L and Roffel, S and Krom, BP and Gibbs, S and Deng, D},
title = {Stable reconstructed human gingiva-microbe interaction model: Differential response to commensals and pathogens.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {991128},
pmid = {36339338},
issn = {2235-2988},
mesh = {Humans ; *Gingiva/microbiology ; *Elafin ; Agar ; Aggregatibacter actinomycetemcomitans ; Cytokines ; },
abstract = {Background: To investigate human oral health and disease, models are required which represent the interactions between the oral mucosa and microbiome. Our aim was to develop an organotypic model which maintains viability of both host and microbes for an extended period of time.<br><br>Methods: Reconstructed Human Gingiva (RHG) were cultured air-lifted with or without penicillin-streptomycin (PS) and topically exposed to Streptococcus gordonii (commensal) or Aggregatibacter actinomycetemcomitans (pathogen) for 72 hours in agar. RHG histology, viability and cytokines (ELISA), and bacterial viability (colony forming units) and location (FISH) were assessed.<br><br>Results: The low concentration of topically applied agar did not influence RHG viability. Topically applied bacteria in agar remained localized and viable for 72 hours and did not spill over to infect RHG culture medium. PS in RHG culture medium killed topically applied bacteria. Co-culture with living bacteria did not influence RHG viability (Ki67 expression, MTT assay) or histology (epithelium differentiation, Keratin10 expression). RHG exposed to S. gordonii (with or without PS) did not influence low level of IL-6, IL-8, CCL2, CCL5, CCL20 or CXCL1 secretion. However, all cytokines increased (except CCL2) when RHG were co-cultured with A. actinomycetemcomitans. The effect was significantly more in the presence of living, rather than dead, A. actinomycetemcomitans. Both bacteria resulted in increased expression of RHG antimicrobial peptides (AMPs) Elafin and HBD-2, with S. gordonii exposure resulting in the most Elafin secretion.<br><br>Conclusion: This technical advance enables living human oral host-microbe interactions to be investigated during a 72-hour period and shows differences in innate immunology triggered by S. gordonii and A. actinomycetemcomitans.},
}
@article {pmid36339270,
year = {2022},
author = {Bartlett, A and Kleiner, M},
title = {Dietary protein and the intestinal microbiota: An understudied relationship.},
journal = {iScience},
volume = {25},
number = {11},
pages = {105313},
pmid = {36339270},
issn = {2589-0042},
abstract = {Diet has a profound impact on the microbial community in the gastrointestinal tract, the intestinal microbiota, to the benefit or detriment of human health. To understand the influence of diet on the intestinal microbiota, research has focused on individual macronutrients. Some macronutrients (e.g. fiber) have been studied in great detail and have been found to strongly influence the intestinal microbiota. The relationship between dietary protein, a vital macronutrient, and the intestinal microbiota has gone largely unexplored. Emerging evidence suggests that dietary protein strongly impacts intestinal microbiota composition and function and that protein-microbiota interactions can have critical impacts on host health. In this review, we focus on recent studies investigating the impact of dietary protein quantity and source on the intestinal microbiota and resulting host health consequences. We highlight major open questions critical to understanding health outcomes mediated by interactions between dietary protein and the microbiota.},
}
@article {pmid36339093,
year = {2022},
author = {Goldsmith, R and Aburahma, A and Pachhain, S and Choudhury, SR and Phuntumart, V and Larsen, R and Ward, CS and Sprague, JE},
title = {Reversal of temperature responses to methylone mediated through bi-directional fecal microbiota transplantation between hyperthermic tolerant and naïve rats.},
journal = {Temperature (Austin, Tex.)},
volume = {9},
number = {4},
pages = {318-330},
pmid = {36339093},
issn = {2332-8940},
abstract = {The synthetic cathinone ("bath salt") methylone induces a hyperthermia response and with chronic administration tolerance to this hyperthermia has been reported. The microbiome-gut-brain axis has been implicated in multiple bodily systems and pathologies, and intentional manipulation of the gut-microbiome has yielded clinically significant results. Here, we examined the effects of bi-directional Fecal Microbiota Transplantation (FMT) between methylone-induced hyperthermic tolerant (MHT) and methylone-naïve (MN) rats. Rats treated with methylone once per week developed tolerance to methylone-induced hyperthermia by the fourth week. Once tolerant, daily bi-directional FMT between the two groups were performed for seven days prior to the next methylone treatment. The FMT abated the developed tolerance in the MHT group. When treated with methylone for the first time following FMT, recipient MN rats displayed significant tolerance to hyperthermia despite it being their initial drug treatment. Post-FMT, MHT rats displayed elevations in norepinephrine and expression of UCP1, UCP3 and TGR5 in brown adipose tissue, with reductions in expression of TGR5 and UCP3 in skeletal muscle. The pre- and post-FMT methylone tolerance phenotypes of transplant recipients are concurrent with changes in the relative abundance of several classes of Proteobacteria, most evident for Gammaproteobacteria and Alphaproteobacteria. MHT recipients demonstrated a marked increase in the relative proportion of the Firmicutes class Erysipelotrichia. These findings suggest that transplantation of gut-microbiomes can confer phenotypic responses to a drug and that the microbiome may be playing a major role in sympathomimetic-mediated hyperthermia. Abbreviations: 3,4-methylenedioxymethamphetamine (MDMA); methylone-induced hyperthermic tolerant (MHT); methylone-naïve (MN); fecal microbiota transplantation (FMT); uncoupling protein (UCP); subcutaneous (sc); intraperitoneal (ip); brown adipose tissue (BAT); skeletal muscle (SKM); sympathetic nervous system (SNS); norepinephrine (NE); quantitative PCR (qRT-PCR); quantification cycle (Cq); High Performance Liquid Chromatography-Electrochemical Detection (HPLC-EC); amplicon sequence variants (ASVs); principal coordinates analysis (PCoA); permutational multivariate analysis (PERMANOVA).},
}
@article {pmid36338834,
year = {2022},
author = {Zhou, X and Wang, B and Demkowicz, PC and Johnson, JS and Chen, Y and Spakowicz, DJ and Zhou, Y and Dorsett, Y and Chen, L and Sodergren, E and Kuchel, GA and Weinstock, GM},
title = {Exploratory studies of oral and fecal microbiome in healthy human aging.},
journal = {Frontiers in aging},
volume = {3},
number = {},
pages = {1002405},
pmid = {36338834},
issn = {2673-6217},
abstract = {Growing evidence has linked an altered host fecal microbiome composition with health status, common chronic diseases, and institutionalization in vulnerable older adults. However, fewer studies have described microbiome changes in healthy older adults without major confounding diseases or conditions, and the impact of aging on the microbiome across different body sites remains unknown. Using 16S ribosomal RNA gene sequencing, we reconstructed the composition of oral and fecal microbiomes in young (23-32; mean = 25 years old) and older (69-94; mean = 77 years old) healthy community-dwelling research subjects. In both body sites, we identified changes in minor bacterial operational taxonomic units (OTUs) between young and older subjects. However, the composition of the predominant bacterial species of the healthy older group in both microbiomes was not significantly different from that of the young cohort, which suggests that dominant bacterial species are relatively stable with healthy aging. In addition, the relative abundance of potentially pathogenic genera, such as Rothia and Mycoplasma, was enriched in the oral microbiome of the healthy older group relative to the young cohort. We also identified several OTUs with a prevalence above 40% and some were more common in young and others in healthy older adults. Differences with aging varied for oral and fecal samples, which suggests that members of the microbiome may be differentially affected by aging in a tissue-specific fashion. This is the first study to investigate both oral and fecal microbiomes in the context of human aging, and provides new insights into interactions between aging and the microbiome within two different clinically relevant sites.},
}
@article {pmid36338832,
year = {2022},
author = {Rabe, A and Gesell Salazar, M and Michalik, S and Kocher, T and Below, H and Völker, U and Welk, A},
title = {Impact of different oral treatments on the composition of the supragingival plaque microbiome.},
journal = {Journal of oral microbiology},
volume = {14},
number = {1},
pages = {2138251},
pmid = {36338832},
issn = {2000-2297},
abstract = {Background: Dental plaque consists of a diverse microbial community embedded in a complex structure of exopolysaccharides. Dental biofilms form a natural barrier against pathogens but lead to oral diseases in a dysbiotic state.<br><br>Objective: Using a metaproteome approach combined with a standard plaque-regrowth study, this pilot study examined the impact of different concentrations of lactoperoxidase (LPO) on early plaque formation, and active biological processes.<br><br>Design: Sixteen orally healthy subjects received four local treatments as a randomized single-blind study based on a cross-over design. Two lozenges containing components of the LPO-system in different concentrations were compared to a placebo and Listerine®. The newly formed dental plaque was analyzed by mass spectrometry (nLC-MS/MS).<br><br>Results: On average 1,916 metaproteins per sample were identified, which could be assigned to 116 genera and 1,316 protein functions. Listerine® reduced the number of metaproteins and their relative abundance, confirming the plaque inhibiting effect. The LPO-lozenges triggered mainly higher metaprotein abundances of early and secondary colonizers as well as bacteria associated with dental health but also periodontitis. Functional information indicated plaque biofilm growth.<br><br>Conclusion: In conclusion, the mechanisms on plaque biofilm formation of Listerine® and the LPO-system containing lozenges are different. In contrast to Listerine®, the lozenges led to a higher bacterial diversity.},
}
@article {pmid36338471,
year = {2022},
author = {Weinroth, MD and Oakley, B and Ramírez, GA and Reyes, A and Harris, CE and Buhr, RJ},
title = {16S rRNA gene-based assessment of common broiler chicken sampling methods: Evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {996654},
pmid = {36338471},
issn = {1664-042X},
abstract = {16S rRNA gene sequencing for characterization of microbiomes has become more common in poultry research and can be used to both answer specific research questions and help inform experimental design choices. The objective of this study was to use 16S rRNA gene sequencing to examine common sampling practices in broiler chicken studies such as: the required number of birds selected from a flock to adequately capture microbiome diversity, the differences between cecal pairs within the same bird, and whether cloacal swabs are representative of other alimentary tract (AT) locations. To do this, nine market age broilers were euthanized and immediately sampled in ten AT locations: crop, gizzard, proventriculus, duodenum, jejunum, ileum, cecal samples from each pouch, colon, and cloacal swab. DNA was extracted and subjected to 16S rRNA gene amplification and sequencing. Each location within the broiler AT hosts distinct microbial communities. When each sampling location was considered, it was found that sampling after 2.8 birds (range 2-4) resulted in less than 10% new amplicon sequencing variants (ASV) being added while sampling after 7.6 birds (range 6-10) increases new observed ASVs by less than 1%. Additionally, when cecal pairs from the same bird were evaluated, it was found that cecal pair mates are an adequate replication if interested in the total cecal microbiome but may be less useful if a rare lineage is of interest. Furthermore, when compared to other AT locations, the cecal microbiome was enriched in Firmicutes and Bacteroides while several lineages, most notably Lactobacillus, were under-represented. Finally, when cloacal swabs were compared to other AT locations, community similarity exhibited a direct distance relationship, i.e., the more aborad samples were the more similar they were to the swab. These findings indicate that while cloacal swabs can approximate overall changes in microbiome composition, they are not adequate for inferring changes to specific taxa in other parts of the AT tract-even those that are highly abundant within the microbial community. These data provide new insights guiding appropriate sample size selection within flocks and add to the consensus data regarding cecal pair similarity and destructive versus non-destructive sampling methods.},
}
@article {pmid36338447,
year = {2021},
author = {Beaver, A and Petersen, C and Weary, DM and Finlay, BB and von Keyserlingk, MAG},
title = {Differences in the fecal microbiota of dairy calves reared with differing sources of milk and levels of maternal contact.},
journal = {JDS communications},
volume = {2},
number = {4},
pages = {200-206},
pmid = {36338447},
issn = {2666-9102},
abstract = {The practice of rearing cows and calves together is gaining popularity on dairy farms, with different systems currently under assessment in mainland Europe, the United Kingdom, and Oceania. Research into the effects of cow-calf rearing has primarily focused on direct health and welfare implications, and little work has examined the role of different rearing paradigms on calf microbiota. We trialed a cow-calf rearing system on a Canadian dairy farm and compared fecal microbiota of these calves with the microbiota of calves reared according to the conventional practice of the same farm (separated from the dam and fed waste milk). At 4 wk, the conventionally reared calves had reduced relative abundance of Lactobacillus and higher relative abundance of other taxa, including Sutterella, Prevotella, and Bacteroides. We also detected predicted functional differences, such as reduced l-tryptophan biosynthesis in conventionally reared calves. These results suggest that maternal contact may influence the calf microbiota, but the observed differences are also likely related to other aspects of the rearing environment independent of maternal contact (e.g., potential exposure to antibiotic residues in waste milk). These findings provide preliminary evidence of the effects of early rearing environments on the establishment of the dairy calf fecal microbiota. This research is needed, given the critical role of the bovine gut microbiome in behavioral, metabolic, and immune development.},
}
@article {pmid36338247,
year = {2022},
author = {Campbell, CD and Barnett, C and Sulaiman, I},
title = {A clinicians' review of the respiratory microbiome.},
journal = {Breathe (Sheffield, England)},
volume = {18},
number = {1},
pages = {210161},
pmid = {36338247},
issn = {1810-6838},
abstract = {The respiratory microbiome and its impact in health and disease is now well characterised. With the development of next-generation sequencing and the use of other techniques such as metabolomics, the functional impact of microorganisms in different host environments can be elucidated. It is now clear that the respiratory microbiome plays an important role in respiratory disease. In some diseases, such as bronchiectasis, examination of the microbiome can even be used to identify patients at higher risk of poor outcomes. Furthermore, the microbiome can aid in phenotyping. Finally, development of multi-omic analysis has revealed interactions between the host and microbiome in some conditions. This review, although not exhaustive, aims to outline how the microbiome is investigated, the healthy respiratory microbiome and its role in respiratory disease.<br><br>Educational aims: To define the respiratory microbiome and describe its analysis.To outline the respiratory microbiome in health and disease.To describe future directions for microbiome research.},
}
@article {pmid36338100,
year = {2022},
author = {Jiang, C and Liu, Y and Li, H and Zhu, S and Sun, X and Wu, K and Shui, W},
title = {The characterization of microbial communities and associations in karst tiankeng.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1002198},
pmid = {36338100},
issn = {1664-302X},
abstract = {The karst tiankeng is a special and grand negative terrain on the surface, that maintains a unique ecosystem. However, knowledge about bacterial and fungal communities in karst tiankengs is still limited. Therefore, soil samples from five karst tiankengs were collected and subjected to high-throughput sequencing of 16S rRNA and ITS genes, and multivariate statistical analysis. The results showed abundant and diversified bacterial and fungal communities in karst tiankeng. The bacterial communities were dominated by Proteobacteria and Acidobacteria, and the fungal communities were dominated by Ascomycota and Basidiomycota. Statistical analysis revealed significant differences in bacterial and fungal communities among the five karst tiankengs, which may indicate that the distribution of bacterial and fungal communities was driven by separate karst tiankengs. The co-occurrence network structure was characterized by highly modularized assembly patterns and more positive interactions. The keystone taxa were mainly involved in nutrient cycling and energy metabolism. The null model analysis results showed that the stochastic process, especially dispersal limitation, tended to be more important in controlling the development of bacterial and fungal communities in karst tiankeng. The bacterial community structure was significantly associated with soil properties (SWC, TN, AN, and BD), while the fungal community structure was significantly associated with soil properties (SWC and TP) and plant diversity. These results can expand our knowledge of the karst tiankeng microbiome.},
}
@article {pmid36338096,
year = {2022},
author = {Yang, X and Tai, Y and Ma, Y and Xu, Z and Hao, J and Han, D and Li, J and Deng, X},
title = {Cecum microbiome and metabolism characteristics of Silky Fowl and White Leghorn chicken in late laying stages.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {984654},
pmid = {36338096},
issn = {1664-302X},
abstract = {Cecal microflora plays a key role in the production performance and immune function of chickens. White Leghorn (WL) is a well-known commercial layer line chicken with high egg production rate. In contrast, Silky Fowl (SF), a Chinese native chicken variety, has a low egg production rate, but good immune performance. This study analyzed the composition of cecal microbiota, metabolism, and gene expression in intestinal tissue of these varieties and the correlations among them. Significant differences were observed in the cecal microbes: Bacteroides was significantly enriched in WL, whereas Veillonellaceae and Parabacteroides were significantly enriched in SF. Carbohydrate biosynthesis and metabolism pathways were significantly upregulated in WL cecum, which might provide more energy to the host, leading to persistently high levels of egg production. The higher Parabacteroides abundance in SF increased volicitin content, enhanced α-linolenic acid metabolism, and significantly negatively correlated with metabolites of propanoate metabolism and carbohydrate metabolism. Genes related to lipid metabolism, immunity, and melanogenesis were significantly upregulated in the SF cecum, regulating lipid metabolism, and participating in the immune response, while genes related to glucose metabolism and bile acid metabolism were expressed at higher levels in WL, benefiting energy support. This study provided a mechanism for intestinal microorganisms and metabolic pathways to regulate chicken egg-laying performance and immunity.},
}
@article {pmid36338092,
year = {2022},
author = {Chen, J and Liu, K and Sun, X and Shi, X and Zhao, G and Yang, Z},
title = {Microbiome landscape of lesions and adjacent normal mucosal areas in oral lichen planus patient.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {992065},
pmid = {36338092},
issn = {1664-302X},
abstract = {The pathogenesis of oral lichen planus (OLP) remains unclear, and microbial dysbiosis has been proposed to play a role in the pathogenesis of OLP. Oral mucosal swabs from 77 OLP patients and 76 healthy subjects were collected. The bacterial community among the OLP lesion, the adjacent normal mucosal, and the oral mucosal surface in healthy people were analyzed by 16S sequencing. The factor of gender and age that may affect the flora distribution of OLP patients were explored. Results indicate no significant difference in microbiota between OLP and the adjacent group. Compared with the healthy group, Neisseria, Haemophilus, Fusobacterium, Porphyromonas, Rothia, Actinomyces, and Capnocytophaga significantly increased in the OLP group. Actinomyces increased in male OLP patients, and the other six bacteria increased in female OLP patients. In female OLP patients, Lautropia and Dialister were positively correlated with age. While in male OLP patients, Moraxella, Porphyromonas, and Fusobacterium were positively correlated with age. Functional enrichment analysis suggested that abnormal energy metabolism related to ATP synthases, abnormal transport and metabolism of glycans, amino acids, and vitamins, and disorders of the local immune microenvironment might exist in OLP lesion.},
}
@article {pmid36338085,
year = {2022},
author = {Ding, P and Ming, Z and Liu, J and Erill, I and Zhang, Z},
title = {Editorial: Microbiome and microbial informatics.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1054811},
doi = {10.3389/fmicb.2022.1054811},
pmid = {36338085},
issn = {1664-302X},
}
@article {pmid36338082,
year = {2022},
author = {Bhar, A and Gierse, LC and Meene, A and Wang, H and Karte, C and Schwaiger, T and Schröder, C and Mettenleiter, TC and Urich, T and Riedel, K and Kaderali, L},
title = {Application of a maximal-clique based community detection algorithm to gut microbiome data reveals driver microbes during influenza A virus infection.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {979320},
pmid = {36338082},
issn = {1664-302X},
abstract = {Influenza A Virus (IAV) infection followed by bacterial pneumonia often leads to hospitalization and death in individuals from high risk groups. Following infection, IAV triggers the process of viral RNA replication which in turn disrupts healthy gut microbial community, while the gut microbiota plays an instrumental role in protecting the host by evolving colonization resistance. Although the underlying mechanisms of IAV infection have been unraveled, the underlying complex mechanisms evolved by gut microbiota in order to induce host immune response following IAV infection remain evasive. In this work, we developed a novel Maximal-Clique based Community Detection algorithm for Weighted undirected Networks (MCCD-WN) and compared its performance with other existing algorithms using three sets of benchmark networks. Moreover, we applied our algorithm to gut microbiome data derived from fecal samples of both healthy and IAV-infected pigs over a sequence of time-points. The results we obtained from the real-life IAV dataset unveil the role of the microbial families Ruminococcaceae, Lachnospiraceae, Spirochaetaceae and Prevotellaceae in the gut microbiome of the IAV-infected cohort. Furthermore, the additional integration of metaproteomic data enabled not only the identification of microbial biomarkers, but also the elucidation of their functional roles in protecting the host following IAV infection. Our network analysis reveals a fast recovery of the infected cohort after the second IAV infection and provides insights into crucial roles of Desulfovibrionaceae and Lactobacillaceae families in combating Influenza A Virus infection. Source code of the community detection algorithm can be downloaded from https://github.com/AniBhar84/MCCD-WN.},
}
@article {pmid36338055,
year = {2022},
author = {Yang, Z and Fu, H and Su, H and Cai, X and Wang, Y and Hong, Y and Hu, J and Xie, Z and Wang, X},
title = {Multi-omics analyses reveal the specific changes in gut metagenome and serum metabolome of patients with polycystic ovary syndrome.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1017147},
pmid = {36338055},
issn = {1664-302X},
abstract = {Objective: The purpose of this study was to investigate the specific alterations in gut microbiome and serum metabolome and their interactions in patients with polycystic ovary syndrome (PCOS).<br><br>Methods: The stool samples from 32 PCOS patients and 18 healthy controls underwent the intestinal microbiome analysis using shotgun metagenomics sequencing approach. Serum metabolome was analyzed by ultrahigh performance liquid chromatography quadrupole time-of-flight mass spectrometry. An integrative network by combining metagenomics and metabolomics datasets was constructed to explore the possible interactions between gut microbiota and circulating metabolites in PCOS, which was further assessed by fecal microbiota transplantation (FMT) in a rat trial.<br><br>Results: Fecal metagenomics identified 64 microbial strains significantly differing between PCOS and healthy subjects, half of which were enriched in patients. These changed species showed an ability to perturb host metabolic homeostasis (including insulin resistance and fatty acid metabolism) and inflammatory levels (such as PI3K/Akt/mTOR signaling pathways) by expressing sterol regulatory element-binding transcription factor-1, serine/threonine-protein kinase mTOR, and 3-oxoacyl-[acyl-cattier-protein] synthase III, possibly suggesting the potential mechanisms of gut microbiota underlying PCOS. By integrating multi-omics datasets, the panel comprising seven strains (Achromobacter xylosoxidans, Pseudomonas sp. M1, Aquitalea pelogenes, Porphyrobacter sp. HL-46, Vibrio fortis, Leisingera sp. ANG-Vp, and Sinorhizobium meliloti) and three metabolites [ganglioside GM3 (d18:0/16:0), ceramide (d16:2/22:0), and 3Z,6Z,9Z-pentacosatriene] showed the highest predictivity of PCOS (AUC: 1.0) with sensitivity of 0.97 and specificity of 1.0. Moreover, the intestinal microbiome modifications by FMT were demonstrated to regulate PCOS phenotypes including metabolic variables and reproductive hormones.<br><br>Conclusion: Our findings revealed key microbial and metabolite features and their interactions underlying PCOS by integrating multi-omics approaches, which may provide novel insights into discovering clinical diagnostic biomarkers and developing efficient therapeutic strategies for PCOS.},
}
@article {pmid36338053,
year = {2022},
author = {Koczorski, P and Furtado, BU and Gołębiewski, M and Hulisz, P and Thiem, D and Baum, C and Weih, M and Hrynkiewicz, K},
title = {Mixed growth of Salix species can promote phosphate-solubilizing bacteria in the roots and rhizosphere.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1006722},
pmid = {36338053},
issn = {1664-302X},
abstract = {Phosphorus (P) is an essential plant nutrient that can limit plant growth due to low availability in the soil. P-solubilizing bacteria in the roots and rhizosphere increase the P use efficiency of plants. This study addressed the impact of plant species, the level of plant association with bacteria (rhizosphere or root endophyte) and environmental factors (e.g., seasons, soil properties) on the abundance and diversity of P-solubilizing bacteria in short-rotation coppices (SRC) of willows (Salix spp.) for biomass production. Two willow species (S. dasyclados cv. Loden and S. schwerinii × S. viminalis cv. Tora) grown in mono-and mixed culture plots were examined for the abundance and diversity of bacteria in the root endosphere and rhizosphere during two seasons (fall and spring) in central Sweden and northern Germany. Soil properties, such as pH and available P and N, had a significant effect on the structure of the bacterial community. Microbiome analysis and culture-based methods revealed a higher diversity of rhizospheric bacteria than endophytic bacteria. The P-solubilizing bacterial isolates belonged mainly to Proteobacteria (85%), Actinobacteria (6%) and Firmicutes (9%). Pseudomonas was the most frequently isolated cultivable bacterial genus from both the root endosphere and the rhizosphere. The remaining cultivable bacterial isolates belonged to the phyla Actinobacteria and Firmicutes. In conclusion, site-specific soil conditions and the level of plant association with bacteria were the main factors shaping the bacterial communities in the willow SRCs. In particular, the concentration of available P along with the total nitrogen in the soil controlled the total bacterial diversity in willow SRCs. A lower number of endophytic and rhizospheric bacteria was observed in Loden willow species compared to that of Tora and the mix of the two, indicating that mixed growth of Salix species promotes P-solubilizing bacterial diversity and abundance. Therefore, a mixed plant design was presented as a management option to increase the P availability for Salix in SRCs. This design should be tested for further species mixtures.},
}
@article {pmid36338051,
year = {2022},
author = {Peter, TK and Withanage, MHH and Comnick, CL and Pendleton, C and Dabdoub, S and Ganesan, S and Drake, D and Banas, J and Xie, XJ and Zeng, E},
title = {Systematic review and meta-analysis of oral squamous cell carcinoma associated oral microbiome.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {968304},
pmid = {36338051},
issn = {1664-302X},
abstract = {The intersection between the human oral microbiome and oral health is an emerging area of study which has gained momentum over the last decade. This momentum has motivated a search for associations between the oral microbiome and oral cancer, in hopes of identifying possible biomarkers that facilitate earlier diagnosis and improved prognosis for patients with that disease. The present study examined the relationship between the microbiome in the human oral cavity and oral squamous cell carcinoma (OSCC). We searched the literature for case-control studies which focused on the relationship between the human oral microbiome and OSCC. We aggregated three types of data from these studies: bacteriome data at the genus level, predicted functional pathway data, and gene abundance data. From these data, we noted several microbial genera which may be associated with oral cancer status, including Fusobacterium. We also identified functional pathways which merit further investigation, including RNA degradation (ko03018) and primary immunodeficiency (ko05340). In addition, our analysis of gene abundance data identified the gene K06147 (ATP-binding cassette, subfamily B, bacterial) as being over abundant in OSCC samples. Our results are generalizations which identified some currents that we believe could guide further research. Our work faced several limitations related to the heterogeneity of the available data. Wide variation in methods for sample collection, methods for controlling for known behavioral risk factors, computing platform choice, and methods for case-control design all posed confounding factors in this work. We examined the current methods of data collection, data processing, and data reporting in order to offer suggestions toward the establishment of best practices within this field. We propose that these limitations should be addressed through the implementation of standardized data analytic practices that will conform to the rigor and reproducibility standards required of publicly funded research.},
}
@article {pmid36338039,
year = {2022},
author = {Meyer, KM and Deines, P and Wei, Z and Busby, PE and Lindow, SE and Bohannan, BJM},
title = {Editorial: The role of dispersal and transmission in structuring microbial communities.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1054498},
doi = {10.3389/fmicb.2022.1054498},
pmid = {36338039},
issn = {1664-302X},
}
@article {pmid36337626,
year = {2022},
author = {Dong, S and Wu, C and He, W and Zhong, R and Deng, J and Tao, Y and Zha, F and Liao, Z and Fang, X and Wei, H},
title = {Metagenomic and metabolomic analyses show correlations between intestinal microbiome diversity and microbiome metabolites in ob/ob and ApoE-/- mice.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {934294},
pmid = {36337626},
issn = {2296-861X},
abstract = {Obesity and atherosclerosis are the most prevalent metabolic diseases. ApoE-/- and ob/ob mice are widely used as models to study the pathogenesis of these diseases. However, how gut microbes, gut bacteriophages, and metabolites change in these two disease models is unclear. Here, we used wild-type C57BL/6J (Wt) mice as normal controls to analyze the intestinal archaea, bacteria, bacteriophages, and microbial metabolites of ob/ob and ApoE-/- mice through metagenomics and metabolomics. Analysis of the intestinal archaea showed that the abundances of Methanobrevibacter and Halolamina were significantly increased and decreased, respectively, in the ob/ob group compared with those in the Wt and ApoE-/- groups (p < 0.05). Compared with those of the Wt group, the relative abundances of the bacterial genera Enterorhabdus, Alistipes, Bacteroides, Prevotella, Rikenella, Barnesiella, Porphyromonas, Riemerella, and Bifidobacterium were significantly decreased (p < 0.05) in the ob/ob mice, and the relative abundance of Akkermansia was significantly decreased in the ApoE-/- group. The relative abundances of A. muciniphila and L. murinus were significantly decreased and increased, respectively, in the ob/ob and ApoE-/- groups compared with those of the Wt group (p < 0.05). Lactobacillus_ prophage_ Lj965 and Lactobacillus _ prophage _ Lj771 were significantly more abundant in the ob/ob mice than in the Wt mice. Analysis of the aminoacyl-tRNA biosynthesis metabolic pathway revealed that the enriched compounds of phenylalanine, glutamine, glycine, serine, methionine, valine, alanine, lysine, isoleucine, leucine, threonine, tryptophan, and tyrosine were downregulated in the ApoE-/- mice compared with those of the ob/ob mice. Aminoacyl-tRNA synthetases are considered manifestations of metabolic diseases and are closely associated with obesity, atherosclerosis, and type 2 diabetes. These data offer new insight regarding possible causes of these diseases and provide a foundation for studying the regulation of various food nutrients in metabolic disease models.},
}
@article {pmid36337625,
year = {2022},
author = {Muratore, E and Leardini, D and Baccelli, F and Venturelli, F and Prete, A and Masetti, R},
title = {Nutritional modulation of the gut microbiome in allogeneic hematopoietic stem cell transplantation recipients.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {993668},
pmid = {36337625},
issn = {2296-861X},
abstract = {Allogeneic hematopoietic stem cell transplantation (allo-HSCT) represents a potentially curative strategy for many oncological and non-oncological diseases, but it is associated with marked morbidity and mortality. The disruption of gut microbiota (GM) eubiosis has been linked to major allo-HSCT complications, including infections and acute graft vs. host disease (aGvHD), and correlates with mortality. This increasing knowledge on the role of the GM in the allo-HSCT procedure has led to fascinating ideas for modulating the intestinal ecosystem in order to improve clinical outcomes. Nutritional strategies, either by changing the route of nutritional supplementation or by administering specific molecules, are increasingly being considered as cost- and risk-effective methods of modulating the GM. Nutritional support has also emerged in the past several years as a key feature in supportive care for allo-HSCT recipients, and deterioration of nutritional status is associated with decreased overall survival and higher complication rates during treatment. Herein we provide a complete overview focused on nutritional modulation of the GM in allo-HSCT recipients. We address how pre transplant diet could affect GM composition and its ability to withstand the upsetting events occurring during transplantation. We also provide a complete overview on the influence of the route of nutritional administration on the intestinal ecosystem, with a particular focus on the comparison between enteral and parenteral nutrition (PN). Moreover, as mounting evidence are showing how specific components of post-transplant diet, such as lactose, could drastically shape the GM, we will also summarize the role of prebiotic supplementation in the modulation of the intestinal flora and in allo-HSCT outcomes.},
}
@article {pmid36337619,
year = {2022},
author = {Akimbekov, NS and Digel, I and Yerezhepov, AY and Shardarbek, RS and Wu, X and Zha, J},
title = {Nutritional factors influencing microbiota-mediated colonization resistance of the oral cavity: A literature review.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {1029324},
pmid = {36337619},
issn = {2296-861X},
abstract = {The oral cavity is a key biocenosis for many distinct microbial communities that interact with both the external environment and internal body systems. The oral microbiota is a vital part of the human microbiome. It has been developed through mutual interactions among the environment, host physiological state, and microbial community composition. Indigenious microbiota of the oral cavity is one of the factors that prevent adhesion and invasion of pathogens on the mucous membrane, i.e., the development of the infectious process and thereby participating in the implementation of one of the mechanisms of local immunity-colonization resistance. The balance between bacterial symbiosis, microbial virulence, and host resistance ensures the integrity of the oral cavity. In this review we have tried to address how nutritional factors influence integrity of the oral indigenous microbiota and its involvement in colonization resistance.},
}
@article {pmid36337613,
year = {2022},
author = {Dhakal, S and Dey, M},
title = {Resistant starch type-4 intake alters circulating bile acids in human subjects.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {930414},
pmid = {36337613},
issn = {2296-861X},
abstract = {Background: Resistant starch (RS) type 4 (RS4) is a type of RS, a class of non-digestible prebiotic dietary fibers with a range of demonstrated metabolic health benefits to the host. On the other hand, bile acids (BA) have recently emerged as an important class of metabolic function mediators that involve host-microbiota interactions. RS consumption alters fecal and cecal BA in humans and rodents, respectively. The effect of RS intake on circulating BA concentrations remains unexplored in humans.<br><br>Methods and results: Using available plasma and stool samples from our previously reported double-blind, controlled, 2-arm crossover nutrition intervention trial (Clinicaltrials.gov: NCT01887964), a liquid-chromatography/mass-spectrometry-based targeted multiple reaction monitoring, and absolute quantifications, we assessed BA changes after 12 weeks of an average 12 g/day RS4-intake. Stool BA concentrations were lower post RS4 compared to the control, the two groups consuming similar macronutrients (n = 14/group). Partial least squares-discriminant analysis revealed distinct BA signatures in stool and plasma post interventions. The increased circulating BA concentrations were further investigated using linear mixed-effect modeling that controlled for potential confounders. A higher plasma abundance of several BA species post RS4 was observed (fold increase compared to control in parenthesis): taurocholic acid (1.92), taurodeoxycholic acid (1.60), glycochenodeoxycholic acid (1.58), glycodeoxycholic acid (1.79), and deoxycholic acid (1.77) (all, p < 0.05). Distinct microbiome ortholog-signatures were observed between RS4 and control groups (95% CI), derived using the Piphillin function-prediction algorithm and principal component analysis (PCA) of pre-existing 16S rRNA gene sequences. Association of Bifidobacterium adolescentis with secondary BA such as, deoxycholic acid (rho = 0.55, p = 0.05), glycodeoxycholic acid (rho = 0.65, p = 0.02), and taurodeoxycholic acid (rho = 0.56, p = 0.04) were observed in the RS4-group, but not in the control group (all, p > 0.05).<br><br>Conclusion: Our observations indicate a previously unknown in humans- RS4-associated systemic alteration of microbiota-derived secondary BA. Follow-up investigations of BA biosynthesis in the context of RS4 may provide molecular targets to understand and manipulate microbiome-host interactions.},
}
@article {pmid36337184,
year = {2022},
author = {Kim, SW and Kim, JH},
title = {Establishing an experimental model for canine atopic dermatitis through epicutaneous application of Dermatophagoides farinae.},
journal = {Frontiers in veterinary science},
volume = {9},
number = {},
pages = {1015915},
pmid = {36337184},
issn = {2297-1769},
abstract = {There is no established protocol for the development of an experimental canine atopic dermatitis model in laboratory beagles. This study aimed to establish an experimental model that mimics spontaneous canine atopic dermatitis (CAD) clinically, immunologically, and microbiologically, by repeated epicutaneous applications of mite antigens and to describe the entire process including sensitization and provocation in detail for reproducibility. Six intact male laboratory beagle dogs aged 14 months were included in this study. During the sensitization and provocation phase, the house dust mite (HDM) paste consisted of Dermatophagoides farinae (Der f) and mineral oil, which was applied focally to the 10 × 10 cm area of the right groin as evenly as possible. Further, 120 mg of Der f was applied to each dog twice a week for 12 weeks during the sensitization phase and 25 mg and 120 mg was applied to each dog for the first 2 weeks and subsequent 2 weeks, respectively, during the provocation phase. Thereafter, the applied area was covered with a dressing. Skin lesions including erythema, hyperpigmentation, excoriation, and lichenification were induced and exacerbated gradually through the experimental time course in all six dogs. The canine atopic dermatitis extent and severity index (CADESI) score and transepidermal water loss (TEWL) significantly increased after sensitization and provocation. IL-13 and IL-31 levels increased significantly after provocation as a result of the activation of the T helper-2 (Th2) response. On the contrary, the IL-10 levels decreased significantly after sensitization, which suggested a suppression of Tregs activity. After the completion of provocation, skin microbiome analysis showed that Firmicutes was the most abundant phylum, which indicated bacterial dysbiosis. This study demonstrated that epicutaneous application of HDM in beagle dogs resulted in the elevation of serum HDM-specific IgE levels and clinical atopic scores, a high TEWL, and microbiome dysbiosis resembling spontaneous CAD. These results suggest that this tailored protocol of epicutaneous exposure to Der f may provide support for the development of the experimental CAD model in laboratory beagles.},
}
@article {pmid36336856,
year = {2022},
author = {Jiao, J and Shen, Y and Wang, P and Zuo, K and Yang, X and Chen, M and Dong, Y and Li, J},
title = {Characterization of the Intestinal Microbiome in Healthy Adults over Sars-Cov-2 Vaccination.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {27},
number = {10},
pages = {280},
doi = {10.31083/j.fbl2710280},
pmid = {36336856},
issn = {2768-6698},
mesh = {Adult ; Humans ; SARS-CoV-2 ; *Gastrointestinal Microbiome ; COVID-19 Vaccines ; *COVID-19/prevention &amp; control ; Vaccination ; },
abstract = {BACKGROUND: In response to the outbreak of coronavirus disease 2019 (COVID-19) worldwide, inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are implemented. Dysbiosic gut microbiota is implicated in the COVID-19 patients. Whereas, how intestinal microbiota are affected by vaccination remains elusive, and it is important to investigate the microbial shifts during vaccines treatment.<br><br>METHODS: In the present study, we assessed the gut microbial composition in healthy adults, and performed comparison before and post an inactivated SARS-CoV-2 vaccine candidate, BBIBP-CorV vaccination.<br><br>RESULTS: Microbial diversity in shannon, pielou evenness, simpson and invsimpson index was remarkably suppressed by vaccination. Ruminococcus and Actinomyces were observed to be strikingly deficient, and Faecalibacterium was dramatically augmented after BBIBP-CorV treatment. Potential functional profiles of gut microbiome in amino acid metabolism, lipid biosynthesis proteins and steroid biosynthesis were remarkably increased, while the capacity in renin-angiotensin system was remarkably decreased following vaccines.<br><br>CONCLUSIONS: Our study suggests that inactivated BBIBP-CorV against SARS-CoV-2 could elicit modulations on gut microbial composition and functions, which might favor host immune response and protect from COVID-19.},
}
@article {pmid36336802,
year = {2022},
author = {Yang, M and Luo, F and Song, Y and Ma, S and Ma, Y and Fazal, A and Yin, T and Lu, G and Sun, S and Qi, J and Wen, Z and Li, Y and Yang, Y},
title = {The host niches of soybean rather than genetic modification or glyphosate application drive the assembly of root-associated microbial communities.},
journal = {Microbial biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-7915.14164},
pmid = {36336802},
issn = {1751-7915},
support = {31870495//National Natural Science Foundation of China/ ; 32101383//National Natural Science Foundation of China/ ; 2022M711562//China Postdoctoral Science Foundation/ ; 2016ZX08011-003//National Important Science &amp; Technology Specific Project/ ; IRT_14R27//Program for Changjiang Scholars and Innovative Research Team in University from the Ministry of Education of China/ ; },
abstract = {Plant roots significantly influence soil microbial diversity, and soil microorganisms play significant roles in both natural and agricultural ecosystems. Although the genetically modified (GM) crops with enhanced insect and herbicide resistance are thought to have unmatched yield and stress resistance advantages, thorough and in-depth case studies still need to be carried out in a real-world setting due to the potential effects of GM plants on soil microbial communities. In this study, three treatments were used: a recipient soybean variety Jack, a triple transgenic soybean line JD321, and the glyphosate-treated JD321 (JD321G). Three sampling stages (flowering, seed filling and maturing), as well as three host niches of soybean rhizosphere [intact roots (RT), rhizospheric soil (RS) and surrounding soil (SS)] were established. In comparison to Jack, the rhizospheric soil of JD321G had higher urease activity and lower nitrite reductase at the flowering stage. Different treatments and different sampling stages existed no significant effects on the compositions of microbial communities at different taxonomic levels. However, at the genus level, the relative abundance of three plant growth-promoting fungal genera (i.e. Mortierella, Chaetomium and Pseudombrophila) increased while endophytic bacteria Chryseobacterium and pathogenic bacteria Streptomyces decreased from the inside to the outside of the roots (i.e. RT → RS → SS). Moreover, two bacterial genera, Bradyrhizobium and Ensifer were more abundant in RT than in RS and SS, as well as three species, Agrobacterium radiobacter, Ensifer fredii and Ensifer meliloti, which are closely related to nitrogen-fixation. Furthermore, five clusters of orthologous groups (COGs) associated to nitrogen-fixation genes were higher in RT than in RS, whereas only one COG annotated as dinitrogenase iron-molybdenum cofactor biosynthesis protein was lower. Overall, the results imply that the rhizosphere host niches throughout the soil-plant continuum largely control the composition and function of the root-associated microbiome of triple transgenic soybean.},
}
@article {pmid36336781,
year = {2022},
author = {Zhang, Q and Yang, J and Zhou, X and Ding, Y and Wang, Y and Zhu, X and Xu, F and Liu, J and Wang, Z and Zhang, J and Xu, W},
title = {Soil-borne bacterium Klebsiella pneumoniae promotes cluster root formation in white lupin through ethylene mediation.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.18600},
pmid = {36336781},
issn = {1469-8137},
abstract = {Cluster roots of white lupin are induced by low phosphorus (LP) to efficiently access unavailable P, but how soil-borne microbes are associate with cluster root formation (CRF) is unclear. We investigated the roles of soil-borne bacteria in CRF response to LP by high-throughput sequencing and root-bacteria interactions. Cluster root number was significantly decreased in plants grown in sterilized soil compared with non-sterilized soil. Proteobacteria was enriched in CR, as shown by microbiome analysis of soil (bulk, rhizosphere and rhizosheath) and roots (main, lateral and CR). Large-scale gene expression level implicated ethylene mediation in CRF. Klebsiella pneumoniae (P7), a soil-borne bacterium belonging to Proteobacteria, was isolated from CR. Among 11 isolated strains, P7 exhibited the highest 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity; this enzyme inhibits the biosynthesis of ethylene in plants by the cleavage of the ethylene precursor ACC and promotes CRF under LP. We constructed an ACCD-deficit mutant accd in the P7 genetic background. The loss-of-function mutation failed to promote CRF under LP conditions. Also, auxin responses may be involved in K. pneumoniae-ethylene-mediated CRF. Overall, we propose that soil-borne bacterium K. pneumoniae promotes CRF of white lupin in response to LP by ethylene mediation.},
}
@article {pmid36336607,
year = {2022},
author = {Langdahl, BL and Uitterlinden, AG and Ralston, SH},
title = {Where is bone science taking us?.},
journal = {Best practice &amp; research. Clinical rheumatology},
volume = {},
number = {},
pages = {101791},
doi = {10.1016/j.berh.2022.101791},
pmid = {36336607},
issn = {1532-1770},
abstract = {Bone science has over the last decades unraveled many important pathways in bone and mineral metabolism and the interplay between genetic factors and the environment. Some of these discoveries have led to the development of pharmacological treatments of osteoporosis and rare bone diseases. Other scientific avenues have uncovered a role for the gut microbiome in regulating bone mass, which have led to investigations on the possible therapeutic role of probiotics in the prevention of osteoporosis. Huge advances have been made in identifying the genes that cause rare bone diseases, which in some cases have led to therapeutic interventions. Advances have also been made in understanding the genetic basis of the more common polygenic bone diseases, including osteoporosis and Paget's disease of bone (PDB). Polygenic profiles are used for establishing genetic risk scores aiming at early diagnosis and intervention, but also in Mendelian randomization (MR) studies to investigate both desired and undesired effects of targets for drug design.},
}
@article {pmid36336154,
year = {2022},
author = {Lu, Y and Zhu, X and Hu, C and Li, P and Zhao, M and Lu, J and Xia, G},
title = {A fucoidan-gelatin wound dressing accelerates wound healing by enhancing antibacterial and anti-inflammatory activities.},
journal = {International journal of biological macromolecules},
volume = {223},
number = {Pt A},
pages = {36-48},
doi = {10.1016/j.ijbiomac.2022.10.255},
pmid = {36336154},
issn = {1879-0003},
abstract = {Microbial infections and the slow regression of inflammation are major impediments to wound healing. Herein, a tilapia fish skin gelatin-fucose gum-tannic acid (Gel&amp;Fuc-TA) hydrogel wound dressing (Gel&amp;Fuc-TA) was designed to promote wound healing by mixing and reacting tannic acid (TA) with tilapia fish skin gelatin (Gel) and fucoidan (Fuc). Gel&amp;Fuc-TA hydrogel has a good network structure as well as swelling and release properties, and shows excellent antibacterial, antioxidant, cell compatibility, and hemostatic properties. Gel&amp;Fuc-TA hydrogel can promote the expression of vascular endothelial growth factor (VEGF), platelet endothelial cell adhesion molecule-1 (CD-31), and alpha-smooth muscle actin (α-SMA), enhance collagen deposition, and accelerate wound repair. Gel&amp;Fuc-TA hydrogel can change the wound microbiome, reduce wound microbiome colonization, and decrease the expression of microbiome-related proinflammatory factors, such as lipopolysaccharide (LPS), Toll-like receptor 2 (TLR2), and Toll-like receptor 4 (TLR4). Gel&amp;Fuc-TA hydrogel effectively regulates the conversion of wound macrophages to the M2 (anti-inflammatory phenotype) phenotype, decreases the expression of interleukin-6 (IL-6), interleukin-1β (IL-1β) and tumor necrosis factor-alpha (TNF-α), and increases the expression of arginase-1 (Arg-1), interleukin-10 (IL-10) and transforming growth factor-beta (TGF-β), thereby reducing the inflammatory response. In summary, Gel&amp;Fuc-TA hydrogel prepared using a rational green cross-linking reaction can effectively accelerate wound healing.},
}
@article {pmid36336131,
year = {2022},
author = {Zhang, H and Zou, Y and Xue, Q and Li, M and Yang, H and Cheng, H and Gu, Y and Shen, C and Tian, Q and Wang, S},
title = {Elemene oral emulsion attenuates colitis in mice by altering gut microbiome and regulating amino acids metabolism.},
journal = {Microbial pathogenesis},
volume = {173},
number = {Pt A},
pages = {105821},
doi = {10.1016/j.micpath.2022.105821},
pmid = {36336131},
issn = {1096-1208},
}
@article {pmid36336091,
year = {2022},
author = {Koner, S and Chen, JS and Rathod, J and Hussain, B and Hsu, BM},
title = {Unravelling the ultramafic rock-driven serpentine soil formation leading to the geo-accumulation of heavy metals: An impact on the resident microbiome, biogeochemical cycling and acclimatized eco-physiological profiles.},
journal = {Environmental research},
volume = {},
number = {},
pages = {114664},
doi = {10.1016/j.envres.2022.114664},
pmid = {36336091},
issn = {1096-0953},
abstract = {In the present study, we have underpinned the serpentine rock, serpentinized ultramafic soil and rhizosphere's microbial communities, signifying their heavy metals-exposed taxa signatures and functional repertoires in comparison to non-serpentine soils. The results revealed that the serpentine rock embedded soil highlighted the geo-accumulation of higher amount of Cr and Ni impacting soil microbial diversity negatively by metal stress-driven selection. Biolog Ecoplate CLPP defined a restricted spectrum of C-utilization in the higher heavy metal-containing serpentine samples compared to non-serpentine. The linear discriminant analysis (LDA) score identified a higher abundance of Desulfobacterota, Opitutales, and Bacteroidales in low Cr and Ni-stressed non-serpentine-exposed samples. Whereas the abundance of Propionibacteriales and Actinobacteriota were significantly enriched in the serpentine niche. Further, the C, N, S, Fe, and methane biogeochemical cycles linked functional members were identified, and showing higher functional diversity in low Cr and Ni concentration-containing rhizosphere JS-soils. The Pearson correlation coefficient (r) value confirmed the abundance of functional members linked to specific biogeochemical cycle, positively correlated with relevant pathway enrichment. Ultimately, this study highlighted the heavy metal stress within a serpentine setting that could limit the resident microbial community's metabolic diversity and further select the bacteria that could thrive in the serpentine-associated heavy metal-stressed soils. These acclimatized microbes could pave the way for the future applications in the soil conservation and management.},
}
@article {pmid36336059,
year = {2022},
author = {Bian, J and Wang, H and Ding, H and Song, Y and Zhang, X and Tang, X and Zhong, Y and Zhao, C},
title = {Unveiling the dynamics of antibiotic resistome, bacterial communities, and metals from the feces of patients in a typical hospital wastewater treatment system.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {159907},
doi = {10.1016/j.scitotenv.2022.159907},
pmid = {36336059},
issn = {1879-1026},
abstract = {Bacterial pathogens and antibiotic resistance genes (ARGs) are extensively disseminated into the environment via hospital wastewater (HWW), as it contains large quantities of feces from resident patients. However, studies on the antibiotic resistome and pathogenic bacteria from the gut of resident patients within the hospital wastewater treatment plant (hWWTP) are limited. Here, we examined and compared the occurrence and abundance of ARGs, mobile genetic elements (MGEs), metals, and bacterial communities from the feces of patients in a typical hWWTP system and determined the pathogenic hosts responsible for transferring ARGs. There were 176 ARGs and 43 MGEs detected in the feces of hospitalized patients, 129 genes were persistent, and 88 genes were enriched after HWW treatment, particularly for the blaVEB, blaNDM, and class 1 integron (intI1), with an average of 659-fold, 202-fold, and seven-fold enrichment, respectively. MGEs, especially Is613, in the feces of hospitalized patients were exceptionally abundant and even surpassed the abundance of total ARGs, which explained the persistence of ARGs in hWWTPs due to possible gene mobilization events. Bacteroidetes and Firmicutes were the most abundant phyla in these feces, accounting for 81 % of the total gut microbiota, while Epsilonbacteraeota and Proteobacteria dominated the hWWTPs. Additionally, 54 possible bacterial pathogens were found in the hospital environment, including four "ESKAPE" pathogens and 14 cancer-related pathogens. Many of them were strongly associated with different types of ARGs. Notably, Bacteroides was the major potential ARG-harboring pathogenic genus, as determined by the network analysis, and was highly abundant after the treatment. The altered microbial community was the major contributing factor shaping antibiotic resistome. This study might provide a comprehensive insight into the distribution profiles of ARGs and pathogens from the gut of inpatients throughout the HWW treatment system, which could be used as a reference for optimizing HWW treatment and monitoring public risk.},
}
@article {pmid36335804,
year = {2022},
author = {Cuozzo, S and de Moreno de LeBlanc, A and LeBlanc, JG and Hoffmann, N and Tortella, GR},
title = {Streptomyces genus as a source of probiotics and its potential for its use in health.},
journal = {Microbiological research},
volume = {266},
number = {},
pages = {127248},
doi = {10.1016/j.micres.2022.127248},
pmid = {36335804},
issn = {1618-0623},
abstract = {The effect of a probiotic on gut microbiota depends not only on the species of microorganism but specifically on the strain. In human beings, as in other animals, specific probiotics have been associated with numerous beneficial properties, which include weight modulation (gain or loss), immune modulation, and prevention of many disorders such as lactose intolerance, cardiovascular diseases, and antibiotic-associated diarrhoea. Streptomyces are an essential group of soil bacteria in the Actinomycetes family. They are related to producing a wide range of secondary metabolites known for their beneficial effects on human health. However, according to the human microbiome analysis, a lower prevalence of Streptomyces genus exists than in other non-human microbiomes. This difference can be associated with current lifestyles. In this article, we review the benefits associated with different compounds produced by Streptomyces, with a particular focus on the production of exopolysaccharides, antibiotics, and other secondary metabolites and the potential innovative use of Streptomyces spp. as probiotics.},
}
@article {pmid36335803,
year = {2022},
author = {Yu, S and Zhang, H and Wan, L and Xue, M and Zhang, Y and Gao, X},
title = {The association between the respiratory tract microbiome and clinical outcomes in patients with COPD.},
journal = {Microbiological research},
volume = {266},
number = {},
pages = {127244},
doi = {10.1016/j.micres.2022.127244},
pmid = {36335803},
issn = {1618-0623},
abstract = {Though it has been widely accepted that infections of the respiratory tract is associated with aetiology of acute exacerbation of chronic obstructive pulmonary disease (AECOPD), more recent techniques have shown emerging evidence on the importance of alterations of diversity and composition of microbiota itself in the disease process. Specifically, these alterations is widely present in COPD patients from a variety of populations, and is associated with severity of disease, frequency of acute exacerbation, as well as prediction of exacerbation. In addition, the microbiota from respiratory tract contributes to disease mechanisms, and more recently have been shown to interact with gut microbiota in a bidirectional way. Therefore, updating progress in the field is crucial as it not only reveals potential underlying mechanisms of the disease, but also highlights the potential utilisation of microbiota as a biomarker for disease prediction and as a target for treatment. In this narrative review, we summarize current updates on microbiota dysbiosis in COPD, including techniques for sampling and analysis of microbiota, recent findings on the presence of microbiota dysbiosis and its correlation with clinical prediction and prognosis of the disease, as well as its potential roles in disease mechanisms. In addition, how gut-lung axis contributes to COPD progression is also discussed. Finally, we addressed the utilisation of prebiotic and probiotic treatment for COPD. Together, we hope to provide useful information to advocate the use of microbial parameters as important tools for diagnosis, treatment and long-term follow-up for COPD patients.},
}
@article {pmid36335740,
year = {2022},
author = {Ponsuksili, S and Hadlich, F and Perdomo-Sabogal, A and Reyer, H and Oster, M and Trakooljul, N and Iqbal, MA and Schmucker, S and Stefanski, V and Roth, C and Silva, AC and Huber, K and Sommerfeld, V and Rodehutscord, M and Wimmers, K},
title = {The dynamics of molecular, immune and physiological features of the host and the gut microbiome, and their interactions before and after onset of laying in two hen strains.},
journal = {Poultry science},
volume = {102},
number = {1},
pages = {102256},
doi = {10.1016/j.psj.2022.102256},
pmid = {36335740},
issn = {1525-3171},
abstract = {Aggregation of data, including deep sequencing of mRNA and miRNA data in jejunum mucosa, abundance of immune cells, metabolites, or hormones in blood, composition of microbiota in digesta and duodenal mucosa, and production traits collected along the lifespan, provides a comprehensive picture of lifelong adaptation processes. Here, respective data from two laying hen strains (Lohmann Brown-Classic (LB) and Lohmann LSL-Classic (LSL) collected at 10, 16, 24, 30, and 60 wk of age were analyzed. Data integration revealed strain- and stage-specific biosignatures, including elements indicative of molecular pathways discriminating the strains. Although the strains performed the same, they differed in the activity of immunological and metabolic functions and pathways and showed specific gut-microbiota-interactions in different production periods. The study shows that both strains employ different strategies to acquire and maintain their capabilities under high performance conditions, especially during the transition phase. Furthermore, the study demonstrates the capacity of such integrative analyses to elucidate molecular pathways that reflect functional biodiversity. The bioinformatic reduction of the multidimensional data provides good guidance for further manual review of the data.},
}
@article {pmid36332998,
year = {2022},
author = {Liu, JL and Woo, JMP and Parks, CG and Costenbader, KH and Jacobsen, S and Bernatsky, S},
title = {Systemic Lupus Erythematosus Risk: The Role of Environmental Factors.},
journal = {Rheumatic diseases clinics of North America},
volume = {48},
number = {4},
pages = {827-843},
doi = {10.1016/j.rdc.2022.06.005},
pmid = {36332998},
issn = {1558-3163},
mesh = {Humans ; *Environmental Exposure/adverse effects ; Ultraviolet Rays/adverse effects ; *Lupus Erythematosus, Systemic/epidemiology/etiology ; Smoking ; Risk Factors ; },
abstract = {Systemic lupus erythematosus (SLE) is a complex, chronic autoimmune disease. The etiology of SLE is multifactorial and includes potential environmental triggers, which may occur sequentially (the "multi-hit" hypothesis). This review focuses on SLE risk potentially associated with environmental factors including infections, the microbiome, diet, respirable exposures (eg, crystalline silica, smoking, air pollution), organic pollutants, heavy metals, and ultraviolet radiation.},
}
@article {pmid36335441,
year = {2022},
author = {Floca, E and Gaga, R and Sur, G and Lupan, I and Armat, I and Samasca, G and Sur, LM},
title = {A new autoimmune disease: atopic dermatitis in children.},
journal = {Allergologia et immunopathologia},
volume = {50},
number = {6},
pages = {17-21},
pmid = {36335441},
issn = {1578-1267},
abstract = {Atopic dermatitis (AD) is mainly considered an allergy, exacerbated by allergic factors. Is there evidence to suggest the existence of autoimmune components in the pathophysiology of the illness? Studies in the literature that dealt with the occurrence of autoimmunity in children with AD were analyzed. We followed the studies published in PubMed for 10 years, from 2001 to 2021. Clinical signs and symptoms were similar to other autoimmune diseases, having periods of remission and relapses. Other correlations between AD and autoimmune diseases have been described, and patients with AD can also present with a wide range of autoimmune comorbidities. Three major factors contribute to the pathogenesis of AD: damage of the skin barrier, disorders of the immune response, and imbalances of the skin microbiome-all based on genetic changes and influenced by environmental factors. Predominant activation of Th 2 cells, with the increase of Th 1, Th 17, and Th 22 subsets, promotes skin inflammation. All this evidence suggests that AD might be classified as an autoimmune disease, not just as an allergic reaction.},
}
@article {pmid36334897,
year = {2022},
author = {Altaha, B and Heddes, M and Pilorz, V and Niu, Y and Gorbunova, E and Gigl, M and Kleigrewe, K and Oster, H and Haller, D and Kiessling, S},
title = {Genetic and environmental circadian disruption induce weight gain through changes in the gut microbiome.},
journal = {Molecular metabolism},
volume = {},
number = {},
pages = {101628},
doi = {10.1016/j.molmet.2022.101628},
pmid = {36334897},
issn = {2212-8778},
abstract = {OBJECTIVE: Internal clocks time behavior and physiology, including the gut microbiome, in a circadian (∼24 h) manner. Mismatch between internal and external time, e.g. during shift work, disrupts circadian system coordination promoting the development of obesity and type 2 diabetes (T2D). Conversely, body weight changes induce microbiota dysbiosis. The relationship between circadian disruption and microbiota dysbiosis in metabolic diseases, however, remains largely unknown.<br><br>METHODS: Core and accessory clock gene expression in different gastrointestinal (GI) tissues were determined by qPCR in two different models of circadian disruption - mice with Bmal1 deficiency in the circadian pacemaker, the suprachiasmatic nucleus (Bmal1SCNfl/-), and wild-type mice exposed to simulated shift work (SSW). Body composition and energy balance were evaluated by nuclear magnetic resonance (NMR), bomb calorimetry, food intake and running-wheel activity. Intestinal permeability was measured in an Ussing chamber. Microbiota composition and functionality were evaluated by 16S rRNA gene amplicon sequencing, PICRUST2.0 analysis and targeted metabolomics. Finally, microbiota transfer was conducted to evaluate the functional impact of SSW-associated microbiota on the host's physiology.<br><br>RESULTS: Both chronodisruption models show desynchronization within and between peripheral clocks in GI tissues and reduced microbial rhythmicity, in particular in taxa involved in short-chain fatty acid (SCFA) fermentation and lipid metabolism. In Bmal1SCNfl/- mice, loss of rhythmicity in microbial functioning associates with previously shown increased body weight, dysfunctional glucose homeostasis and adiposity. Similarly, we observe an increase in body weight in SSW mice. Germ-free colonization experiments with SSW-associated microbiota mechanistically link body weight gain to microbial changes. Moreover, alterations in expression of peripheral clock genes as well as clock-controlled genes (CCGs) relevant for metabolic functioning of the host were observed in recipients, indicating a bidirectional relationship between microbiota rhythmicity and peripheral clock regulation.<br><br>CONCLUSIONS: Collectively, our data suggest that loss of rhythmicity in bacteria taxa and their products, which likely originates in desynchronization of intestinal clocks, promotes metabolic abnormalities during shift work.},
}
@article {pmid36334830,
year = {2022},
author = {Almeida, P and Jesus, H and Pereira, P and Vieira, C and Bianchini, A and Martins, C and Santos, HF},
title = {The microbial profile of rivers and lagoons three years after the impact of the world's largest mining disaster (Fundão dam, Brazil).},
journal = {Environmental research},
volume = {},
number = {},
pages = {114710},
doi = {10.1016/j.envres.2022.114710},
pmid = {36334830},
issn = {1096-0953},
abstract = {The collapse of the Fundão tailings dam (Minas Gerais, Brazil) was the largest environmental disaster in Brazil's history and in the world mining industry. This disaster carried approximately 55 million m3 of iron ore tailings along the rivers and the lagoons of the Doce river basin. Although multiple studies assessed the impact on microbial communities in those rivers and lagoons right after the dam rupture, it is not known whether the microbiome in those environments remains impacted years after the disaster. Assessing the microbiome is very important to evaluate impacts and evaluate the health of the environment, due to the several ecological roles played by microorganisms. Here, we evaluated the impact of the dam failure on water and sediment bacteriome and archaeome by high-throughput next-generation sequencing. Samples were taken from two rivers and six lagoons during the dry and rainy seasons approximately three years post disturbance. The results showed a large number and abundance of microbial groups associated with the presence of heavy metals and mine tailings sediments. Some of these microorganisms were also reported in large abundance in the impacted rivers shortly after the Fundão dam rupture. Among the most abundant microorganisms in the Doce River, we can highlight the bacteria hgcI clade and the archaea Nitrososphera sp. in the water, and the bacteria Anaerolineaceae sp. in the sediment. These results suggest that the microbiome of the rivers and the lagoons in the Doce river basin remains severely impacted by the Fundão tailings dam failure even three years after the disaster. The presence of those microorganisms can also help to assess the occurrence of the Fundão dam sediment in other environments.},
}
@article {pmid36334762,
year = {2022},
author = {Korenblik, V and Brouwer, ME and Korosi, A and Denys, D and Bockting, CLH and Brul, S and Lok, A},
title = {Are neuromodulation interventions associated with changes in the gut microbiota? A systematic review.},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {109318},
doi = {10.1016/j.neuropharm.2022.109318},
pmid = {36334762},
issn = {1873-7064},
abstract = {The microbiota-gut-brain axis (MGBA) refers to the bidirectional communication between the brain and the gut microbiota and recent studies have linked the MGBA to health and disease. Research has so far investigated this axis mainly from microbiota to brain but less is known about the other direction. One approach to examine the MGBA from brain to microbiota is through understanding if and how neuromodulation might impact microbiota. Neuromodulation encompasses a wide range of stimulation techniques and is used to treat neurological, psychiatric and metabolic disorders, like Parkinson's Disease, depression and obesity. Here, we performed a systematic review to investigate whether neuromodulation is associated with subsequent changes in the gut microbiota. Searches in PsycINFO and MEDLINE were performed up to March 2022. Included studies needed to be clinical or preclinical studies comparing the effects of deep brain stimulation, electroconvulsive therapy, repetitive transcranial magnetic stimulation, transcranial direct current stimulation or vagal nerve stimulation on the gut microbiota before and after treatment or between active and control groups. Seven studies were identified. Neuromodulation was associated with changes in relative bacterial abundances, but not with (changes in) α-diversity or β-diversity. Summarizing, currently reported findings suggest that neuromodulation interventions are associated with moderate changes in the gut microbiome. However, findings remain inconclusive due to the limited number and varying quality of included studies, as well as the large heterogeneity between studies. More research is required to more conclusively establish whether, and if so, via which mechanism(s) of action neuromodulation interventions might influence the gut microbiota.},
}
@article {pmid36334702,
year = {2022},
author = {Shipp, CL and Gergen, PJ and Gern, JE and Matsui, EC and Guilbert, TW},
title = {Asthma Management in Children.},
journal = {The journal of allergy and clinical immunology. In practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaip.2022.10.031},
pmid = {36334702},
issn = {2213-2201},
abstract = {Asthma is a common, complex heterogeneous disease often beginning in early life and is characterized by reversible airflow obstruction. The phenotypic differences that exist in children with asthma may impact underlying comorbid conditions and pharmacologic treatment choices. Prenatal factors for increased risk of asthma could include maternal diet and the maternal microbiome. Evidence also suggests that postnatal microbial exposures and colonization contribute to the risk of allergic diseases and asthma. After confirming the diagnosis, asthma management in children centers on 3 broad areas: pharmacologic treatment, treatment of underlying comorbidities, and education of the patient and caregivers on the importance of adherence and device technique. Moreover, social determinants of health significantly impact on symptom burden and treatment response.},
}
@article {pmid36334333,
year = {2022},
author = {Zhang, Y and Zhang, J and Xia, Y and Sun, J},
title = {Bacterial translocation and barrier dysfunction enhance colonic tumorigenesis.},
journal = {Neoplasia (New York, N.Y.)},
volume = {35},
number = {},
pages = {100847},
doi = {10.1016/j.neo.2022.100847},
pmid = {36334333},
issn = {1476-5586},
abstract = {In the development of colon cancer, the intestinal dysbiosis and disruption of barrier function are common manifestations. In the current study, we hypothesized that host factors, e.g., vitamin D receptor deficiency or adenomatous polyposis coli (APC) mutation, contribute to the enhanced dysbiosis and disrupted barrier in the pathogenesis of colorectal cancer (CRC). Using the human CRC database, we found enhanced tumor-invading bacteria and reduced colonic VDR expression, which was correlated with a reduction of Claudin-10 mRNA and protein. In the colon of VDRΔIEC mice, deletion of intestinal epithelial VDR led to lower protein of tight junction protein Claudin-10. Lacking VDR and a reduction of Claudin-10 are associated with an increased number of tumors in the mice without myeloid VDR. Intestinal permeability was significantly increased in the mice with myeloid VDR conditional deletion. Further, mice with conditional colonic APC mutation showed reduced mucus layer, enhanced bacteria in tumors, and loss of Claudin-10. Our data from human samples and colon cancer models provided solid evidence- on the host factor regulation of bacterial translocation and dysfunction on barriers in colonic tumorigenesis. Studies on the host factor regulation of microbiome and barriers could be potentially applied to risk assessment, early detection, and prevention of colon cancer.},
}
@article {pmid36334179,
year = {2022},
author = {Tripathi, S and Purchase, D and Govarthanan, M and Chandra, R and Yadav, S},
title = {Regulatory and innovative mechanisms of bacterial quorum sensing-mediated pathogenicity: a review.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {1},
pages = {75},
pmid = {36334179},
issn = {1573-2959},
support = {YSS/2015/000768//DST(SERB), New Delhi/ ; },
abstract = {Quorum sensing (QS) is a system of bacteria in which cells communicate with each other; it is linked to cell density in the microbiome. The high-density colony population can provide enough small molecular signals to enable a range of cellular activities, gene expression, pathogenicity, and antibiotic resistance that cause damage to the hosts. QS is the basis of chronic illnesses in human due to microbial sporulation, expression of virulence factors, biofilm formation, secretion of enzymes, or production of membrane vesicles. The transfer of antimicrobial resistance gene (ARG) among antibiotic resistance bacteria is a major public health concern. QS-mediated biofilm is a hub for ARG horizontal gene transfer. To develop innovative approach to prevent microbial pathogenesis, it is essential to understand the role of QS especially in response to environmental stressors such as exposure to antibiotics. This review provides the latest knowledge on the relationship of QS and pathogenicity and explore the novel approach to control QS via quorum quenching (QQ) using QS inhibitors (QSIs) and QQ enzymes. The state-of-the art knowledge on the role of QS and the potential of using QQ will help to overcome the threats of rapidly emerging bacterial pathogenesis.},
}
@article {pmid36334119,
year = {2022},
author = {Zhao, F and Guo, Z and Kwok, LY and Zhao, Z and Wang, K and Li, Y and Sun, Z and Zhao, J and Zhang, H},
title = {Bifidobacterium lactis Probio-M8 improves bone metabolism in patients with postmenopausal osteoporosis, possibly by modulating the gut microbiota.},
journal = {European journal of nutrition},
volume = {},
number = {},
pages = {},
pmid = {36334119},
issn = {1436-6215},
support = {2021ZD0014//Inner Mongolia Science and Technology Major Projects/ ; },
abstract = {PURPOSE: Postmenopausal osteoporosis (PMO) is usually managed by conventional drug treatment. However, prolonged use of these drugs cause side effects. Gut microbiota may be a potential target for treatment of PMO. This work was a three-month intervention trial aiming to evaluate the added effect of probiotics as adjunctive treatment for PMO.<br><br>METHODS: Forty patients with PMO were randomized into probiotic (n = 20; received Bifidobacterium animalis subsp. lactis Probio-M8 [Probio-M8], calcium, calcitriol) and placebo (n = 20; received placebo material, calcium, calcitriol) groups. The bone mineral density of patients was measured at month 0 (0 M; baseline) and month 3 (3 M; after three-month intervention). Blood and fecal samples were collected 0 M and 3 M. Only 15 and 12 patients from Probio-M8 and placebo groups, respectively, provided complete fecal samples for gut microbiota analysis.<br><br>RESULTS: No significant change was observed in the bone mineral density of patients at 3 M. Co-administering Probio-M8 improved the bone metabolism, reflected by an increased vitamin D3 level and decreased PTH and procalcitonin levels in serum at 3 M. Fecal metagenomic analysis revealed modest changes in the gut microbiome in both groups at 3 M. Interestingly, Probio-M8 co-administration affected the gut microbial interactive correlation network, particularly the short-chain fatty acid-producing bacteria. Probio-M8 co-administration significantly increased genes encoding some carbohydrate metabolism pathways (including ABC transporters, the phosphotransferase system, and fructose and mannose metabolism) and a choline-phosphate cytidylyltransferase.<br><br>CONCLUSIONS: Co-administering Probio-M8 with conventional drugs/supplements was more efficacious than conventional drugs/supplements alone in managing PMO. Our study shed insights into the beneficial mechanism of probiotic adjunctive treatment.<br><br>Chinese Clinical Trial Registry (identifier number: ChiCTR1800019268).},
}
@article {pmid36334085,
year = {2022},
author = {Ordinola-Zapata, R and Costalonga, M and Nixdorf, D and Dietz, M and Schuweiller, D and Lima, BP and Staley, C},
title = {Taxonomic Abundance in Primary and Secondary Root Canal Infections.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.13864},
pmid = {36334085},
issn = {1365-2591},
abstract = {AIM: To evaluate the root canal microbiome composition in cases of primary and secondary apical periodontitis.<br><br>METHODOLOGY: Thirty-nine samples from patients with primary root canal infections obtained before root canal treatment, and forty samples obtained during root-end resection procedures from previously filled cases with apical periodontitis were evaluated using 16S rRNA next-generation sequencing analysis (NGS). Demographic and clinical factors included age, sex, infection type, percussion sensitivity, and presence of pain. Differences in abundances of genera were evaluated using Kruskal-Wallis test. Alpha and beta diversity indices were calculated using mothur. The Shannon and Chao1 indices were used to measure alpha diversity. The Bray-Curtis dissimilarity was used to measure beta diversity. Differences in community composition were evaluated using analysis of similarity (ANOSIM) with Bonferroni correction for multiple comparisons.<br><br>RESULTS: Significantly fewer OTUs values were observed from samples from secondary infections (P < 0.0001). While no significant differences were observed in the Chao 1 index between primary and secondary infections, the Shannon alpha diversity was significantly lower in secondary relative to primary infections (P = 0.001). Among samples, sex, age (adult vs older adult), percussion sensitivity, and presence of pain all showed no significant effects on community composition via an ANOSIM. However, community composition was significantly different depending on whether the sample was from a primary or secondary infection (R = 0.051, P = 0.03). Nine microbial genera comprised the predominant taxa observed among samples (>3.3%) and included Parvimonas, Fusobacterium, Campylobacter, Arachnia, Eubacterium, Prevotella, Peptostreptococcus, Fretibacterirum, and Pseudoramibacter Significantly greater relative abundances of Prevotella, Peptostreptococcus, Veillonella, Lactucaseibacillus and Dialister were observed in primary infections.<br><br>CONCLUSIONS: Primary endodontic infections are more diverse than secondary infections. The microbial composition is not associated with the clinical manifestations of apical periodontitis.},
}
@article {pmid36333950,
year = {2022},
author = {Hammer, TJ and Easton-Calabria, A and Moran, NA},
title = {Microbiome assembly and maintenance across the lifespan of bumble bee workers.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16769},
pmid = {36333950},
issn = {1365-294X},
abstract = {How a host's microbiome changes over its lifespan can influence development and aging. As these temporal patterns have only been described in detail for a handful of hosts, an important next step is to compare microbiome succession more broadly and investigate why it varies. Here we characterize the temporal dynamics and stability of the bumble bee worker gut microbiome. Bumble bees have simple and host-specific gut microbiomes, and their microbial dynamics may influence health and pollination services. We used 16S rRNA gene sequencing, qPCR, and metagenomics to characterize gut microbiomes over the lifespan of Bombus impatiens workers. We also sequenced gut transcriptomes to examine host factors that may control the microbiome. At the community level, microbiome assembly is highly predictable and similar to patterns of primary succession observed in the human gut. But at the strain level, partitioning of bacterial variants among colonies suggests stochastic colonization events similar to those observed in flies and nematodes. We also find strong differences in temporal dynamics among symbiont species, suggesting ecological differences among microbiome members in colonization and persistence. Finally, we show that both the gut microbiome and host transcriptome-including expression of key immunity genes-stabilize, as opposed to senesce, with age. We suggest that in highly social groups such as bumble bees, maintenance of both microbiomes and immunity contribute to the inclusive fitness of workers, and thus remain under selection even in old age. Our findings provide a foundation for exploring the mechanisms and functional outcomes of bee microbiome succession.},
}
@article {pmid36333915,
year = {2022},
author = {Berry, O and Briand, E and Bagot, A and Chaigné, M and Meslet-Cladière, L and Wang, J and Grovel, O and Jansen, JJ and Ruiz, N and Robiou du Pont, T and Pouchus, YF and Hess, P and Bertrand, S},
title = {Deciphering interactions between the marine dinoflagellate Prorocentrum lima and the fungus Aspergillus pseudoglaucus.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16271},
pmid = {36333915},
issn = {1462-2920},
abstract = {The comprehension of microbial interactions is one of the key challenges in marine microbial ecology. This study focused on exploring chemical interactions between the toxic dinoflagellate Prorocentrum lima and a filamentous fungal species, Aspergillus pseudoglaucus, which has been isolated from the microalgal culture. Such interspecies interactions are expected to occur even though they were rarely studied. Here, a co-culture system was designed in a dedicated microscale marine-like condition. This system allowed to explore microalgal-fungal physical and metabolic interactions in presence and absence of the bacterial consortium. Microscopic observation showed an unusual physical contact between the fungal mycelium and dinoflagellate cells. To delineate specialized metabolome alterations during microalgal-fungal co-culture metabolomes were monitored by high-performance liquid chromatography coupled to high-resolution mass spectrometry. In-depth multivariate statistical analysis using dedicated approaches highlighted (1) the metabolic alterations associated with microalgal-fungal co-culture, and (2) the impact of associated bacteria in microalgal metabolome response to fungal interaction. Unfortunately, only a very low number of highlighted features were fully characterised. However, an up-regulation of the dinoflagellate toxins okadaic acid and dinophysistoxin 1 was observed during co-culture in supernatants. Such results highlight the importance to consider microalgal-fungal interactions in the study of parameters regulating toxin production. This article is protected by copyright. All rights reserved.},
}
@article {pmid36333752,
year = {2022},
author = {Kim, G and Yoon, Y and Park, JH and Park, JW and Noh, MG and Kim, H and Park, C and Kwon, H and Park, JH and Kim, Y and Sohn, J and Park, S and Kim, H and Im, SK and Kim, Y and Chung, HY and Nam, MH and Kwon, JY and Kim, IY and Kim, YJ and Baek, JH and Kim, HS and Weinstock, GM and Cho, B and Lee, C and Fang, S and Park, H and Seong, JK},
title = {Bifidobacterial carbohydrate/nucleoside metabolism enhances oxidative phosphorylation in white adipose tissue to protect against diet-induced obesity.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {188},
pmid = {36333752},
issn = {2049-2618},
support = {6-2018-0098//Faculty research grant from the Yonsei University College of Medicine/ ; HI18C0012//Ministry of Health &amp; Welfare/ ; NRF-2017M3A9F3046536//Ministry of Science and ICT, South Korea/ ; 2013M3A9D5072550//Korea Mouse Phenotyping Project/ ; },
abstract = {BACKGROUND: Comparisons of the gut microbiome of lean and obese humans have revealed that obesity is associated with the gut microbiome plus changes in numerous environmental factors, including high-fat diet (HFD). Here, we report that two species of Bifidobacterium are crucial to controlling metabolic parameters in the Korean population.<br><br>RESULTS: Based on gut microbial analysis from 99 Korean individuals, we observed the abundance of Bifidobacterium longum and Bifidobacterium bifidum was markedly reduced in individuals with increased visceral adipose tissue (VAT), body mass index (BMI), blood triglyceride (TG), and fatty liver. Bacterial transcriptomic analysis revealed that carbohydrate/nucleoside metabolic processes of Bifidobacterium longum and Bifidobacterium bifidum were associated with protecting against diet-induced obesity. Oral treatment of specific commercial Bifidobacterium longum and Bifidobacterium bifidum enhanced bile acid signaling contributing to potentiate oxidative phosphorylation (OXPHOS) in adipose tissues, leading to reduction of body weight gain and improvement in hepatic steatosis and glucose homeostasis. Bifidobacterium longum or Bifidobacterium bifidum manipulated intestinal sterol biosynthetic processes to protect against diet-induced obesity in germ-free mice.<br><br>CONCLUSIONS: Our findings support the notion that treatment of carbohydrate/nucleoside metabolic processes-enriched Bifidobacterium longum and Bifidobacterium bifidum would be a novel therapeutic strategy for reprograming the host metabolic homeostasis to protect against metabolic syndromes, including diet-induced obesity. Video Abstract.},
}
@artic