@article {pmid38034829,
year = {2023},
author = {Monleón-Getino, A and Pujol-Muncunill, G and Méndez Viera, J and Álvarez Carnero, L and Sanseverino, W and Paytuví-Gallart, A and Martín de Carpí, J},
title = {A pilot study of the use of the oral and faecal microbiota for the diagnosis of ulcerative colitis and Crohn's disease in a paediatric population.},
journal = {Frontiers in pediatrics},
volume = {11},
number = {},
pages = {1220976},
pmid = {38034829},
issn = {2296-2360},
abstract = {Crohn's disease (CD) and ulcerative colitis (UC) are chronic inflammatory bowel diseases (IBD) that affect the gastrointestinal tract. Changes in the microbiome and its interaction with the immune system are thought to play a key role in their development. The aim of this study was to determine whether metagenomic analysis is a feasible non-invasive diagnostic tool for IBD in paediatric patients. A pilot study of oral and faecal microbiota was proposed with 36 paediatric patients divided in three cohorts [12 with CD, 12 with UC and 12 healthy controls (HC)] with 6 months of follow-up. Finally, 30 participants were included: 13 with CD, 11 with UC and 8 HC (6 dropped out during follow-up). Despite the small size of the study population, a differential pattern of microbial biodiversity was observed between IBD patients and the control group. Twenty-one bacterial species were selected in function of their discriminant accuracy, forming three sets of potential markers of IBD. Although IBD diagnosis requires comprehensive medical evaluation, the findings of this study show that faecal metagenomics or a reduced set of bacterial markers could be useful as a non-invasive tool for an easier and earlier diagnosis.},
}

@article {pmid38034672,
year = {2023},
author = {Oyeyemi, BF and Kaur, US and Paramraj, A and Chintamani, and Tandon, R and Kumar, A and Bhavesh, NS},
title = {Microbiome analysis of saliva from oral squamous cell carcinoma (OSCC) patients and tobacco abusers with potential biomarkers for oral cancer screening.},
journal = {Heliyon},
volume = {9},
number = {11},
pages = {e21773},
pmid = {38034672},
issn = {2405-8440},
abstract = {Oral squamous cell carcinoma (OSCC) is the most common type of oral cancer and accounts for about 95% of all head and neck cancers with high mortality, usually at a late stage. Dysbiosis in the oral microbiome can lead to chronic inflammatory responses and may predispose to the development and progression of OSCC. Tobacco abuse plays an essential role in oral microbiome dysregulation and OSCC pathogenesis. We used 16S rRNA gene amplicon next-generation sequencing to examine microbial signatures unique to saliva from OSCC patients, tobacco abusers (TA) and controls (n = 10 for each group) to elucidate oral microbiome changes associated with tobacco abuse and OSCC. Overall, the oral microbiome compositions of class Betaproteobacteria and Epsilonproteobacteria, order Neisseriales, Burkholderiales and Campylobacterales, family Burkholderiaceae and Campylobacteraceae and genera Campylobacter and Leptotrichia revealed significant differences among OSCC patients, TA and control. Our preliminary pilot study not only serves as a basis for future studies with large sample size but also gives an indication of microbiome-based potential non-invasive biomarkers for early screening and monitoring of oral carcinogenesis transition due to tobacco abuse.},
}

@article {pmid38034657,
year = {2023},
author = {Fu, J and Liang, Y and Shi, Y and Yu, D and Wang, Y and Chen, P and Liu, S and Lu, F},
title = {HuangQi ChiFeng decoction maintains gut microbiota and bile acid homeostasis through FXR signaling to improve atherosclerosis.},
journal = {Heliyon},
volume = {9},
number = {11},
pages = {e21935},
pmid = {38034657},
issn = {2405-8440},
abstract = {Huangqi Chifeng Decoction (HQCFT), a traditional Chinese medicine preparation, has long been used to treat cardiovascular and cerebrovascular diseases. However, the mechanism of the beneficial effect of HQCFT on atherosclerosis remains to be explored. In this work, to investigate the effects of HQCFT on bile acid (BA) metabolism and the gut microbiome in atherosclerosis, ApoE[-/-] mice were fed a with high-fat diet for 16 weeks to establish the AS model. HQCFT(1.95 g kg[-1] and 3.9 g kg[-1] per day) was administered intragastrically for 8 weeks to investigate the regulatory effects of HQCFT on gut microbiota and bile acid metabolism and to inhibit the occurrence and development of AS induced by a high-fat diet. Histopathology, liver function and blood lipids were used to assess whether HQCFT can reduce plaque area, regulate lipid levels and alleviate liver steatosis in AS mice. In addition, 16S rDNA sequencing was used to screen the gut microbiota structure, and ultrahigh-performance liquid chromatography-tandem mass spectrometry (UPLC‒MS/MS) was used to determine the bile acid profile. The mRNA and protein expression levels of bile acid metabolism were detected by RT‒PCR and WB to find the potential correlation. Results: HQCFT can regulate gut microbiota disorders, which was achieved by increasing gut microbiota diversity and altering Proteobacteria, Desulfobacterota, Deferribacteres, Rodentibacter, Parasutterella, and Mucispirillum interference abundance to improve AS-induced gut microbiota. HQCFT can also adjust the content of bile acids (TCA, LCA, DCA, TDCA, TLCA, UDCA, etc.), regulate bile acid metabolism, relieve liver fat accumulation, and inhibit the process of AS. In addition, HQCFT can restore the abnormal metabolism of bile acid caused by AS by regulating the expression of farnesoid X receptor (FXR), liver X receptor α (LXRα), ABCA1, ABCG1 and CYP7A1. Conclusion: HQCFT may play a part in the prevention of atherosclerosis by inhibiting the FXR/LXRα axis, increasing the expression of CYP7A1 in the liver, and regulating the interaction between the gut microbiota and bile acid metabolism.},
}

@article {pmid38034621,
year = {2023},
author = {Jiang, W and Lu, G and Qiao, T and Yu, X and Luo, Q and Tong, J and Fan, S and Chai, L and Gao, D and Wang, R and Deng, C and Lv, Z and Li, D},
title = {Integrated microbiome and metabolome analysis reveals a distinct microbial and metabolic signature in Graves' disease and hypothyroidism.},
journal = {Heliyon},
volume = {9},
number = {11},
pages = {e21463},
pmid = {38034621},
issn = {2405-8440},
abstract = {Recent studies reveal that imbalanced microbiota is related to thyroid diseases. However, studies on the alterations in fecal metabolites in Graves' disease and clinical hypothyroidism patients are insufficient. Here, we identified 21 genera and 53 metabolites that were statistically significant among Graves' disease patients, hypothyroidism patients, and controls integrating microbiome and untargeted metabolome analysis. Disease groups revealed a decreased abundance in butyrate-producing microbiota and an increased abundance in potentially pathogenic microbiota. Lipids molecules were the major differential metabolites identified in all fecal samples. Network analysis recognized that microbiota may affect thyroid function by targeting specific metabolites. We further identified specific microbiota and metabolites that could distinguish Graves' disease patients, hypothyroidism patients, and controls. Our study reveals a distinct microbial and metabolic signature in hypothyroidism patients and Graves' disease patients and further validates the potential role of microbiota in thyroid diseases, providing new ideas for future research into the etiology and clinical intervention of thyroid diseases.},
}

@article {pmid38034569,
year = {2023},
author = {Xia, K and Feng, Z and Zhang, X and Zhou, Y and Zhu, H and Yao, Q},
title = {Potential functions of the shared bacterial taxa in the citrus leaf midribs determine the symptoms of Huanglongbing.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1270929},
pmid = {38034569},
issn = {1664-462X},
abstract = {INSTRUCTION: Citrus is a globally important fruit tree whose microbiome plays a vital role in its growth, adaptability, and resistance to stress.

METHODS: With the high throughput sequencing of 16S rRNA genes, this study focused on analyzing the bacterial community, especially in the leaf midribs, of healthy and Huanglongbing (HLB)-infected plants.

RESULTS: We firstly identified the shared bacterial taxa in the midribs of both healthy and HLB-infected plants, and then analyzed their functions. Results showed that the shared bacterial taxa in midribs belonged to 62 genera, with approximately 1/3 of which modified in the infected samples. Furthermore, 366 metabolic pathways, 5851 proteins, and 1833 enzymes in the shared taxa were predicted. Among these, three metabolic pathways and one protein showed significant importance in HLB infection. With the random forest method, six genera were identified to be significantly important for HLB infection. Notably, four of these genera were also among the significantly different shared taxa. Further functional characterization of these four genera revealed that Pseudomonas and Erwinia likely contributed to plant defense against HLB, while Streptomyces might have implications for plant defense against HLB or the pathogenicity of Candidatus Liberibacter asiaticus (CLas).

DISCCUSION: Overall, our study highlights that the functions of the shared taxa in leaf midribs are distinguished between healthy and HLB-infected plants, and these microbiome-based findings can contribute to the management and protection of citrus crops against CLas.},
}

@article {pmid38034470,
year = {2023},
author = {Mukhi, S and Dhanashree, B and Srikantiah, RM and Manjrekar, P and Harish, S},
title = {Evaluation of Minimum Inhibitory Concentration of Heavy Metals Contained in Packaging Material Digest on Prominent Gut Microbiota.},
journal = {International journal of food science},
volume = {2023},
number = {},
pages = {3840795},
pmid = {38034470},
issn = {2314-5765},
abstract = {Several scientific investigations have revealed that the leaching of metals from packaging material into the packed food is an unavoidable process. Hence, this study is aimed at investigating the effect of leached heavy metals from food packing materials on normal human gut flora. We analysed the effect of vanadium, arsenic, cadmium, and mercury present in digested packaging materials (DPM) on standard strains of Escherichia coli ATCC 25923, Pseudomonas aeruginosa ATCC 27853, Klebsiella pneumoniae ATCC 70063, and Enterococcus faecalis ATCC 29212. The minimum inhibitory concentration (MIC) of laboratory-grade heavy metal salts and heavy metals present in DPM was determined by the agar dilution method. For all four bacteria, the MIC of cadmium and arsenic in the DPM was 7 μg/ml and 1.6 μg/ml, respectively. The MIC of mercury in DPM was 1.6 μg/ml for E. coli, K. pneumoniae, and E. faecalis and 1.4 μg/ml for P. aeruginosa. MIC of vanadium for E. coli, P. aeruginosa, and E. faecalis was 2.2 μg/ml, and for K. pneumoniae was 2.0 μg/ml. The difference in MICs of heavy metals in DPMs and heavy metal salts was not statistically significant. MICs were within CODEX-specified permissible levels. Though heavy metals in packaging material have not shown a deleterious effect on representative human gut flora, there is scope to study their effect on the gut microbiome. Thus, understanding the risk of heavy metal ingestion through unknown sources and avoiding any possible ingestion is crucial to preventing chronic diseases.},
}

@article {pmid38034007,
year = {2023},
author = {Abuqwider, J and Corrado, A and Scidà, G and Lupoli, R and Costabile, G and Mauriello, G and Bozzetto, L},
title = {Gut microbiome and blood glucose control in type 1 diabetes: a systematic review.},
journal = {Frontiers in endocrinology},
volume = {14},
number = {},
pages = {1265696},
pmid = {38034007},
issn = {1664-2392},
abstract = {OBJECTIVE: The risk of developing micro- and macrovascular complications is higher for individuals with type 1 diabetes (T1D). Numerous studies have indicated variations in gut microbial composition between healthy individuals and those with T1D. These changes in the gut ecosystem may lead to inflammation, modifications in intestinal permeability, and alterations in metabolites. Such effects can collectively impact the metabolic regulation system, thereby influencing blood glucose control. This review aims to explore the relationship between the gut microbiome, inflammation, and blood glucose parameters in patients with T1D.

METHODS: Google Scholar, PubMed, and Web of Science were systematically searched from 2003 to 2023 using the following keywords: "gut microbiota," "gut microbiome," "bacteria," "T1D," "type 1 diabetes," "autoimmune diabetes," "glycemic control," "glucose control," "HbA1c," "inflammation," "inflammatory," and "cytokine." The examination has shown 18,680 articles with relevant keywords. After the exclusion of irrelevant articles, seven observational papers showed a distinct gut microbial signature in T1D patients.

RESULTS: This review shows that, in T1D patients, HbA1c level was negatively correlated with abundance of Prevotella, Faecalibacterium, and Ruminococcaceae and positively correlated with abundance of Dorea formicigenerans, Bacteroidetes, Lactobacillales, and Bacteriodes. Instead, Bifidobacteria was negatively correlated with fasting blood glucose. In addition, there was a positive correlation between Clostridiaceae and time in range. Furthermore, a positive correlation between inflammatory parameters and gut dysbiosis was revealed in T1D patients.

CONCLUSION: We draw the conclusion that the gut microbiome profiles of T1D patients and healthy controls differ. Patients with T1D may experience leaky gut, bacterial translocation, inflammation, and poor glucose management due to microbiome dysbiosis. Direct manipulation of the gut microbiome in humans and its effects on gut permeability and glycemic control, however, have not been thoroughly investigated. Future research should therefore thoroughly examine other potential pathophysiological mechanisms in larger studies.},
}

@article {pmid38033919,
year = {2023},
author = {Bautista-Becerril, B and Budden, KF and Falfán-Valencia, R},
title = {Editorial: Microbiota and asthma.},
journal = {Frontiers in allergy},
volume = {4},
number = {},
pages = {1297425},
pmid = {38033919},
issn = {2673-6101},
}

@article {pmid38033643,
year = {2023},
author = {Centeno-Martinez, RE and Klopp, RN and Koziol, J and Boerman, JP and Johnson, TA},
title = {Dynamics of the nasopharyngeal microbiome of apparently healthy calves and those with clinical symptoms of bovine respiratory disease from disease diagnosis to recovery.},
journal = {Frontiers in veterinary science},
volume = {10},
number = {},
pages = {1297158},
pmid = {38033643},
issn = {2297-1769},
abstract = {INTRODUCTION: Bovine respiratory disease (BRD) is a multifactorial disease complex in which bacteria in the upper respiratory tract play an important role in disease development. Previous studies have related the presence of four BRD-pathobionts (Mycoplasma bovis, Histophilus somni, Pasteurella multocida, and Mannheimia haemolytica) in the upper respiratory tract to BRD incidence and mortalities in the dairy and beef cattle industry, but these studies typically only use one time point to compare the abundance of BRD-pathobionts between apparently healthy and BRD-affected cattle. The objective of this study was to characterize the longitudinal development of the nasopharyngeal (NP) microbiome from apparently healthy calves, and in calves with clinical signs of BRD, the microbiota dynamics from disease diagnosis to recovery.

METHODS: Deep nasopharyngeal swabs were taken from all calves immediately after transport (day 0). If a calf was diagnosed with BRD (n = 10), it was sampled, treated with florfenicol or tulathromycin, and sampled again 1, 5, and 10 days after antibiotic administration. Otherwise, healthy calves (n = 20) were sampled again on days 7 and 14. Bacterial community analysis was performed through 16S rRNA gene amplicon sequencing.

RESULTS: The NP microbiome of the healthy animals remained consistent throughout the study, regardless of time. The NP microbiota beta diversity and community composition was affected by tulathromycin or florfenicol administration. Even though BRD-pathobionts were identified by 16S rRNA gene sequencing in BRD-affected animals, no difference was observed in their relative abundance between the BRD-affected and apparently healthy animals. The abundance of BRD-pathobionts was not predictive of disease development while the relative abundance of BRD pathobionts was unique to each BRD-affected calf. Interestingly, at the end of the study period, the genera Mycoplasma was the most abundant genus in the healthy group, while Lactobacillus was the most abundant genus in the animals that recovered from BRD.

DISCUSSION: This study highlights that injected antibiotics seem to improve the NP microbiome composition (higher abundance of Lactobacillus and lower abundance of Mycoplasma), and that the relative abundance of BRD-pathobionts differs between individual calves but is not strongly predictive of BRD clinical signs, indicating that additional factors are likely important in the clinical progression of BRD.},
}

@article {pmid38033611,
year = {2023},
author = {Lin, Y and Lourenco, JM and Olukosi, OA},
title = {Effects of xylanase, protease, and xylo-oligosaccharides on growth performance, nutrient utilization, short chain fatty acids, and microbiota in Eimeria-challenged broiler chickens fed high fiber diet.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {15},
number = {},
pages = {430-442},
pmid = {38033611},
issn = {2405-6383},
abstract = {A 21-d experiment was conducted to study the effect of xylanase, protease, and xylo-oligosaccharides on growth performance, nutrient utilization, gene expression of nutrient transporters, cecal short-chain fatty acids (SCFA), and cecal microbiota profile of broilers challenged with mixed Eimeria spp. The study utilized 392 zero-d-old male broiler chicks allocated to 8 treatments in a 4 × 2 factorial arrangement, as follows: corn-soybean meal diet with no enzyme (Con); Con plus xylanase alone (XYL); Con plus xylanase combined with protease (XYL + PRO); or Con plus xylo-oligosaccharides (XOS); with or without Eimeria challenge. Diets were based on a high-fiber (100 g/kg soluble fibers and 14 g/kg insoluble fibers) basal diet. At d 15, birds in challenged treatment were gavaged with a solution containing Eimeria maxima, Eimeria acervulina, and Eimeria tenella oocysts. At d 21, birds were sampled. Eimeria depressed (P < 0.01) growth performance and nutrient utilization, whereas supplementation had no effect. There were significant Eimeria × supplementation interactions for the sugar transporters GLUT5 (P = 0.02), SGLT1 (P = 0.01), SGLT4 (P < 0.01), and peptide transporter PepT1 (P < 0.01) in jejunal mucosa. Eimeria challenge increased the expression of GM-CSF2 (P < 0.01) and IL-17 (P = 0.04) but decreased (P = 0.03) IL-1β expression in the cecal tonsil. Eimeria × supplementation interactions for cecal acetate, butyrate, and total SCFA showed that concentrations increased or tended to be greater in the supplemented treatments, but only in non-challenged birds. Birds challenged with Eimeria spp. had higher concentrations of isobutyrate (P < 0.01), isovalerate (P < 0.01), and valerate (P = 0.02) in cecal content. Eimeria challenge significantly (P < 0.01) decreased the microbial richness and diversity, and increased (P < 0.01) the proportion of Anaerostipes butyraticus, Bifidobacterium pseudolongum, and Lactobacillus pontis. In conclusion, Eimeria infection depressed growth performance, nutrient utilization with regulating nutrient transporters. Furthermore, Eimeria challenge shifted the microbial profile and reduced microbial richness and diversity. On the other hand, enzyme supplementation showed limited benefits, which included increased concentrations of SCFA.},
}

@article {pmid38033603,
year = {2023},
author = {Yuan, L and Zhu, C and Gu, F and Zhu, M and Yao, J and Zhu, C and Li, S and Wang, K and Hu, P and Zhang, Y and Cai, D and Liu, HY},
title = {Lactobacillus johnsonii N5 from heat stress-resistant pigs improves gut mucosal immunity and barrier in dextran sodium sulfate-induced colitis.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {15},
number = {},
pages = {210-224},
pmid = {38033603},
issn = {2405-6383},
abstract = {Developing effective strategies to prevent diarrhea and associated-gut disorders in mammals has gained great significance. Owing to the many health benefits provided by the commensal microbiota of the intestinal tract, such as against environmental perturbation, we explored the host phenotype-associated microbes and their probiotic potential. Based on the observations that the chronic heat stress-exposed weaned piglets present as heat stress-susceptible (HS-SUS) or heat stress-resistant (HS-RES) individuals, we confirmed the phenotypic difference between the two on growth performance (P < 0.05), diarrhea index (P < 0.001), intestinal heat shock protein 70 (HSP70) regulation (P < 0.01), and inflammatory responses (P < 0.01). By comparing the gut microbiome using 16S rRNA gene sequencing and KEGG functional analysis, we found that Lactobacillus johnsonii exhibited significantly higher relative abundance in the HS-RES piglets than in the HS-SUS ones (P < 0.05). Further experiments using a mouse model for chemical-induced inflammation and intestinal injury demonstrated that oral administration of a representative L. johnsonii N5 (isolated from the HS-RES piglets) ameliorated the clinical and histological signs of colitis while suppressing intestinal pro-inflammatory cytokines TNF-α and IL-6 production (P < 0.05). We found that N5 treatment enhanced tight junction proteins ZO-1 and occludin and cytoprotective HSP70 levels under physiological condition and restored their mucosal expressions in colitis (P < 0.05). In support of the high production of the anti-inflammatory cytokine IL-10, N5 promoted the intestinal Peyer's patches MHCII[+] and CD103[+] dendritic cell populations (P < 0.05), increased the regulatory T (Treg) cell numbers (P < 0.05), and decreased the Th17 population and its IL-17a production under physiological condition and during colitis (P < 0.01). Our results shed light on understanding the interaction between commensal Lactobacillus and the host health, and provide L. johnsonii N5 as an alternative to antibiotics for preventing diarrhea and intestinal diseases.},
}

@article {pmid38033594,
year = {2023},
author = {Fujita, H and Ushio, M and Suzuki, K and Abe, MS and Yamamichi, M and Okazaki, Y and Canarini, A and Hayashi, I and Fukushima, K and Fukuda, S and Kiers, ET and Toju, H},
title = {Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1261137},
pmid = {38033594},
issn = {1664-302X},
abstract = {Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).},
}

@article {pmid38033589,
year = {2023},
author = {Liu, Z and Liu, X},
title = {Gut microbiome, metabolome and alopecia areata.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1281660},
pmid = {38033589},
issn = {1664-302X},
abstract = {Alopecia areata (AA) is a type of dermatological disease characterized by rapid and non-scarring hair loss of the scalp or body skin that may be related to genetic, immunological and physiological factors. It is now believed that AA is associated with oxidative stress, autoimmune disease, neuropsychological factors, pathogens, immune checkpoint inhibitors and microecological imbalance under the premise of host genetic susceptibility. In recent years, studies have revealed the significant role of the gut microbiome or metabolome in many aspects of human health. Diverse studies have revealed that the gut microbiome and metabolome have an important influence on skin conditions. This review highlights the relationship between AA and the gut microbiome or metabolome to provide novel directions for the prevention, clinical diagnosis and treatment of AA.},
}

@article {pmid38033568,
year = {2023},
author = {Seo, JY and You, SW and Gu, KN and Kim, H and Shin, JG and Leem, S and Hwang, BK and Kim, Y and Kang, NG},
title = {Longitudinal study of the interplay between the skin barrier and facial microbiome over 1 year.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1298632},
pmid = {38033568},
issn = {1664-302X},
abstract = {Skin is a diverse ecosystem that provides a habitat for microorganisms. The skin condition and the skin microbiome interact each other under diverse environmental conditions. This study was conducted on 10 study participants for a one-year, from September 2020 to August 2021, to investigate the variability of skin microbiome and skin biophysical parameters [TEWL, hydration, and elasticity (R5)] according to season, and to understand the interplay between skin microbiome and skin characteristics. We identified that Cutibacterium, Corynebacterium, Staphyloccocus, unclassified genus within Neisseriaceae, and Streptococcus were major skin microbial taxa at the genus level, and fluctuated with the seasons. Cutibacterium was more abundant in winter, while Corynebacterium, Staphylococcus, and Streptococcus were more abundant in summer. Notably, Cutibacterium and skin barrier parameter, TEWL, exhibited a co-decreasing pattern from winter to summer and showed a significant association between Cutibacterium and TEWL. Furthermore, functional profiling using KEGG provided clues on the impact of Cutibacterium on the host skin barrier. This study enhances our understanding of the skin microbiome and its interplay with skin characteristics and highlights the importance of seasonal dynamics in shaping skin microbial composition.},
}

@article {pmid38033481,
year = {2023},
author = {Bai, J and Wei, JQ and Tian, Q and Xue, F and Zhang, W and He, H},
title = {The impact of electroacupuncture on anxiety-like behavior and gut microbiome in a mouse model of chronic restraint stress.},
journal = {Frontiers in behavioral neuroscience},
volume = {17},
number = {},
pages = {1292835},
pmid = {38033481},
issn = {1662-5153},
abstract = {INTRODUCTION: Electroacupuncture (EA) is a beneficial physiotherapy approach for addressing neuropsychiatric disorders. Nevertheless, the impact of EA on the gut microbiome in relation to anxiety disorders remains poorly understood.

METHODS: To address this gap, we conducted a study using a chronic restraint stress (CRS) mouse model to investigate the anti-anxiety outcome of EA and its influence on gut microbiota. Our research involved behavioral tests and comprehensive sequencing of full-length 16S rRNA microbiomes.

RESULTS: Our findings revealed that CRS led to significant anxiety-like behaviors and an imbalance in the gut microbiota. Specifically, we identified 13 species that exhibited changes associated with anxiety-like behaviors. Furthermore, EA partially alleviated both behaviors related to anxiety and the dysbiosis induced by CRS.

DISCUSSION: In summary, this study sheds light on the alterations in gut microbiota species resulting from CRS treatment and brings new light into the connection between EA's anti-anxiety effects and the gut microbiota.},
}

@article {pmid38032916,
year = {2023},
author = {Sondo, M and Wonni, I and Koïta, K and Rimbault, I and Barro, M and Tollenaere, C and Moulin, L and Klonowska, A},
title = {Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0287084},
pmid = {38032916},
issn = {1932-6203},
abstract = {Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.},
}

@article {pmid38032828,
year = {2023},
author = {Micks, E and Reed, S and Mitchell, C},
title = {The Postmenopausal Vaginal Microbiome and Genitourinary Syndrome of Menopause.},
journal = {Clinical obstetrics and gynecology},
volume = {},
number = {},
pages = {},
pmid = {38032828},
issn = {1532-5520},
abstract = {This review summarizes our current understanding of associations of the postmenopausal vaginal microbiome with genitourinary syndrome of menopause. We review the normal postmenopausal microbiota, examine the association of the microbiome with vulvovaginal symptoms, describe microbial communities associated with physical and laboratory findings, and report the impact of different treatments for genitourinary syndrome of menopause on microbiota and symptom improvement. Postmenopausal vaginal symptoms have an underlying pathophysiology that has not been fully elucidated. Estrogen treatment may not be sufficient to relieve symptoms of vaginal discomfort in all postmenopausal individuals. In addition, other interventions targeted at changing the microbiota or pH do not consistently improve symptom severity.},
}

@article {pmid38032704,
year = {2023},
author = {Lednovich, KR and Gough, S and Priyadarshini, M and Pandya, N and Nnyamah, C and Xu, K and Wicksteed, B and Mishra, S and Jain, S and Zapater, JL and Cordoba-Chacon, J and Yadav, H and Layden, B},
title = {Intestinal FFA2 promotes obesity by altering food intake in Western diet-fed mice.},
journal = {The Journal of endocrinology},
volume = {},
number = {},
pages = {},
doi = {10.1530/JOE-23-0184},
pmid = {38032704},
issn = {1479-6805},
abstract = {Short-chain fatty acids (SCFAs) are key nutrients that play a diverse set of roles in physiological function, including regulating metabolic homeostasis. Generated through the fermentation of dietary fibers in the distal colon by the gut microbiome, SCFAs and their effects are partially mediated by their cognate receptors, including free fatty acid receptor 2 (FFA2). FFA2 is highly expressed in the intestinal epithelial, where its putative functions are controversial, with numerous in vivo studies relying on global knockout mouse models to characterize intestine-specific roles of the receptor. Here, we used the Villin-Cre mouse line to generate a novel, intestine-specific knockout mouse model for FFA2 (Vil-FFA2) to investigate receptor function within the intestine. Because dietary changes are known to affect the composition of the gut microbiome, and can thereby alter SCFA production, we performed an obesogenic challenge on male Vil-FFA2 mice and their littermate controls (FFA2-floxed, FFA2fl/fl) to identify physiological changes on a high-fat, high-sugar "Western diet" (WD) compared to a low-fat control diet (CD). We found that the WD-fed Vil-FFA2 mice were transiently protected from the obesogenic effects of the WD, and had lower fat mass and improved glucose homeostasis compared to the WD-fed FFA2fl/fl control group during the first half of the study. Additionally, major differences in respiratory exchange ratio and energy expenditure were observed in the WD-fed Vil-FFA2 mice, and food intake was found to be significantly reduced at multiple points in the study. Taken together, this study uncovers a novel role of intestinal FFA2 in mediating the development of obesity.},
}

@article {pmid38032526,
year = {2023},
author = {Dong, X and Deng, L and Su, Y and Han, X and Yao, S and Wu, W and Cao, J and Tian, L and Bai, Y and Wang, G and Ren, W},
title = {Curcumin alleviates traumatic brain injury induced by gas explosion through modulating gut microbiota and suppressing the LPS/TLR4/MyD88/NF-κB pathway.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {38032526},
issn = {1614-7499},
support = {U2004102//National Natural Science Foundation of China/ ; U1904209//National Natural Science Foundation of China/ ; 232102311071//Henan Provincial Science and Technology Research Project/ ; 202300410312//Natural Science Foundation of Henan Province/ ; },
abstract = {Gas explosions (GE) are a prevalent and widespread cause of traumatic brain injury (TBI) in coal miners. However, the impact and mechanism of curcumin on GE-induced TBI in rats remain unclear. In this study, we simulated GE-induced TBI in rats and administered curcumin orally at a dose of 100 mg/kg every other day for 7 days to modulate the gut microbiota in TBI rats. We employed 16S rRNA sequencing and LC-MS/MS metabolomic analysis to investigate changes in the intestinal flora and its metabolic profile. Additionally, we utilized ELISA, protein assays, and immunohistochemistry to assess neuroinflammatory signaling molecules for validation. In a rat TBI model, GE resulted in weight loss, pathological abnormalities, and cortical hemorrhage. Treatment with curcumin significantly mitigated histological abnormalities and microscopic mitochondrial structural changes in brain tissue. Furthermore, curcumin treatment markedly ameliorated GE-induced brain dysfunction by reducing the levels of several neuroinflammatory signaling molecules, including neuron-specific enolase, interleukin (IL)-1β, IL-6, and cryptothermic protein 3. Notably, curcumin reshaped the gut microbiome by enhancing evenness, richness, and composition. Prevotella_9, Alloprevotella, Bacilli, Lactobacillales, Proteobacteria, and Gammaproteobacteria were identified as prominent members of the gut microbiota, increasing the linear discriminant analysis scores and specifically enhancing the abundance of bacteria involved in the nuclear factor (NF)-κB signaling pathway, such as Lachnospiraceae and Roseburia. Additionally, there were substantial alterations in serum metabolites associated with metabolic NF-κB signaling pathways in the model group. Curcumin administration reduced serum lipopolysaccharide levels and downregulated downstream Toll-like receptor (TLR)4/myeloid differentiation primary response 88 (MyD88)/NF-κB signaling. Furthermore, curcumin alleviated GE-induced TBI in rats by modulating the gut microbiota and its metabolites. Based on these protective effects, curcumin may exert its influence on the gut microbiota and the TLR4/MyD88/NF-κB signaling pathways to ameliorate GE-induced TBI.},
}

@article {pmid38032332,
year = {2023},
author = {Zawadzka-Głos, L},
title = {Microbiota and antibiotic therapy in rhinosinusitis.},
journal = {Otolaryngologia polska = The Polish otolaryngology},
volume = {77},
number = {5},
pages = {36-42},
doi = {10.5604/01.3001.0053.8709},
pmid = {38032332},
issn = {2300-8423},
mesh = {Humans ; *Sinusitis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; *Microbiota ; *Nasal Polyps ; },
abstract = {Rhinosinusitis is one of the most frequently diagnosed diseases in patients seeking medical consultation. Sinusitis is a heterogeneous group of diseases and can be acute or chronic. The current state of knowledge on rhinosinusitis is presented in the recommendations of the European Position Paper on Rhinosynusitis and Nasal Polyps 2020 (EPOS 2020). More and more attention is paid to the condition of the microbiota in the context of inflammatory changes in the sinuses. There is also a negative effect of excessively prescribed antibiotics on the increase in bacterial resistance to drugs and significant changes in the disturbance in the composition of the microbiota during antibiotic therapy. Since the most common etiology of acute sinusitis is viral, the use of antibiotics in uncomplicated sinusitis is unjustified. New therapeutic solutions are sought, including the use of herbal medicines. The EPOS 2020 document recommends the use of BNO 1016 in uncomplicated acute rhinosinusitis. New models of treatment also take into account the use of biological drugs, especially in the treatment of chronic rhinosinusitis.},
}

Humans
*Sinusitis/drug therapy
Anti-Bacterial Agents/therapeutic use
*Microbiota
*Nasal Polyps

@article {pmid38032239,
year = {2023},
author = {Bowen, M and Farag, IF and Main, CR and Biddle, JF},
title = {Reference library for microbial source tracking in the mid-Atlantic United States.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0067423},
doi = {10.1128/MRA.00674-23},
pmid = {38032239},
issn = {2576-098X},
abstract = {Microbial source tracking can determine fecal contamination but requires a relevant, sizable reference library for analysis. We provide a reference library of 100+ fecal microbiome samples relevant to mid-Atlantic United States ecosystems. Included are wild and domesticated fauna, wastewater, and septic samples applicable to Delaware source tracking studies.},
}

@article {pmid38032203,
year = {2023},
author = {Tahiri, M and Johnsrud, C and Steffensen, IL},
title = {Evidence and hypotheses on adverse effects of the food additives carrageenan (E 407)/processed Eucheuma seaweed (E 407a) and carboxymethylcellulose (E 466) on the intestines: a scoping review.},
journal = {Critical reviews in toxicology},
volume = {},
number = {},
pages = {1-51},
doi = {10.1080/10408444.2023.2270574},
pmid = {38032203},
issn = {1547-6898},
abstract = {This scoping review provides an overview of publications reporting adverse effects on the intestines of the food additives carrageenan (CGN) (E 407)/processed Eucheuma seaweed (PES) (E 407a) and carboxymethylcellulose (CMC) (E 466). It includes evidence from human, experimental mammal and in vitro research publications, and other evidence. The databases Medline, Embase, Scopus, Web of Science Core Collection, Cochrane Database of Systematic Reviews and Epistemonikos were searched without time limits, in addition to grey literature. The publications retrieved were screened against predefined criteria. From two literature searches, 2572 records were screened, of which 224 records were included, as well as 38 records from grey literature, making a total of 262 included publications, 196 on CGN and 101 on CMC. These publications were coded and analyzed in Eppi-Reviewer and data gaps presented in interactive maps. For CGN, five, 69 and 33 research publications on humans, experimental mammals and in vitro experiments were found, further separated as degraded or native (non-degraded) CGN. For CMC, three human, 20 animal and 14 in vitro research publications were obtained. The most studied adverse effects on the intestines were for both additives inflammation, the gut microbiome, including fermentation, intestinal permeability, and cancer and metabolic effects, and immune effects for CGN. Further studies should focus on native CGN, in the form and molecular weight used as food additive. For both additives, randomized controlled trials of sufficient power and with realistic dietary exposure levels of single additives, performed in persons of all ages, including potentially vulnerable groups, are needed.},
}

@article {pmid38031529,
year = {2023},
author = {Sanders, WB},
title = {The disadvantages of current proposals to redefine lichens: A comment on Hawksworth & Grube (2020): 'Lichens redefined as complex ecosystems'.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19321},
pmid = {38031529},
issn = {1469-8137},
}

@article {pmid38031491,
year = {2023},
author = {Kim, SH and Choi, Y and Oh, J and Lim, EY and Lee, JE and Song, EJ and Nam, YD and Kim, H},
title = {Associations among the Duodenal Ecosystem, Gut Microbiota, and Nutrient Intake in Functional Dyspepsia.},
journal = {Gut and liver},
volume = {},
number = {},
pages = {},
doi = {10.5009/gnl230130},
pmid = {38031491},
issn = {2005-1212},
abstract = {BACKGROUND/AIMS: : Functional dyspepsia (FD) has long been regarded as a syndrome because its pathophysiology is multifactorial. However, recent reports have provided evidence that changes in the duodenal ecosystem may be the key. This study aimed to identify several gastrointestinal factors and biomarkers associated with FD, specifically changes in the duodenal ecosystem that may be key to understanding its pathophysiology.

METHODS: : In this case-control study, 28 participants (12 with FD and 16 healthy control individuals) were assessed for dietary nutrients, gastrointestinal symptom severity, immunological status of the duodenal mucosa, and microbiome composition from oral, duodenal, and fecal samples. Integrated data were analyzed using immunohistochemistry, real-time polymerase chain reaction, 16S rRNA sequencing, and network analysis.

RESULTS: : Duodenal mucosal inflammation and impaired expression of tight junction proteins were confirmed in patients with FD. The relative abundance of duodenal Streptococcus (p=0.014) and reductions in stool Butyricicoccus (p=0.047) were confirmed. These changes in the gut microbiota were both correlated with symptom severity. Changes in dietary micronutrients, such as higher intake of valine, were associated with improved intestinal barrier function and microbiota.

CONCLUSIONS: : This study emphasizes the relationships among dietary nutrition, oral and gut microbiota, symptoms of FD, impaired function of the duodenal barrier, and inflammation. Assessing low-grade inflammation or increased permeability in the duodenal mucosa, along with changes in the abundance of stool Butyricicoccus, is anticipated to serve as effective biomarkers for enhancing the objectivity of FD diagnosis and monitoring.},
}

@article {pmid38031487,
year = {2023},
author = {Hawksworth, DL and Grube, M},
title = {Reflections on lichens as ecosystems.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19418},
pmid = {38031487},
issn = {1469-8137},
}

@article {pmid38031339,
year = {2023},
author = {Kamenova, S and de Muinck, EJ and Veiberg, V and Utsi, TA and Steyaert, SMJG and Albon, SD and Loe, LE and Trosvik, P},
title = {Gut microbiome biogeography in reindeer supersedes millennia of ecological and evolutionary separation.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiad157},
pmid = {38031339},
issn = {1574-6941},
abstract = {Ruminants are dependent on their gut microbiomes for nutrient extraction from plant diets. However, knowledge about the composition, diversity, function, and spatial structure of gut microbiomes, especially in wild ruminants, is limited, largely because analysis has been restricted to faeces or the rumen. In two geographically separated reindeer subspecies, 16S rRNA gene amplicon sequencing revealed strong spatial structuring, and pronounced differences in microbial diversity of at least 33 phyla across the stomach, small intestine, and large intestine (including faeces). The main structural feature was the Bacteroidota to Firmicutes ratio, which declined from the stomachs to the large intestine, likely reflecting functional adaptation. Metagenome shotgun sequencing also revealed highly significant structuring in the relative occurrence of carbohydrate-active enzymes (CAZymes). CAZymes were enriched in the rumen relative to the small and large intestine. Interestingly, taxonomic diversity was highest in the large intestine, suggesting an important and understudied role for this organ. Despite the two study populations being separated by an ocean and six millennia of evolutionary history, gut microbiome structuring was remarkably consistent. Our study suggests a strong selection for gut microbiome biogeography along the gastrointestinal tract in reindeer subspecies.},
}

@article {pmid38031252,
year = {2023},
author = {Crossland, NA and Beck, S and Tan, WY and Lo, M and Mason, JB and Zhang, C and Guo, W and Crott, JW},
title = {Fecal microbiota transplanted from old mice promotes more colonic inflammation, proliferation, and tumor formation in azoxymethane-treated A/J mice than microbiota originating from young mice.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2288187},
doi = {10.1080/19490976.2023.2288187},
pmid = {38031252},
issn = {1949-0984},
abstract = {Aging is a strong risk factor for colorectal cancer (CRC). It is well established that gut microbial dysbiosis can play a role in the etiology of CRC. Although the composition of the gut microbial community changes with age and is reported to become more pro-inflammatory, it is unclear whether such changes are also pro-tumorigenic for the colon. To address this gap, we conducted fecal microbiota transplants (FMT) from young (DY, ~6 wk) and old (DO, ~72 wk) donor mice into young (8 wk) recipient mice that were pre-treated with antibiotics. After initiating tumorigenesis with azoxymethane, recipients were maintained for 19 wk during which time they received monthly FMT boosters. Compared to recipients of young donors (RY), recipients of old donors (RO) had an approximately 3-fold higher prevalence of histologically confirmed colon tumors (15.8 vs 50%, Chi2 P = .03), approximately 2-fold higher proliferating colonocytes as well as significantly elevated colonic IL-6, IL-1β and Tnf-α. Transcriptomics analysis of the colonic mucosa revealed a striking upregulation of mitochondria-related genes in the RO mice, a finding corroborated by increased mitochondrial abundance. Amongst the differences in fecal microbiome observed between DY and DO mice, the genera Ruminoclostridium, Lachnoclostridium and Marvinbryantia were more abundant in DY mice while the genera Bacteroides and Akkermansia were more abundant in DO mice. Amongst recipients, Ruminoclostridium and Lachnoclostridium were higher in RY mice while Bacteroides was higher in RO mice. Differences in fecal microbiota were observed between young and old mice, some of which persisted upon transplant into recipient mice. Recipients of old donors displayed significantly higher colonic proliferation, inflammation and tumor abundance compared to recipients of young donors. These findings support an etiological role for altered gut microbial communities in the increased risk for CRC with increasing age and establishes that such risk can be transmitted between individuals.},
}

@article {pmid38031142,
year = {2023},
author = {Holm, JB and France, MT and Gajer, P and Ma, B and Brotman, RM and Shardell, M and Forney, L and Ravel, J},
title = {Integrating compositional and functional content to describe vaginal microbiomes in health and disease.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {259},
pmid = {38031142},
issn = {2049-2618},
support = {R01-NR015495/NR/NINR NIH HHS/United States ; },
abstract = {BACKGROUND: A Lactobacillus-dominated vaginal microbiome provides the first line of defense against adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this gap, we developed metagenomic community state types (mgCSTs) which use metagenomic sequences to describe and define vaginal microbiomes based on both composition and functional potential.

RESULTS: MgCSTs are categories of microbiomes classified using taxonomy and the functional potential encoded in their metagenomes. MgCSTs reflect unique combinations of metagenomic subspecies (mgSs), which are assemblages of bacterial strains of the same species, within a microbiome. We demonstrate that mgCSTs are associated with demographics such as age and race, as well as vaginal pH and Gram stain assessment of vaginal smears. Importantly, these associations varied between mgCSTs predominated by the same bacterial species. A subset of mgCSTs, including three of the six predominated by Gardnerella vaginalis mgSs, as well as mgSs of L. iners, were associated with a greater likelihood of bacterial vaginosis diagnosed by Amsel clinical criteria. This L. iners mgSs, among other functional features, encoded enhanced genetic capabilities for epithelial cell attachment that could facilitate cytotoxin-mediated cell lysis. Finally, we report a mgSs and mgCST classifier for which source code is provided and may be adapted for use by the microbiome research community.

CONCLUSIONS: MgCSTs are a novel and easily implemented approach to reduce the dimension of complex metagenomic datasets while maintaining their functional uniqueness. MgCSTs enable the investigation of multiple strains of the same species and the functional diversity in that species. Future investigations of functional diversity may be key to unraveling the pathways by which the vaginal microbiome modulates the protection of the genital tract. Importantly, our findings support the hypothesis that functional differences between vaginal microbiomes, including those that may look compositionally similar, are critical considerations in vaginal health. Ultimately, mgCSTs may lead to novel hypotheses concerning the role of the vaginal microbiome in promoting health and disease, and identify targets for novel prognostic, diagnostic, and therapeutic strategies to improve women's genital health. Video Abstract.},
}

@article {pmid38031016,
year = {2023},
author = {Li, P and Jiang, J and Li, Y and Lan, Y and Yang, F and Wang, J and Xie, Y and Xiong, F and Wu, J and Liu, H and Fan, Z},
title = {Metagenomic analysis reveals distinct changes in the gut microbiome of obese Chinese children.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {721},
pmid = {38031016},
issn = {1471-2164},
support = {No. 2023YFS0034 and 2020YFS0109//the Science and Technology Bureau of Sichuan Province/ ; No. KL119//the Clinical Discipline Development Fund of West China Second Hospital, Sichuan University/ ; SCU2022D022//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: The prevalence of obese children in China is increasing, which poses a great challenge to public health. Gut microbes play an important role in human gut health, and changes in gut status are closely related to obesity. However, how gut microbes contribute to obesity in children remains unclear. In our study, we performed shotgun metagenomic sequencing of feces from 23 obese children, 8 overweight children and 22 control children in Chengdu, Sichuan, China.

RESULTS: We observed a distinct difference in the gut microbiome of obese children and that of controls. Compared with the controls, bacterial pathogen Campylobacter rectus was significantly more abundant in obese children. In addition, functional annotation of microbial genes revealed that there might be gut inflammation in obese children. The guts of overweight children might belong to the transition state between obese and control children due to a gradient in relative abundance of differentially abundant species. Finally, we compared the gut metagenomes of obese Chinese children and obese Mexican children and found that Trichuris trichiura was significantly more abundant in the guts of obese Mexican children.

CONCLUSIONS: Our results contribute to understanding the changes in the species and function of intestinal microbes in obese Chinese children.},
}

@article {pmid38030903,
year = {2023},
author = {Lutz, S and Bodenhausen, N and Hess, J and Valzano-Held, A and Waelchli, J and Deslandes-Hérold, G and Schlaeppi, K and van der Heijden, MGA},
title = {Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi.},
journal = {Nature microbiology},
volume = {8},
number = {12},
pages = {2277-2289},
pmid = {38030903},
issn = {2058-5276},
support = {GRS-072/17//Gebert Rüf Stiftung (Gebert Rüf Foundation)/ ; GRS-088/20//Gebert Rüf Stiftung (Gebert Rüf Foundation)/ ; GRS-072/17//Gebert Rüf Stiftung (Gebert Rüf Foundation)/ ; 40IN40_215832 / 1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 40IN40_215832 / 1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 40IN40_215832 / 1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {Alternative solutions to mineral fertilizers and pesticides that reduce the environmental impact of agriculture are urgently needed. Arbuscular mycorrhizal fungi (AMF) can enhance plant nutrient uptake and reduce plant stress; yet, large-scale field inoculation trials with AMF are missing, and so far, results remain unpredictable. We conducted on-farm experiments in 54 fields in Switzerland and quantified the effects on maize growth. Growth response to AMF inoculation was highly variable, ranging from -12% to +40%. With few soil parameters and mainly soil microbiome indicators, we could successfully predict 86% of the variation in plant growth response to inoculation. The abundance of pathogenic fungi, rather than nutrient availability, best predicted (33%) AMF inoculation success. Our results indicate that soil microbiome indicators offer a sustainable biotechnological perspective to predict inoculation success at the beginning of the growing season. This predictability increases the profitability of microbiome engineering as a tool for sustainable agricultural management.},
}

@article {pmid38030898,
year = {2023},
author = {Gancz, AS and Farrer, AG and Nixon, MP and Wright, S and Arriola, L and Adler, C and Davenport, ER and Gully, N and Cooper, A and Britton, K and Dobney, K and Silverman, JD and Weyrich, LS},
title = {Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain.},
journal = {Nature microbiology},
volume = {8},
number = {12},
pages = {2315-2325},
pmid = {38030898},
issn = {2058-5276},
support = {DGE1255832//National Science Foundation (NSF)/ ; DGE1255832//National Science Foundation (NSF)/ ; },
abstract = {The prevalence of chronic, non-communicable diseases has risen sharply in recent decades, especially in industrialized countries. While several studies implicate the microbiome in this trend, few have examined the evolutionary history of industrialized microbiomes. Here we sampled 235 ancient dental calculus samples from individuals living in Great Britain (∼2200 BCE to 1853 CE), including 127 well-contextualized London adults. We reconstructed their microbial history spanning the transition to industrialization. After controlling for oral geography and technical biases, we identified multiple oral microbial communities that coexisted in Britain for millennia, including a community associated with Methanobrevibacter, an anaerobic Archaea not commonly prevalent in the oral microbiome of modern industrialized societies. Calculus analysis suggests that oral hygiene contributed to oral microbiome composition, while microbial functions reflected past differences in diet, specifically in dairy and carbohydrate consumption. In London samples, Methanobrevibacter-associated microbial communities are linked with skeletal markers of systemic diseases (for example, periostitis and joint pathologies), and their disappearance is consistent with temporal shifts, including the arrival of the Second Plague Pandemic. This suggests pre-industrialized microbiomes were more diverse than previously recognized, enhancing our understanding of chronic, non-communicable disease origins in industrialized populations.},
}

@article {pmid38030815,
year = {2023},
author = {Zhang, N and Zhu, W and Zhang, S and Liu, T and Gong, L and Wang, Z and Zhang, W and Cui, Y and Wu, Q and Li, J and Yu, H and El-Omar, EM and Hao, J and Lu, W},
title = {A Novel Bifidobacterium/Klebsiella Ratio in Characterization Analysis of the Gut and Bile Microbiota of CCA Patients.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {5},
pmid = {38030815},
issn = {1432-184X},
abstract = {Cholangiocarcinoma (CCA) is a serious health problem worldwide. The gut and bile microbiota have not been clearly characterized in patients with CCA, and better noninvasive diagnostic approaches for CCA need to be established. The aim of this study was to investigate the characteristics of the gut and bile microbiota in CCA patients. Forty-two CCA patients and 16 healthy normal controls (HNCs) were enrolled. DNA was extracted from fecal and bile samples and subjected to 16S rRNA gene analysis. We found that there were significant differences in the species diversity, structure, and composition of the microbial communities between the CCA group and the HNC grouAt the phylum level, compared with that in the HNC group, the relative abundance of Firmicutes and Actinobacteriota was significantly decreased in the CCA group, whereas Proteobacteria and Bacteroidota were significantly enriched. The Firmicutes/Bacteroidota (F/B) ratio significantly decreased in the CCA group compared to the HNC grouThe relative abundance of Klebsiella in the CCA group was significantly higher than that in the HNC group, while the relative abundance of Bifidobacterium was significantly decreased. The Bifidobacterium/Klebsiella (B/K) ratio was established as a novel biomarker and was found to be significantly decreased in the CCA group compared with the HNC grouOur findings provide evidence supporting the use of Klebsiella and Bifidobacterium as noninvasive intestinal microbiomarkers for improving the diagnosis of CCA.},
}

@article {pmid38030736,
year = {2023},
author = {Gajecka, M and Gutaj, P and Jaskiewicz, K and Rydzanicz, M and Szczapa, T and Kaminska, D and Kosewski, G and Przyslawski, J and Ploski, R and Wender-Ozegowska, E},
title = {Effects of maternal type 1 diabetes and confounding factors on neonatal microbiomes.},
journal = {Diabetologia},
volume = {},
number = {},
pages = {},
pmid = {38030736},
issn = {1432-0428},
support = {PSNC-534//Poznan Supercomputing and Networking Center/ ; Professor Artur Czyżyk' Scientific Grant 2015//Polish Diabetes Association/ ; Professor Artur Czyżyk' Scientific Grant 2017//Polish Diabetes Association/ ; 502-01-01110142-05618//Uniwersytet Medyczny im. Karola Marcinkowskiego w Poznaniu/ ; 502-14-03301402-09911//Uniwersytet Medyczny im. Karola Marcinkowskiego w Poznaniu/ ; },
abstract = {AIMS/HYPOTHESIS: Body niche-specific microbiota in maternal-neonatal dyads from gravidae with type 1 diabetes have not been quantitatively and functionally examined. Similarly, the impact of pregnancy-specific factors, such as the presence of comorbidities known to occur more frequently among gravidae with type 1 diabetes, including Caesarean delivery, as well as antibiotic prophylaxis, level of glycaemic control during each trimester of pregnancy and insulin administration, has not been adequately considered. The aims of this study were to characterise the maternal and neonatal microbiomes, assess aspects of microbiota transfer from the maternal microbiomes to the neonatal microbiome and explore the impact of type 1 diabetes and confounding factors on the microbiomes.

METHODS: In this observational case-control study, we characterised microbiome community composition and function using 16S rRNA amplicon sequencing in a total of 514 vaginal, rectal and ear-skin swabs and stool samples derived from 92 maternal-neonatal dyads (including 50 gravidae with type 1 diabetes) and in-depth clinical metadata from throughout pregnancy and delivery.

RESULTS: Type 1 diabetes-specific microbiota were identified among gravidae with type 1 diabetes and their neonates. Neonatal microbiome profiles of ear-skin swabs and stool samples were established, indicating the taxa more prevalent among neonates born to mothers with type 1 diabetes compared with neonates born to control mothers. Without taking into account the type 1 diabetes status of mothers, both delivery mode and intrapartum antibiotic prophylaxis were found to have an influence on neonatal microbiota composition (both p=0.001). In the logistic regression analysis involving all confounding variables, neonatal ear-skin microbiome variation was explained by maternal type 1 diabetes status (p=0.020) and small for gestational age birthweight (p=0.050). Moreover, in women with type 1 diabetes, a relationship was found between HbA1c levels >55 mmol/mol (>7.2%) measured in the first trimester of pregnancy and neonatal ear-skin microbiota composition (p=0.008). In the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) assessment, pathways concerning carbohydrate biosynthesis were predicted as key elements of the microbial functional profiles dysregulated in type 1 diabetes. Additionally, in SourceTracker analysis, we found that, on average, 81.0% of neonatal microbiota was attributed to maternal sources. An increase in the contribution of maternal rectum microbiota and decrease in the contribution of maternal cervix microbiota were found in ear-skin samples of vaginally delivered neonates of mothers with type 1 diabetes compared with neonates born to control mothers (83.2% vs 59.5% and 0.7% vs 5.2%, respectively).

CONCLUSIONS/INTERPRETATION: These findings indicate that, in addition to maternal type 1 diabetes, glycaemic dysregulation before/in the first trimester of pregnancy, mode of delivery and intrapartum antibiotic prophylaxis may contribute to the inoculation and formation of the neonatal microbiomes.

DATA AVAILABILITY: The BioProject (PRJNA961636) and associated SRA metadata are available at http://www.ncbi.nlm.nih.gov/bioproject/961636 . Processed data on probiotic supplementation and the PICRUSt analysis are available in the Mendeley Data Repository (https://doi.org/10.17632/g68rwnnrfk.1).},
}

@article {pmid38030652,
year = {2023},
author = {Bacci, G and Meriggi, N and Cheng, CLY and Ng, KH and Iannucci, A and Mengoni, A and Cavalieri, D and Cannicci, S and Fratini, S},
title = {Species-specific gill's microbiome of eight crab species with different breathing adaptations.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {21033},
pmid = {38030652},
issn = {2045-2322},
support = {207080320.088562.26020.430.01//Hong Kong Government/ ; 260008686.088562.26000.400.01//TUYF Charitable Trust funds, Hong Kong/ ; CN00000033//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; },
abstract = {Transitions to physically different environments, such as the water-to-land transition, proved to be the main drivers of relevant evolutionary events. Brachyuran crabs evolved remarkable morphological, behavioral, and physiological adaptations to terrestrial life. Terrestrial species evolved new respiratory structures devoted to replace or support the gills, a multifunctional organ devoted to gas exchanges, ion-regulation and nitrogen excretion. It was hypothesized that microorganisms associated with respiratory apparatus could have facilitated the processes of osmoregulation, respiration, and elimination of metabolites along this evolutionary transition. To test if crab species with different breathing adaptations may host similar microbial communities on their gills, we performed a comparative targeted-metagenomic analysis, selecting two marine and six terrestrial crabs belonging to different families and characterised by different breathing adaptations. We analysed anterior and posterior gills separately according to their different and specific roles. Regardless of their terrestrial or marine adaptations, microbial assemblages were strongly species-specific indicating a non-random association between the host and its microbiome. Significant differences were found in only two terrestrial species when considering posterior vs. anterior gills, without any association with species-specific respiratory adaptations. Our results suggest that all the selected species are strongly adapted to the ecological niche and specific micro-habitat they colonise.},
}

@article {pmid38030540,
year = {2023},
author = {Holers, VM},
title = {Are there causal mucosal drivers in the preclinical development of rheumatoid arthritis?.},
journal = {Seminars in arthritis and rheumatism},
volume = {},
number = {},
pages = {152324},
doi = {10.1016/j.semarthrit.2023.152324},
pmid = {38030540},
issn = {1532-866X},
abstract = {BACKGROUND: The causal pathways which drive the development of seropositive rheumatoid arthritis (RA) are incompletely understood, especially in the period of time prior to the first development of signs and symptoms of joint involvement. That asymptomatic period, designated herein as pre-RA, is characterized by the presence of RA-related autoantibodies for many years and is the subject of an increasing number of studies as well as a focus of efforts to prevent the onset of clinically apparent arthritis.

OBJECTIVES: To review the potential causal pathways in pre-RA by examining results of studies which evaluate the systemic peripheral blood and mucosal alterations that have been identified in individuals who are genetically at-risk, and/or who elaborate RA-related autoantibodies, and are defined as in a pre-RA period.

METHODS: Published studies by the author and his colleagues, as well as publications by other groups, which describe the presence of biomarkers at mucosal sites and in the blood were reviewed. From these studies, a hypothesis related to the presence of pre-RA causal drivers was constructed.

RESULTS: The author and his colleagues, as well as other groups, have shown that there are multiple mucosal sites, primarily gut, lung and oral/peridontial, which appear in subsets of individuals in the pre-RA to exhibit inflammation and/or the presence of local production of IgA and IgG RA-related autoantibodies, including anti-citrullinated protein antibodies (ACPA). These findings are reviewed herein. There remain a large number of unanswered questions, though, related to the immune mechanisms that are operative at each site, as well as how these local findings evolve to causal systemic autoimmunity and eventually inflammatory arthritis.

AUTHOR'S CONCLUSIONS: Comprehensive natural history studies are required to understand how multiple mucosal sites which appear to be involved in pre-RA are causally involved in the development of arthritis. Questions remain as to whether there are independent, serially involved, or inter-related causal immune pathways originating from these sites. In addition, the microbiota which may be involved in local immune inflammation and autoantibody production should be identified and characterized.},
}

@article {pmid38030382,
year = {2023},
author = {Song, CH and Kim, N and Nam, RH and Choi, SI and Jang, JY and Kim, EH and Choi, J and Choi, Y and Yoon, H and Lee, SM},
title = {The Possible Preventative Role of Lactate- and Butyrate-Producing Bacteria in Colorectal Carcinogenesis.},
journal = {Gut and liver},
volume = {},
number = {},
pages = {},
doi = {10.5009/gnl230385},
pmid = {38030382},
issn = {2005-1212},
abstract = {BACKGROUND/AIMS: : The gut microbiome has emerged as a key player that mechanistically links various risk factors to colorectal cancer (CRC) etiology. However, the role of the gut microbiome in CRC pathogenesis remains unclear. This study aimed to characterize the gut microbiota in healthy controls (HCs) and patients with colorectal adenoma (AD) and CRC in subgroups based on sex and age.

METHODS: : Study participants who visited the hospital for surveillance of CRC or gastrointestinal symptoms were prospectively enrolled, and the gut microbiome was analyzed based on fecal samples.

RESULTS: : In terms of HC-AD-CRC sequence, commensal bacteria, including lactate-producing (Streptococcus salivarius) and butyrate-producing (Faecalibacterium prausnitzii, Anaerostipes hadrus, and Eubacterium hallii) bacteria, were more abundant in the HC group than in the AD and CRC groups. In the sex comparison, the female HC group had more lactate-producing bacteria (Bifidobacterium adolescentis, Bifidobacterium catenulatum, and Lactobacillus ruminis) than the male HC group. In age comparison, younger subjects had more butyrate-producing bacteria (Agathobaculum butyriciproducens and Blautia faecis) than the older subjects in the HC group. Interestingly, lactate-producing bacteria (B. catenulatum) were more abundant in females than males among younger HC group subjects. However, these sex- and age-dependent differences were not observed in the AD and CRC groups.

CONCLUSIONS: : The gut microbiome, specifically lactate- and butyrate-producing bacteria, which were found to be abundant in the HC group, may play a role in preventing the progression of CRC. In particular, lactate-producing bacteria, which were found to be less abundant in healthy male controls may contribute to the higher incidence of CRC in males.},
}

@article {pmid38030126,
year = {2023},
author = {Ahsan, T and Tian, PC and Gao, J and Wang, C and Liu, C and Huang, YQ},
title = {Effects of microbial agent and microbial fertilizer input on soil microbial community structure and diversity in a peanut continuous cropping system.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2023.11.028},
pmid = {38030126},
issn = {2090-1224},
abstract = {INTRODUCTION: The soil harbors a diverse array of microorganisms, and these are essential components of terrestrial ecosystems. The presence of microorganisms in the soil, particularly in the rhizosphere, is closely linked to plant growth and soil fertility.

OBJECTIVE: The primary objective of this study is to assess the potential advantages of integrating microbial inoculants with compound fertilizer in enhancing peanut yield.

METHODS: We utilized Illumina MiSeq high-throughput sequencing technology to conduct our investigation. The experimental design consists of four treatment groups: compound fertilizers (CF), compound fertilizers supplemented with microbial agents (CF+MA), compound fertilizers supplemented with microbial fertilizers (CF+MF), and compound fertilizers supplemented with both microbial agents and microbial fertilizers (CF+MM).

RESULTS: The experimental results demonstrated a significant increase in peanut yield upon application of CF+MA, CF+MF, and CF+MM treatments. During the blossom stage and pod-setting stage, the soil's catalase, urease, and acid phosphatase activities were significantly increased in the CF+MA, and CF+MM treatments compared to the CF treatment. The application of CF+MA resulted in an increase in bacterial richness in the rhizosphere soil of peanuts, as indicated by the sequencing results. The application of CF+MA, CF+MF, and CF+MM resulted in a reduction of fungal diversity. Proteobacteria, Actinobacteria, and Acidobacteria were the dominant bacterial phyla, while Ascomycota and Basidiomycota were the dominant phyla in the fungal component of the rhizosphere soil microbiome across all experimental treatments.

CONCLUSION: Microbial agents and fertilizers modify the peanut rhizosphere soil's microbial community structure, as per our findings. The abundance of potentially beneficial bacteria (Bradyrhizobium, Rhizobium, and Burkholderia) and fungi (Trichoderma and Cladophialophora) could increase, while pathogenic fungi (Penicillium and Fusarium) decreased, thereby significantly promoting plant growth and yield of peanut.},
}

@article {pmid38030048,
year = {2023},
author = {Gong, X and Ma, Y and Deng, X and Li, A and Li, X and Kong, X and Liu, Y and Liu, X and Guo, K and Yang, Y and Li, Z and Wei, H and Zhou, D and Hong, Z},
title = {Intestinal dysbiosis exacerbates susceptibility to the anti-NMDA receptor encephalitis-like phenotype by changing blood brain barrier permeability and immune homeostasis.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2023.11.030},
pmid = {38030048},
issn = {1090-2139},
abstract = {Changes in the intestinal microbiota have been observed in patients with anti-N-methyl-D-aspartate receptor encephalitis (NMDARE). However, whether and how the intestinal microbiota is involved in the pathogenesis of NMDARE susceptibility needs to be demonstrated. Here, we first showed that germ-free (GF) mice that underwent fecal microbiota transplantation (FMT) from NMDARE patients, whose fecal microbiota exhibited low short-chain fatty acid content, decreased abundance of Lachnospiraceae, and increased abundance of Verrucomicrobiota, Akkermansia, Parabacteroides, Oscillospirales, showed significant behavioral deficits. Then, these FMT mice were actively immunized with an amino terminal domain peptide from the GluN1 subunit (GluN1356-385) to mimic the pathogenic process of NMDARE. We found that FMT mice showed an increased susceptibility to an encephalitis-like phenotype characterized by more clinical symptoms, greater pentazole (PTZ)-induced susceptibility to seizures, and higher levels of T2 weighted image (T2WI) hyperintensities following immunization. Furthermore, mice with dysbiotic microbiota had impaired blood-brain barrier integrity and a proinflammatory condition. In NMDARE-microbiota recipient mice, the levels of Evan's blue (EB) dye extravasation increased, ZO-1 and claudin-5 expression decreased, and the levels of proinflammatory cytokines (IL-1, IL-6, IL-17, TNF-α and LPS) increased. Finally, significant brain inflammation, mainly in hippocampal and cortical regions, with modest neuroinflammation, immune cell infiltration, and reduced expression of NMDA receptors were observed in NMDARE microbiota recipient mice following immunization. Overall, our findings demonstrated that intestinal dysbiosis increased NMDARE susceptibility, suggesting a new target for limiting the occurrence of the severe phenotype of NMDARE.},
}

@article {pmid38030004,
year = {2023},
author = {Liu, Y and Deng, G and Liu, H and Chen, P and Pan, Y and Chen, L and Chen, H and Zhang, G},
title = {Seasonal variations of airborne microbial diversity in waste transfer stations and preventive effect on Streptococcus pneumoniae induced pulmonary inflammation.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168888},
doi = {10.1016/j.scitotenv.2023.168888},
pmid = {38030004},
issn = {1879-1026},
abstract = {Environment, location, and season are important factors that influence the microbiological community, yet, little research on airborne microorganisms in waste transfer stations (WTSs). Here, the airborne bacterial and fungal communities at four WTSs during different seasons were analyzed by high-throughput sequencing. The bacteria were isolated by cultural method and screened bacterium alleviate inflammation induced by Streptococcus pneumoniae (Spn) by regulating gut microbiome. The results revealed that collected bioaerosols from the WTSs varied significantly by location and season. Proteobacteria and Pseudomonadota are prevalent in summer and winter, respectively. Ascomycota was predominant in two seasons. Hazard quotients for adults from four WTSs were below one. Three selected potential probiotics were formulated into a microbial preparation with a carrier that effectively prevented inflammation in bacterial and animal experiments. The expression levels of interleukin-1β, interleukin-6, and tumor necrosis factor-α in Pre group (0.11, 0.17, and 0.48-fold) were significantly lower than Spn group (2.75, 1.71, and 5.01-fold). These mechanisms are associated with changes in gut microbiota composition and short-chain fatty acids (SCFAs) levels, such as affecting Lachnospiraceae lachnospira abundance and acetic acid content. This study provides insights into the potential application of probiotics derived from WTSs as an alternative approach to preventing respiratory infections.},
}

@article {pmid38029942,
year = {2023},
author = {Xie, Z and Zhou, J and Zhang, X and Li, Z},
title = {Clinical potential of microbiota in thyroid cancer therapy.},
journal = {Biochimica et biophysica acta. Molecular basis of disease},
volume = {1870},
number = {2},
pages = {166971},
doi = {10.1016/j.bbadis.2023.166971},
pmid = {38029942},
issn = {1879-260X},
abstract = {Thyroid cancer is one of the most common tumors of the endocrine system because of its rapid and steady increase in incidence and prevalence. In recent years, a growing number of studies have identified a key role for the gut, thyroid tissue and oral microbiota in the regulation of metabolism and the immune system. A growing body of evidence has conclusively demonstrated that the microbiota influences tumor formation, prevention, diagnosis, and treatment. We provide extensive information in which oral, gut, and thyroid microbiota have an effect on thyroid cancer development in this review. In addition, we thoroughly discuss the various microbiota species, their potential functions, and the underlying mechanisms for thyroid cancer. The microbiome offers a unique opportunity to improve the effectiveness of immunotherapy and radioiodine therapy thyroid cancer by maintaining the right type of microbiota, and holds great promise for improving clinical outcomes and quality of life for thyroid cancer patients.},
}

@article {pmid38029921,
year = {2023},
author = {Lian, V and Hinrichs, H and Young, M and Faerber, A and Özler, O and Xie, Y and Ballentine, SJ and Tarr, PI and Davidson, NO and Thompson, MD},
title = {MATERNAL OBESOGENIC DIET ATTENUATES MICROBIOME DEPENDENT OFFSPRING WEANING REACTION WITH WORSENING OF STEATOTIC LIVER DISEASE.},
journal = {The American journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajpath.2023.11.006},
pmid = {38029921},
issn = {1525-2191},
abstract = {The mechanisms by which maternal obesity increases the susceptibility to steatotic liver disease (SLD) in offspring are incompletely understood and models using different maternal obesogenic diets (MODEs) display phenotypic variability, likely reflecting the influence of timing and diet composition. Here we compare three maternal obesogenic diets using standardized exposure times to identify differences in offspring disease progression. We found that the severity of hepatic inflammation and fibrosis in offspring depends on the composition of maternal obesogenic diet. Offspring cecal microbiome composition was shifted in all MODE groups relative to control. Decreased alpha-diversity in some MODE offspring with shifts in abundance of multiple genera suggestive of delayed maturation of the microbiome. Next we demonstrated that the weaning reaction typically characterized by a spike in intestinal expression of Tnfa and Ifng is attenuated in MODE offspring in an early microbiome dependent manner shown using cross-fostering. Cross-fostering also switched the severity of disease progression in offspring dependent on the diet of the fostering dam. These results identify maternal diet composition and timing of exposure as modifiers in mediating transmissible changes in the microbiome. These changes in the early microbiome alter a critical window during weaning that drives susceptibility to progressive liver disease in offspring.},
}

@article {pmid38029741,
year = {2023},
author = {Meyer, KM and Muscettola, IE and Vasconcelos, ALS and Sherman, JK and Metcalf, CJE and Lindow, SE and Koskella, B},
title = {Conspecific versus heterospecific transmission shapes host specialization of the phyllosphere microbiome.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2023.11.002},
pmid = {38029741},
issn = {1934-6069},
abstract = {In disease ecology, pathogen transmission among conspecific versus heterospecific hosts is known to shape pathogen specialization and virulence, but we do not yet know if similar effects occur at the microbiome level. We tested this idea by experimentally passaging leaf-associated microbiomes either within conspecific or across heterospecific plant hosts. Although conspecific transmission results in persistent host-filtering effects and more within-microbiome network connections, heterospecific transmission results in weaker host-filtering effects but higher levels of interconnectivity. When transplanted onto novel plants, heterospecific lines are less differentiated by host species than conspecific lines, suggesting a shift toward microbiome generalism. Finally, conspecific lines from tomato exhibit a competitive advantage on tomato hosts against those passaged on bean or pepper, suggesting microbiome-level host specialization. Overall, we find that transmission mode and previous host history shape microbiome diversity, with repeated conspecific transmission driving microbiome specialization and repeated heterospecific transmission promoting microbiome generalism.},
}

@article {pmid38029703,
year = {2023},
author = {Liu, H and Feng, X and Wang, D and Liu, L and Liu, Y and Liu, B and Zhu, L and Zhang, C and Yang, W},
title = {Altered metabolome and microbiome features provide clues in predicting recurrence of ulcerative colitis.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {239},
number = {},
pages = {115864},
doi = {10.1016/j.jpba.2023.115864},
pmid = {38029703},
issn = {1873-264X},
abstract = {PURPOSE: Many studies have shown that the imbalance of the intestinal flora and metabolite can lead to the development of ulcerative colitis (UC), but their role in recurrent-UC is still unclear. We studied the intestinal flora and metabolites associated with recurrent-UC to elucidate the mechanism and biomarkers of recurrent-UC.

METHODS: Ulcerative colitis (UC) models in active, remission, and recurrence stages were established, and the abundance of intestinal flora was determined by 16 S rRNA sequencing. The changes in the metabolites present in feces and serum were analyzed by UPLC-MS/MS.

RESULTS: We identified 24 metabolites in feces and serum, which might be used as diagnostic and predictive biomarkers of recurrent-UC. The dominant flora of recurrent-UC included Romboutsia, UCG-005, etc. The results of a network analysis found that long-chain fatty acids and phenylalanine were strongly correlated with Firmicutes and Proteobacteria, which indicated that the recurrence of UC might be closely related to metabolites and microorganisms.

CONCLUSION: The changes in intestinal microbiota and metabolites are closely related to the development of UC. Microbiota is an important inducer of UC, which can regulate metabolites through the 'microorganism-gut-metabolite' axis. It may provide a new method for the prediction and treatment of UC.},
}

@article {pmid38029586,
year = {2023},
author = {Fan, Y and Keerthisinghe, TP and Nian, M and Cao, X and Chen, X and Yang, Q and Sampathkumar, K and Loo, JSC and Ng, KW and Demokritou, P and Fang, M},
title = {Comparative secretome metabolic dysregulation by six engineered dietary nanoparticles (EDNs) on the simulated gut microbiota.},
journal = {Journal of hazardous materials},
volume = {465},
number = {},
pages = {133003},
doi = {10.1016/j.jhazmat.2023.133003},
pmid = {38029586},
issn = {1873-3336},
abstract = {The potential use of engineered dietary nanoparticles (EDNs) in diet has been increasing and poses a risk of exposure. The effect of EDNs on gut bacterial metabolism remains largely unknown. In this study, liquid chromatography-mass spectrometry (LC-MS) based metabolomics was used to reveal significantly altered metabolites and metabolic pathways in the secretome of simulated gut microbiome exposed to six different types of EDNs (Chitosan, cellulose nanocrystals (CNC), cellulose nanofibrils (CNF) and polylactic-co-glycolic acid (PLGA); two inorganic EDNs including TiO2 and SiO2) at two dietary doses. We demonstrated that all six EDNs can alter the composition in the secretome with distinct patterns. Chitosan, followed by PLGA and SiO2, has shown the highest potency in inducing the secretome change with major pathways in tryptophan and indole metabolism, bile acid metabolism, tyrosine and phenol metabolism. Metabolomic alterations with clear dose response were observed in most EDNs. Overall, phenylalanine has been shown as the most sensitive metabolites, followed by bile acids such as chenodeoxycholic acid and cholic acid. Those metabolites might be served as the representative metabolites for the EDNs-gut bacteria interaction. Collectively, our studies have demonstrated the sensitivity and feasibility of using metabolomic signatures to understand and predict EDNs-gut microbiome interaction.},
}

@article {pmid38029543,
year = {2023},
author = {Ohkubo, T and Matsumoto, Y and Sasaki, H and Kinoshita, K and Ogasawara, Y and Sugita, T},
title = {Citrobacter koseri inhibits the growth of Staphylococcus epidermidis by suppressing iron utilization.},
journal = {Biochemical and biophysical research communications},
volume = {691},
number = {},
pages = {149277},
doi = {10.1016/j.bbrc.2023.149277},
pmid = {38029543},
issn = {1090-2104},
abstract = {The human skin microbiome consists of many species of bacteria, including Staphylococcus aureus and S. epidermidis. Individuals with atopic dermatitis (AD) have an increased relative abundance of S. aureus, which exacerbates the inflammation of AD. Although S. epidermidis, a main component of healthy skin microbiota, inhibits the growth of S. aureus, the balance between S. epidermidis and S. aureus is disrupted in the skin of individuals with AD. In this study, we found that Citrobacter koseri isolated from patients with AD produces substances that inhibit the growth of S. epidermidis. Heat-treated culture supernatant (CS) of C. koseri inhibited the growth of S. epidermidis but not S. aureus. The genome of C. koseri has gene clusters related to siderophores and the heat-treated CS of C. koseri contained a high concentration of siderophores compared with the control medium. The inhibitory activity of C. koseri CS against the growth of S. epidermidis was decreased by the addition of iron, but not copper or zinc. Deferoxamine, an iron-chelating agent, also inhibited the growth of S. epidermidis, but not that of S. aureus. These findings suggest that C. koseri inhibits the growth of S. epidermidis by interfering with its iron utilization.},
}

@article {pmid38029490,
year = {2023},
author = {Thomas, S and Lappin, DF and Bennett, D and Nile, C and Riggio, MP},
title = {Elevated pro-inflammatory cytokines and chemokines in saliva of cats with feline odontoclastic resorptive lesion.},
journal = {Research in veterinary science},
volume = {166},
number = {},
pages = {105092},
doi = {10.1016/j.rvsc.2023.105092},
pmid = {38029490},
issn = {1532-2661},
abstract = {Feline odontoclastic resorptive lesion (FORL) is an inflammatory oral disease of unknown aetiopathogenesis that affects between 20% to 75% of cats. Twenty immune-associated molecules were measured in saliva of 25 healthy and 40 cats with FORL using a multiplex assay. No statistically significant differences were observed in the levels of these proteins between the healthy group and the diseased group of cats. A two-step cluster analysis of the oral microbiome and salivary cytokine data identified two subgroups of cats with FORL: FORL-1 (subset of cats with a less diverse oral microbiome) and FORL-2 (diseased cats with a microbiome similar to that of healthy animals). The level of some key proinflammatory cytokines (IL-1β, IL-12p40) and chemokines (IL-8, RANTES, KC) were significantly higher in the FORL-1 subgroup than in the FORL-2 subgroup and the healthy group. In addition, TNF-α levels were greater in the FORL-1 subgroup than in the FORL-2 subgroup. These increases in pro-inflammatory cytokines and chemokines indicate active ongoing inflammation that may promote the osteoclastic/odontoclastic activity associated with FORL.},
}

@article {pmid38029259,
year = {2023},
author = {Ogai, K and Nana, BC and Lloyd, YM and Arios, JP and Jiyarom, B and Awanakam, H and Esemu, LF and Hori, A and Matsuoka, A and Nainu, F and Megnekou, R and Leke, RGF and Ekali, GL and Okamoto, S and Kuraishi, T},
title = {Skin microbiome profile in people living with HIV/AIDS in Cameroon.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1211899},
pmid = {38029259},
issn = {2235-2988},
abstract = {The presence of pathogens and the state of diseases, particularly skin diseases, may alter the composition of human skin microbiome. HIV infection has been reported to impair gut microbiome that leads to severe consequences. However, with cutaneous manifestations, that can be life-threatening, due to the opportunistic pathogens, little is known whether HIV infection might influence the skin microbiome and affect the skin homeostasis. This study catalogued the profile of skin microbiome of healthy Cameroonians, at three different skin sites, and compared them to the HIV-infected individuals. Taking advantage on the use of molecular assay coupled with next-generation sequencing, this study revealed that alpha-diversity of the skin microbiome was higher and beta-diversity was altered significantly in the HIV-infected Cameroonians than in the healthy ones. The relative abundance of skin microbes such as Micrococcus and Kocuria species was higher and Cutibacterium species was significantly lower in HIV-infected people, indicating an early change in the human skin microbiome in response to the HIV infection. This phenotypical shift was not related to the number of CD4 T cell count thus the cause remains to be identified. Overall, these data may offer an important lead on the role of skin microbiome in the determination of cutaneous disease state and the discovery of safe pharmacological preparations to treat microbial-related skin disorders.},
}

@article {pmid38029257,
year = {2023},
author = {Liu, H and Hu, Q and Yan, Q and Hao, Z and Liang, C},
title = {Alterations in urinary microbiota composition in urolithiasis patients: insights from 16S rRNA gene sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1266446},
pmid = {38029257},
issn = {2235-2988},
abstract = {OBJECTIVES: To investigate the urinary microbiota composition in urolithiasis patients compared to healthy controls and to identify potential microbial markers and their association with clinical parameters.

METHODS: A total of 66 samples, comprising 45 from urolithiasis patients and 21 from healthy controls, were analyzed. 16S rRNA gene sequencing was employed to determine the microbiota composition. Various statistical and bioinformatics tools, including ANOVA, PCoA, and LEfSe, were utilized to analyze the sequencing data and identify significant differences in microbial abundance.

RESULTS: No significant demographic differences were observed between the two groups. Post-quality control, clean tags ranged from 60,979 to 68,736. Significant differences in α-diversity were observed between the two groups. β-diversity analysis revealed distinct clustering of the urinary microbiota in urolithiasis patients and controls. Notably, Ruminococcaceae was predominant in urolithiasis samples, while Proteobacteria was more prevalent in healthy samples. Lactobacillus was significantly overrepresented in samples from healthy females.

CONCLUSION: The urinary microbiota composition in urolithiasis patients is distinct from that of healthy controls. Specific microbial taxa, such as Ruminococcaceae and Proteobacteria, could serve as potential biomarkers for urolithiasis. The findings pave the way for further exploration of the role of microbiota in urolithiasis and the development of microbiome-based therapeutic strategies.},
}

@article {pmid38029244,
year = {2023},
author = {Zong, Y and Wang, X and Wang, J},
title = {Research progress on the correlation between gut microbiota and preeclampsia: microbiome changes, mechanisms and treatments.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1256940},
pmid = {38029244},
issn = {2235-2988},
abstract = {Preeclampsia is a specific disease during pregnancy and is a significant factor in the increased mortality in perinatal women. Gut microbiota, an intricate and abundant microbial community in the digestive tract, is crucial for host metabolism, immunity, and nutrient absorption. The onset and progression of preeclampsia are closely correlated with the changes in maternal gut microbiota. Research purpose was to compile the existing bits of present scientific data and to close the gap in the knowledge of changes in gut microbiota in preeclampsia and their association with preeclampsia. We searched studies from two electronic databases (PubMed and Web of Science) included from 2014 to 2023. This review is divided into three parts. In the first part, the author elaborates longitudinal differences of maternal gut microbiota during different gestation periods. In the second part, we discuss that gut microbiota can lead to the occurrence of preeclampsia by systemic immune response, influencing the release of active peptides, short-chain fatty acids, trimethylamine-N-oxide (TMAO) and other metabolites, vascular factors and Microorganism-immune axis. In the third part, we proposed that a high-fiber diet combined with drugs and microecological regulators may be therapeutic in enhancing or preventing the emergence and evolution of preeclampsia, which needs further exploration. Although the pathogenesis of preeclampsia is still nebulous and there is no clear and valid clinical treatment, our study provides new ideas for the pathogenesis, prevention and treatment of preeclampsia.},
}

@article {pmid38029238,
year = {2023},
author = {Nie, Q and Wan, X and Tao, H and Yang, Q and Zhao, X and Liu, H and Hu, J and Luo, Y and Shu, T and Geng, R and Gu, Z and Fan, F and Liu, Z},
title = {Multi-function screening of probiotics to improve oral health and evaluating their efficacy in a rat periodontitis model.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1261189},
pmid = {38029238},
issn = {2235-2988},
abstract = {The oral cavity is the second most microbially rich region of the human body, and many studies have shown that there is a strong association between microorganisms and oral health. Some pathogenic bacteria produce biofilms and harmful metabolites in the mouth that may cause oral problems such as oral malodor, periodontitis, and dental caries. Altering the oral microbiota by using probiotics may alleviate oral health problems. Thus, using multi-function screening, we aimed to identify probiotics that can significantly improve oral health. The main parameters were the inhibition of pathogenic bacteria growth, inhibition of biofilm formation, reduction in the production of indole, H2S, and NH3 metabolites that cause halitosis, increase in the production of H2O2 to combat harmful bacteria, and co-aggregation with pathogens to prevent their adhesion and colonization in the oral cavity. Tolerance to cholic acid and choline was also assessed. Bifidobacterium animalis ZK-77, Lactobacillus salivarius ZK-88, and Streptococcus salivarius ZK-102 had antibacterial activity and inhibited biofilm production to prevent caries. They also improved the oral malodor parameter, H2S, NH3, and indole production. The selected probiotics (especially L. salivarius ZK-88) alleviated the inflammation in the oral cavity of rats with periodontitis. The analysis of the gingival crevicular fluid microbiome after probiotic intervention showed that B. animalis ZK-77 likely helped to restore the oral microbiota and maintain the oral microecology. Next, we determined the best prebiotics for each candidate probiotic in order to obtain a formulation with improved effects. We then verified that a probiotics/prebiotic combination (B. animalis ZK-77, L. salivarius ZK-88, and fructooligosaccharides) significantly improved halitosis and teeth color in cats. Using whole-genome sequencing and acute toxicity mouse experiments involving the two probiotics, we found that neither probiotic had virulence genes and they had no significant effects on the growth or development of mice, indicating their safety. Taking the results together, B. animalis ZK-77 and L. salivarius ZK-88 can improve oral health, as verified by in vivo and in vitro experiments. This study provides a reference for clinical research and also provides new evidence for the oral health benefits of probiotics.},
}

@article {pmid38029215,
year = {2023},
author = {Jin, X and Xiao, J and Lu, C and Ma, W and Fan, Y and Xue, X and Xia, Y and Chen, N and Liu, J and Pei, X},
title = {Breastmilk microbiome changes associated with lactational mastitis and treatment with dandelion extract.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1247868},
pmid = {38029215},
issn = {1664-302X},
abstract = {INTRODUCTION: Dandelion (Pugongying) is one of the most frequently used Chinese herbs for treating lactational mastitis (LM). Pugongying granules, a patented medication primarily comprised of dandelion extract, have been approved by CFDA for LM treatment in China. The aims of this study were to investigate the etiology of LM and the mechanism by which Pugongying granules decrease LM symptoms, with a particular focus on the microbial communities found in breastmilk.

METHODS: Participants were recruited from a previously performed randomized controlled trial (Identifier: NCT03756324, ClinicalTrials.gov). Between 2019 and 2020, women diagnosed with unilateral LM at the Beijing University of Chinese Medicine Third Affiliated Hospital were enrolled. In total, 42 paired breastmilk samples from the healthy and affected breasts of the participants were collected. Additionally, 37 paired pre- and post-treatment breastmilk samples from the affected breast were collected from women who received a 3-day course of either Pugongying granules (20 women) or cefdinir (17 women). Clinical outcomes [e.g., body temperature, visual analogue scale (VAS) score for breast pain, the percentage of neutrophils (NE%)] were analyzed pre- and post-treatment, and the breastmilk samples were subjected to 16S rRNA gene sequencing to analyze the alpha and beta diversities and identify significant bacteria. Finally, the relationship between microorganisms and clinical outcomes was analyzed.

RESULTS: There was no significant difference in fever and pain between the Pugongying group and cefdinir group. The most prevalent bacterial genera in breastmilk were Streptococcus and Staphylococcus. Compared to healthy breastmilk, microbial diversity was reduced in affected breastmilk, and there was a higher relative abundance of Streptococcus. After Pugongying treatment, there was an increase in microbial diversity with significantly higher abundance of Corynebacterium. A negative correlation was found between Corynebacterium, VAS score, and NE%. Treatment with cefdinir did not affect microbial diversity. Taken together, our results show a correlation between LM and reduced microbial diversity, as well as an increased abundance of Streptococcus in affected breastmilk.

CONCLUSION: Pugongying granules enhanced microbial diversity in breastmilk samples. Given the substantial variation in individual microbiomes, identifying specific species of Streptococcus and Corynebacterium associated with LM may provide additional insight into LM pathogenesis and treatment.},
}

@article {pmid38029194,
year = {2023},
author = {Smith, JC and Varriano, S and Roach, K and Snipes, Z and Dawson, JL and Shealy, J and Dunn, LL and Snyder, WE and Shariat, NW},
title = {Prevalence and molecular characterization of Salmonella isolated from wild birds in fresh produce environments.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1272916},
pmid = {38029194},
issn = {1664-302X},
abstract = {Wild birds pose a difficult food safety risk to manage because they can avoid traditional wildlife mitigation strategies, such as fences. Birds often use agricultural fields and structures as foraging and nesting areas, which can lead to defecation on crops and subsequent transfer of foodborne pathogens. To assess the food safety risk associated with these events, wild bird feces were collected from produce fields across the southeastern United States during the 2021 and 2022 growing seasons. In total 773 fecal samples were collected from 45 farms across Florida, Georgia, South Carolina, and Tennessee, and 2.1% (n = 16) of samples were Salmonella-positive. Importantly, 75% of Salmonella were isolated from moist feces, showing reduced Salmonella viability when feces dry out. 16S microbiome analysis showed that presence of culturable Salmonella in moist feces correlated to a higher proportion of the Enterobacteriaceae family. From the Salmonella-positive samples, 62.5% (10/16) contained multi-serovar Salmonella populations. Overall, 13 serovars were detected, including six most commonly attributed to human illness (Enteriditis, Newport, Typhimurium, Infantis, Saintpaul, and Muenchen). PCR screening identified an additional 59 Salmonella-positive fecal samples, which were distributed across moist (n = 44) and dried feces (n = 15). On-farm point counts and molecular identification from fecal samples identified 57 bird species, including for 10 Salmonella-positive fecal samples. Overall, there was a low prevalence of Salmonella in fecal samples, especially in dried feces, and we found no evidence of Salmonella transmission to proximal foliage or produce. Fecal samples collected in farms close together shared highly related isolates by whole genome sequencing and also had highly similar Salmonella populations with comparable relative frequencies of the same serovars, suggesting the birds acquired Salmonella from a common source.},
}

@article {pmid38029189,
year = {2023},
author = {Zhang, X and Luo, X and Tian, L and Yue, P and Li, M and Liu, K and Zhu, D and Huang, C and Shi, Q and Yang, L and Xia, Z and Zhao, J and Ma, Z and Li, J and Leung, JW and Lin, Y and Yuan, J and Meng, W and Li, X and Chen, Y},
title = {The gut microbiome dysbiosis and regulation by fecal microbiota transplantation: umbrella review.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1286429},
pmid = {38029189},
issn = {1664-302X},
abstract = {BACKGROUND: Gut microbiome dysbiosis has been implicated in various gastrointestinal and extra-gastrointestinal diseases, but evidence on the efficacy and safety of fecal microbiota transplantation (FMT) for therapeutic indications remains unclear.

METHODS: The gutMDisorder database was used to summarize the associations between gut microbiome dysbiosis and diseases. We performed an umbrella review of published meta-analyses to determine the evidence synthesis on the efficacy and safety of FMT in treating various diseases. Our study was registered in PROSPERO (CRD42022301226).

RESULTS: Gut microbiome dysbiosis was associated with 117 gastrointestinal and extra-gastrointestinal. Colorectal cancer was associated with 92 dysbiosis. Dysbiosis involving Firmicutes (phylum) was associated with 34 diseases. We identified 62 published meta-analyses of FMT. FMT was found to be effective for 13 diseases, with a 95.56% cure rate (95% CI: 93.88-97.05%) for recurrent Chloridoids difficile infection (rCDI). Evidence was high quality for rCDI and moderate to high quality for ulcerative colitis and Crohn's disease but low to very low quality for other diseases.

CONCLUSION: Gut microbiome dysbiosis may be implicated in numerous diseases. Substantial evidence suggests FMT improves clinical outcomes for certain indications, but evidence quality varies greatly depending on the specific indication, route of administration, frequency of instillation, fecal preparation, and donor type. This variability should inform clinical, policy, and implementation decisions regarding FMT.},
}

@article {pmid38029184,
year = {2023},
author = {Ye, L and Zhang, B and Zhang, L and Yang, X and Tan, W and Zhang, X and Li, X},
title = {Pathogenic invasive microbes Trichoderma pleuroticola transform bacterial and fungal community diversity in Auricularia cornea crop production system.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1263982},
pmid = {38029184},
issn = {1664-302X},
abstract = {Pathogenic invasion of Trichoderma pleuroticola profoundly altered microflora in the Auricularia cornea crop production system, impacting diversity and composition in both artificial bed-log and fruiting bodies. A more complex ecological network between the diseased and healthy bodies. Researchers still have poor knowledge about how the important agricultural relationship between the composition of the microbiome of the artificial bed-log and the fruiting bodies is infected by the pathogenic invasive microbes T. pleuroticola, but this knowledge is crucial if we want to use or improve it. Here, we investigated 8 groups (48 biological samples) across 5 growth stages of the A. cornea production system using metagenomic technology. Diseased and healthy fruiting bodies exhibited distinct microbial compositions, while core members in artificial bed-logs remained stable. Core microbiota analysis highlighted Pseudomonas and Pandoraea bacterial genera, as well as Sarocladium, Cephalotrichum, Aspergillus, and Mortierella fungal genera as biomarker species after the bodies were treated with the pathogenic invasive microbes T. pleuroticola. In diseased bodies, these core members upregulated pathways including polymyxin resistance, L-arginine degradation II, superpathway of L-arginine and L-ornithine degradation, glucose degradation (oxidative), glucose and glucose-1-phosphate degradation, promoting fruit spoilage. Our data confirm that T. pleuroticola plays an important role in the early stages of disease development in the A. cornea crop generation system. The exposed volatile core microbiome may play an important role in accelerating T. pleuroticola-induced decay of fruiting bodies.},
}

@article {pmid38029177,
year = {2023},
author = {Rempfert, KR and Kraus, EA and Nothaft, DB and Dildar, N and Spear, JR and Sepúlveda, J and Templeton, AS},
title = {Intact polar lipidome and membrane adaptations of microbial communities inhabiting serpentinite-hosted fluids.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1198786},
pmid = {38029177},
issn = {1664-302X},
abstract = {The generation of hydrogen and reduced carbon compounds during serpentinization provides sustained energy for microorganisms on Earth, and possibly on other extraterrestrial bodies (e.g., Mars, icy satellites). However, the geochemical conditions that arise from water-rock reaction also challenge the known limits of microbial physiology, such as hyperalkaline pH, limited electron acceptors and inorganic carbon. Because cell membranes act as a primary barrier between a cell and its environment, lipids are a vital component in microbial acclimation to challenging physicochemical conditions. To probe the diversity of cell membrane lipids produced in serpentinizing settings and identify membrane adaptations to this environment, we conducted the first comprehensive intact polar lipid (IPL) biomarker survey of microbial communities inhabiting the subsurface at a terrestrial site of serpentinization. We used an expansive, custom environmental lipid database that expands the application of targeted and untargeted lipodomics in the study of microbial and biogeochemical processes. IPLs extracted from serpentinite-hosted fluid communities were comprised of >90% isoprenoidal and non-isoprenoidal diether glycolipids likely produced by archaeal methanogens and sulfate-reducing bacteria. Phospholipids only constituted ~1% of the intact polar lipidome. In addition to abundant diether glycolipids, betaine and trimethylated-ornithine aminolipids and glycosphingolipids were also detected, indicating pervasive membrane modifications in response to phosphate limitation. The carbon oxidation state of IPL backbones was positively correlated with the reduction potential of fluids, which may signify an energy conservation strategy for lipid synthesis. Together, these data suggest microorganisms inhabiting serpentinites possess a unique combination of membrane adaptations that allow for their survival in polyextreme environments. The persistence of IPLs in fluids beyond the presence of their source organisms, as indicated by 16S rRNA genes and transcripts, is promising for the detection of extinct life in serpentinizing settings through lipid biomarker signatures. These data contribute new insights into the complexity of lipid structures generated in actively serpentinizing environments and provide valuable context to aid in the reconstruction of past microbial activity from fossil lipid records of terrestrial serpentinites and the search for biosignatures elsewhere in our solar system.},
}

@article {pmid38029176,
year = {2023},
author = {Jain, U and Poltronieri, P and Fusco, V and Primiceri, E},
title = {Editorial: Latest perspective on microbes detection: from laboratory to on-spot sensor.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1302805},
doi = {10.3389/fmicb.2023.1302805},
pmid = {38029176},
issn = {1664-302X},
}

@article {pmid38029169,
year = {2023},
author = {Nguyen, TQ and Martínez-Álvaro, M and Lima, J and Auffret, MD and Rutherford, KMD and Simm, G and Dewhurst, RJ and Baima, ET and Roehe, R},
title = {Identification of intestinal and fecal microbial biomarkers using a porcine social stress model.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1197371},
pmid = {38029169},
issn = {1664-302X},
abstract = {Understanding the relationships between social stress and the gastrointestinal microbiota, and how they influence host health and performance is expected to have many scientific and commercial implementations in different species, including identification and improvement of challenges to animal welfare and health. In particular, the study of the stress impact on the gastrointestinal microbiota of pigs may be of interest as a model for human health. A porcine stress model based on repeated regrouping and reduced space allowance during the last 4 weeks of the finishing period was developed to identify stress-induced changes in the gut microbiome composition. The application of the porcine stress model resulted in a significant increase in salivary cortisol concentration over the course of the trial and decreased growth performance and appetite. The applied social stress resulted in 32 bacteria being either enriched (13) or depleted (19) in the intestine and feces. Fecal samples showed a greater number of microbial genera influenced by stress than caecum or colon samples. Our trial revealed that the opportunistic pathogens Treponema and Clostridium were enriched in colonic and fecal samples from stressed pigs. Additionally, genera such as Streptococcus, Parabacteroides, Desulfovibrio, Terrisporobacter, Marvinbryantia, and Romboutsia were found to be enriched in response to social stress. In contrast, the genera Prevotella, Faecalibacterium, Butyricicoccus, Dialister, Alloprevotella, Megasphaera, and Mitsuokella were depleted. These depleted bacteria are of great interest because they synthesize metabolites [e.g., short-chain fatty acids (SCFA), in particular, butyrate] showing beneficial health benefits due to inhibitory effects on pathogenic bacteria in different animal species. Of particular interest are Dialister and Faecalibacterium, as their depletion was identified in a human study to be associated with inferior quality of life and depression. We also revealed that some pigs were more susceptible to pathogens as indicated by large enrichments of opportunistic pathogens of Clostridium, Treponema, Streptococcus and Campylobacter. Generally, our results provide further evidence for the microbiota-gut-brain axis as indicated by an increase in cortisol concentration due to social stress regulated by the hypothalamic-pituitary-adrenal axis, and a change in microbiota composition, particularly of bacteria known to be associated with pathogenicity and mental health diseases.},
}

@article {pmid38029159,
year = {2023},
author = {Huang, B and Khan, MZ and Chen, Y and Liang, H and Kou, X and Wang, X and Ren, W and Wang, C and Zhang, Z},
title = {Yeast polysaccharide supplementation: impact on lactation, growth, immunity, and gut microbiota in Dezhou donkeys.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1289371},
pmid = {38029159},
issn = {1664-302X},
abstract = {INTRODUCTION: The Dezhou donkey, a prominent Chinese breed, is known for its remarkable size, rapid growth, and resilience to tough feeding conditions, and disease resistance. These traits are crucial in meeting the growing demand for Ejiao and donkey meat. Yeast polysaccharide (YPS), a functional polysaccharide complex known for its immune-enhancing and growth-promoting properties in livestock and poultry, remains relatively understudied in donkeys.

OBJECTIVES: This study aimed to investigate the impact of YPS supplementation on lactating and growing Dezhou donkey jennies and foals.

MATERIALS AND METHODS: Twelve 45-day-old Dezhou donkey foals and their jennies, matched for body weight and age, were randomly allocated to two dietary groups: a control group receiving a basal diet and an experimental group receiving the basal diet supplemented with 10 g/pen of YPS. The experiment was conducted over a 23-day period, during which donkey foals and lactating jennies were co-housed.

RESULTS AND DISCUSSION: The findings revealed that YPS supplementation had no adverse effects on milk production or composition in Dezhou donkey jennies but significantly increased feed intake. Additionally, YPS was associated with increased plasma glucose and creatinine concentrations in foals, while tending to decrease alkaline phosphatase, white blood cell count, red blood cell count, and hemoglobin levels (p < 0.10). Immune indices demonstrated that YPS supplementation elevated the levels of immunoglobulin A (IgA) and immunoglobulin G (IgG) in jennies (p < 0.05) and increased complement component C4 concentrations in foals (p < 0.05). Moreover, YPS positively influenced the fecal microbiome, promoting the abundance of beneficial microorganisms such as Lactobacillus and Prevotella in donkey foals and Terriporobacter and Cellulosilyticum in jennies, all of which contribute to enhanced feed digestion. Additionally, YPS induced alterations in the plasma metabolome for both jennies and foals, with a predominant presence of lipids and lipid-like molecules. Notably, YPS increased the concentrations of specific lipid metabolites, including 13,14-Dihydro PGF2a, 2-Isopropylmalic acid, 2,3-Dinor-TXB2, Triterpenoids, Taurocholic acid, and 3b-Allotetrahydrocortisol, all of which are associated with improved animal growth.

CONCLUSION: In conclusion, this study suggests that dietary supplementation of YPS enhances feed intake, boosts immunity by increasing immunoglobulin levels, stimulates the growth-promoting gut microbiota (Lactobacillus and Prevotella), and exerts no adverse effects on the metabolism of both Dezhou donkey jennies and foals.},
}

@article {pmid38029157,
year = {2023},
author = {Liu, M and Ding, J and Lu, M},
title = {Influence of symbiotic bacteria on the susceptibility of Plagiodera versicolora to Beauveria bassiana infection.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1290925},
pmid = {38029157},
issn = {1664-302X},
abstract = {The symbiotic bacterial microbiota of insects has been shown to play essential roles in processes related to physiology, metabolism, and innate immunity. In this study, the symbiotic microbiome of Plagiodera versicolora at different developmental stages was analyzed using 16S rRNA high-throughput sequencing. The result showed that symbiotic bacteria community in P. versicolora was primarily made up of Actinobacteriota, Proteobacteria, Firmicutes, Bacteroidota, and Dependentiae. The bacterial composition among different age individuals were highly diverse, while 65 core genera were distributed in all samples which recommend core bacterial microbiome. The 8 species core bacteria were isolated from all samples, and all of them were classified as Pseudomonas sp. Among them, five species have been proven to promote the vegetable growth of Beauveria bassiana. Moreover, the virulence of B. bassiana against nonaxenic larvae exceeded B. bassiana against axenic larvae, and the introduction of the Pseudomonas sp. to axenic larvae augmented the virulence of fungi. Taken together, our study demonstrates that the symbiotic bacteria of P. versicolora are highly dissimilar, and Pseudomonas sp. core bacteria can promote host infection by entomopathogenic fungus. This result emphasizes the potential for harnessing these findings in the development of effective pest management strategies.},
}

@article {pmid38029153,
year = {2023},
author = {Wu, C and Lower, BA and Moreira, R and Dorantes, D and Le, T and Giurgiu, C and Shi, Y and van der Donk, WA},
title = {Investigation into the mechanism of action of the antimicrobial peptide epilancin 15X.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1247222},
pmid = {38029153},
issn = {1664-302X},
abstract = {Addressing the current antibiotic-resistance challenge would be aided by the identification of compounds with novel mechanisms of action. Epilancin 15X, a lantibiotic produced by Staphylococcus epidermidis 15 × 154, displays antimicrobial activity in the submicromolar range against a subset of pathogenic Gram-positive bacteria. S. epidermidis is a common member of the human skin or mucosal microbiota. We here investigated the mechanism of action of epilancin 15X. The compound is bactericidal against Staphylococcus carnosus as well as Bacillus subtilis and appears to kill these bacteria by membrane disruption. Structure-activity relationship studies using engineered analogs show that its conserved positively charged residues and dehydroamino acids are important for bioactivity, but the N-terminal lactyl group is tolerant of changes. Epilancin 15X treatment negatively affects fatty acid synthesis, RNA translation, and DNA replication and transcription without affecting cell wall biosynthesis. The compound appears localized to the surface of bacteria and is most potent in disrupting the membranes of liposomes composed of negatively charged membrane lipids in a lipid II independent manner. Epilancin 15X does not elicit a LiaRS response in B. subtilis but did upregulate VraRS in S. carnosus. Treatment of S. carnosus or B. subtilis with epilancin 15X resulted in an aggregation phenotype in microscopy experiments. Collectively these studies provide new information on epilancin 15X activity.},
}

@article {pmid38029152,
year = {2023},
author = {Huang, Z and He, X and Zhang, C and Zhang, M and Wang, J and Hou, Y and Wang, D and Yao, S and Yu, Q and Ji, K},
title = {Microbial communities and functions changed in rhizosphere soil of Pinus massoniana provenances with different carbon storage.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1264670},
pmid = {38029152},
issn = {1664-302X},
abstract = {INTRODUCTION: The average carbon storage of Pinus massoniana is much higher than the average carbon storage of Chinese forests, an important carbon sink tree species in subtropical regions of China. However, there are few studies on the differences in rhizosphere microorganisms of P. massoniana with different carbon storages.

METHODS: To clarify the relationships between plant carbon storage level, environmental parameters and microbial community structure, we identified three carbon storage levels from different P. massoniana provenances and collected rhizosphere soil samples. We determined chemical properties of soil, extracellular enzyme activity, and microbial community structures at different carbon storage levels and examined how soil factors affect rhizosphere microorganisms under different carbon storage levels.

RESULTS: The results revealed that soil organic carbon (SOC), nitrate nitrogen (NO3[-]-N), ammonium nitrogen (NH4[+]-N) contents all increased with increasing carbon storage levels, while pH decreased accordingly. In contrast, the available phosphorus (AP) content did not change significantly. The soil AP content was within the range of 0.91 ~ 1.04 mg/kg. The microbial community structure of P. massoniana changed with different carbon storage, with Acidobacteria (44.27%), Proteobacteria (32.57%), and Actinobacteria (13.43%) being the dominant bacterial phyla and Basidiomycota (73.36%) and Ascomycota (24.64%) being the dominant fungal phyla across the three carbon storage levels. Soil fungi were more responsive to carbon storage than bacteria in P. massoniana. C/N, NH4[+]-N, NO3[-]-N, and SOC were the main drivers (p < 0.05) of changes in rhizosphere microbial communities.

DISCUSSION: The results revealed that in the rhizosphere there were significant differences in soil carbon cycle and microorganism nutrient preferences at different carbon storages of P. massoniana provenance, which were significantly related to the changes in rhizosphere microbial community structure. Jiangxi Anyuan (AY) provenance is more suitable for the construction of high carbon storage plantation.},
}

@article {pmid38029138,
year = {2023},
author = {Portugal, A and Liu, X and Pyzik, A and Trovão, J},
title = {Editorial: Microbiomes of art and their importance in preserving cultural heritage.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1321133},
doi = {10.3389/fmicb.2023.1321133},
pmid = {38029138},
issn = {1664-302X},
}

@article {pmid38029137,
year = {2023},
author = {Qian, X and Fu, Z and Diao, C and Zhang, W and Tao, W and Hu, J and Zhang, S and Zhao, D},
title = {Genetic causal relationship between gut microbiome and psoriatic arthritis: a bidirectional two-sample Mendelian randomization study.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1265786},
pmid = {38029137},
issn = {1664-302X},
abstract = {BACKGROUND: Several observational studies have suggested a potential relationship between gut microbiome and psoriatic arthritis (PsA). However, the causality of this relationship still remains unclear. We aim to explore if the specific gut microbiome is causally associated with PsA at the genetic level and offer valuable insights into the etiology of PsA.

METHODS: In this study, we employed a bidirectional two-sample Mendelian randomization (MR) analysis to investigate the causal effects of the gut microbiome on PsA. Publicly accessible genome-wide association study summary data of gut microbiome were obtained from the MiBioGen consortium (n = 14,306), while the summary statistics of psoriatic arthropathies were sourced from the FinnGen consortium R8 release data (2,776 cases and 221,323 controls). The primary analytical method employed was inverse variance weighted (IVW), complemented by supplementary methods including MR-Egger, weighted median, weighted mode, maximum likelihood, MR-PRESSO, and cML-MA. Reverse MR analysis was performed on the bacteria that were found to be causally associated with PsA in forward MR analysis. Cochran's IVW Q statistic was utilized to assess the heterogeneity of instrumental variables among the selected single nucleotide polymorphisms.

RESULTS: IVW estimates revealed that Ruminococcaceae_UCG-002 (odds ratio (OR) = 0.792, 95% confidence interval (CI), 0.643-0.977, p = 0.029) exhibited a protective effect on PsA. Conversely, Blautia (OR = 1.362, 95% CI, 1.008-1.842, p = 0.044), Eubacterium_fissicatena_group (OR = 1.28, 95% CI, 1.075-1.524, p = 0.006), and Methanobrevibacter (OR = 1.31, 95% CI, 1.059-1.621, p = 0.013) showed a positive correlation with the risk of PsA. No significant heterogeneity, horizontal pleiotropy, or outliers were observed, and the results of the MR analysis remained unaffected by any single nucleotide polymorphisms. According to the results of reverse MR analysis, no significant causal effect of PsA was found on gut microbiome.

CONCLUSION: This study establishes for the first time a causal relationship between the gut microbiome and PsA, providing potential valuable strategies for the prevention and treatment of PsA. Further randomized controlled trials are urgently warranted to support the targeted protective mechanisms of probiotics on PsA.},
}

@article {pmid38029135,
year = {2023},
author = {Maingi, FM and Akutse, KS and Ajene, IJ and Omolo, KM and Khamis, FM},
title = {Immunological responses and gut microbial shifts in Phthorimaea absoluta exposed to Metarhizium anisopliae isolates under different temperature regimes.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1258662},
pmid = {38029135},
issn = {1664-302X},
abstract = {The invasive tomato leaf miner, Phthorimaea absoluta, is conventionally controlled through chemical insecticides. However, the rise of insecticide resistance has necessitated sustainable and eco-friendly alternatives. Entomopathogenic fungi (EPF) have shown potential due to their ability to overcome resistance and have minimal impact on non-target organisms. Despite this potential, the precise physiological mechanisms by which EPF acts on insect pests remain poorly understood. To attain a comprehensive understanding of the complex physiological processes that drive the successful control of P. absoluta adults through EPF, we investigated the impacts of different Metarhizium anisopliae isolates (ICIPE 665, ICIPE 20, ICIPE 18) on the pest's survival, cellular immune responses, and gut microbiota under varying temperatures. The study unveiled that ICIPE 18 caused the highest mortality rate among P. absoluta moths, while ICIPE 20 exhibited the highest significant reduction in total hemocyte counts after 10 days at 25°C. Moreover, both isolates elicited notable shifts in P. absoluta's gut microbiota. Our findings revealed that ICIPE 18 and ICIPE 20 compromised the pest's defense and physiological functions, demonstrating their potential as biocontrol agents against P. absoluta in tomato production systems.},
}

@article {pmid38029134,
year = {2023},
author = {Lartey, I and Benucci, GMN and Marsh, TL and Bonito, GM and Melakeberhan, H},
title = {Characterizing microbial communities associated with northern root-knot nematode (Meloidogyne hapla) occurrence and soil health.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1267008},
pmid = {38029134},
issn = {1664-302X},
abstract = {The northern root-knot nematode (Meloidogyne hapla) causes extensive damage to agricultural crops globally. In addition, M. hapla populations with no known genetic or morphological differences exhibit parasitic variability (PV) or reproductive potential based on soil type. However, why M. hapla populations from mineral soil with degraded soil health conditions have a higher PV than populations from muck soil is unknown. To improve our understanding of soil bio-physicochemical conditions in the environment where M. hapla populations exhibited PV, this study characterized the soil microbial community and core- and indicator-species structure associated with M. hapla occurrence and soil health conditions in 15 Michigan mineral and muck vegetable production fields. Bacterial and fungal communities in soils from where nematodes were isolated were characterized with high throughput sequencing of 16S and internal transcribed spacer (ITS) rDNA. Our results showed that M. hapla-infested, as well as disturbed and degraded muck fields, had lower bacterial diversity (observed richness and Shannon) compared to corresponding mineral soil fields or non-infested mineral fields. Bacterial and fungal community abundance varied by soil group, soil health conditions, and/or M. hapla occurrence. A core microbial community was found to consist of 39 bacterial and 44 fungal sub-operational taxonomic units (OTUs) across all fields. In addition, 25 bacteria were resolved as indicator OTUs associated with M. hapla presence or absence, and 1,065 bacteria as indicator OTUs associated with soil health conditions. Out of the 1,065 bacterial OTUs, 73.9% indicated stable soil health, 8.4% disturbed, and 0.4% degraded condition; no indicators were common to the three categories. Collectively, these results provide a foundation for an in-depth understanding of the environment where M. hapla exists and conditions associated with parasitic variability.},
}

@article {pmid38029126,
year = {2023},
author = {Shah, T and Hou, Y and Jiang, J and Shah, Z and Wang, Y and Li, Q and Xu, X and Wang, Y and Wang, B and Xia, X},
title = {Comparative analysis of the intestinal microbiome in Rattus norvegicus from different geographies.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1283453},
pmid = {38029126},
issn = {1664-302X},
abstract = {Rat species Rattus norvegicus, also known as the brown street rat, is the most abundant mammal after humans in urban areas, where they co-exist with humans and domestic animals. The reservoir role of R. norvegicus of zoonotic pathogens in cities among rodent-borne diseases that could endanger the lives of humans and other mammals. Therefore, understanding the normal microbiome of R. norvegicus is crucial for understanding and preventing zoonotic pathogen transmission to humans and animals. We investigated the intestinal microbiome of free-living R. norvegicus collected from the Ruili, Nujiang, and Lianhe regions of Yunnan, China, using 16S rRNA gene sequence analysis. Proteobacteria, followed by Firmicutes, and Bacteroidetes were abundant in the intestines of R. norvegicus; however, bacterial compositions varied significantly between samples from different locations. Following a similar trend, Gammaproteobacteria, Bacilli, and Clostridia were among the top bacterial classes in most intestinal samples. The situation differed slightly for the Lianhe and Nujiang samples, although Phyla Bacteroidota and Spirochaetota were most prevalent. The Alpha diversity, Chao1, and Simpson indexes revealed microbial richness among the R. norvegicus samples. A slight variation was observed among the samples collected from Ruili, Nujiang, and Lianhe. At species levels, several opportunistic and zoonotic bacterial pathogens, including Lactococcus garvieae, Uruburuella suis, Bartonella australis, Clostridium perfringens, Streptococcus azizii, Vibrio vulnificus, etc., were revealed in the R. norvegicus intestines, implying the need for a regular survey to monitor and control rodent populations. In conclusion, we explored diverse microbial communities in R. norvegicus intestines captured from different regions. Further, we identified several opportunistic and potential bacterial pathogens, which still need to be tested for their underlying pathogenesis. The findings of our current study should be considered a warning to the health authorities to implement rat control and surveillance strategies globally.},
}

@article {pmid38029121,
year = {2023},
author = {Alvarado-Peña, N and Galeana-Cadena, D and Gómez-García, IA and Mainero, XS and Silva-Herzog, E},
title = {The microbiome and the gut-lung axis in tuberculosis: interplay in the course of disease and treatment.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1237998},
pmid = {38029121},
issn = {1664-302X},
abstract = {Tuberculosis is a chronic infectious disease caused by Mycobacterium tuberculosis (MTB) that remains a significant global health challenge. The extensive use of antibiotics in tuberculosis treatment, disrupts the delicate balance of the microbiota in various organs, including the gastrointestinal and respiratory systems. This gut-lung axis involves dynamic interactions among immune cells, microbiota, and signaling molecules from both organs. The alterations of the microbiome resulting from anti-TB treatment can significantly influence the course of tuberculosis, impacting aspects such as complete healing, reinfection, and relapse. This review aims to provide a comprehensive understanding of the gut-lung axis in the context of tuberculosis, with a specific focus on the impact of anti-TB treatment on the microbiome.},
}

@article {pmid38029119,
year = {2023},
author = {Moore, GG and Chalivendra, S and Mack, BM and Gilbert, MK and Cary, JW and Rajasekaran, K},
title = {Microbiota of maize kernels as influenced by Aspergillus flavus infection in susceptible and resistant inbreds.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1291284},
pmid = {38029119},
issn = {1664-302X},
abstract = {BACKGROUND: Nearly everything on Earth harbors a microbiome. A microbiome is a community of microbes (bacteria, fungi, and viruses) with potential to form complex networks that involve mutualistic and antagonistic interactions. Resident microbiota on/in an organism are determined by the external environment, both biotic and abiotic, and the intrinsic adaptability of each organism. Although the maize microbiome has been characterized, community changes that result from the application of fungal biocontrol strains, such as non-aflatoxigenic Aspergillus flavus, have not.

METHODS: We silk channel inoculated field-grown maize separately with a non-aflatoxigenic biocontrol strain (K49), a highly toxigenic strain (Tox4), and a combination of both A. flavus strains. Two maize inbreds were treated, A. flavus-susceptible B73 and A. flavus-resistant CML322. We then assessed the impacts of A. flavus introduction on the epibiota and endobiota of their maize kernels.

RESULTS: We found that the native microbial communities were significantly affected, irrespective of genotype or sampled tissue. Overall, bacteriomes exhibited greater diversity of genera than mycobiomes. The abundance of certain genera was unchanged by treatment, including genera of bacteria (e.g., Enterobacter, Pantoea) and fungi (e.g., Sarocladium, Meyerozyma) that are known to be beneficial, antagonistic, or both on plant growth and health.

CONCLUSION: Beneficial microbes like Sarocladium that responded well to A. flavus biocontrol strains are expected to enhance biocontrol efficacy, while also displacing/antagonizing harmful microbes.},
}

@article {pmid38029106,
year = {2023},
author = {Ying, ZH and Mao, CL and Xie, W and Yu, CH},
title = {Postbiotics in rheumatoid arthritis: emerging mechanisms and intervention perspectives.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1290015},
pmid = {38029106},
issn = {1664-302X},
abstract = {Rheumatoid arthritis (RA) is a prevalent chronic autoimmune disease that affects individuals of all age groups. Recently, the association between RA and the gut microbiome has led to the investigation of postbiotics as potential therapeutic strategies. Postbiotics refer to inactivated microbial cells, cellular components, or their metabolites that are specifically intended for the microbiota. Postbiotics not only profoundly influence the occurrence and development of RA, but they also mediate various inflammatory pathways, immune processes, and bone metabolism. Although they offer a variety of mechanisms and may even be superior to more conventional "biotics" such as probiotics and prebiotics, research on their efficacy and clinical significance in RA with disruptions to the intestinal microbiota remains limited. In this review, we provide an overview of the concept of postbiotics and summarize the current knowledge regarding postbiotics and their potential use in RA therapy. Postbiotics show potential as a viable adjunctive therapy option for RA.},
}

@article {pmid38029089,
year = {2023},
author = {Krishnamurthy, HK and Pereira, M and Bosco, J and George, J and Jayaraman, V and Krishna, K and Wang, T and Bei, K and Rajasekaran, JJ},
title = {Gut commensals and their metabolites in health and disease.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1244293},
pmid = {38029089},
issn = {1664-302X},
abstract = {PURPOSE OF REVIEW: This review comprehensively discusses the role of the gut microbiome and its metabolites in health and disease and sheds light on the importance of a holistic approach in assessing the gut.

RECENT FINDINGS: The gut microbiome consisting of the bacteriome, mycobiome, archaeome, and virome has a profound effect on human health. Gut dysbiosis which is characterized by perturbations in the microbial population not only results in gastrointestinal (GI) symptoms or conditions but can also give rise to extra-GI manifestations. Gut microorganisms also produce metabolites (short-chain fatty acids, trimethylamine, hydrogen sulfide, methane, and so on) that are important for several interkingdom microbial interactions and functions. They also participate in various host metabolic processes. An alteration in the microbial species can affect their respective metabolite concentrations which can have serious health implications. Effective assessment of the gut microbiome and its metabolites is crucial as it can provide insights into one's overall health.

SUMMARY: Emerging evidence highlights the role of the gut microbiome and its metabolites in health and disease. As it is implicated in GI as well as extra-GI symptoms, the gut microbiome plays a crucial role in the overall well-being of the host. Effective assessment of the gut microbiome may provide insights into one's health status leading to more holistic care.},
}

@article {pmid37539715,
year = {2023},
author = {Berenson, CS and Lashner, B and Korman, LY and Hohmann, E and Deshpande, A and Louie, TJ and Sims, M and Pardi, D and Kraft, CS and Wang, EEL and Cohen, SH and Feuerstadt, P and Oneto, C and Misra, B and Pullman, J and De, A and Memisoglu, A and Lombardi, DA and Hasson, BR and McGovern, BH and von Moltke, L and Lee, CH},
title = {Prevalence of Comorbid Factors in Patients With Recurrent Clostridioides difficile Infection in ECOSPOR III, a Randomized Trial of an Oral Microbiota-Based Therapeutic.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {77},
number = {11},
pages = {1504-1510},
doi = {10.1093/cid/ciad448},
pmid = {37539715},
issn = {1537-6591},
support = {//Seres Therapeutics/ ; },
abstract = {BACKGROUND: Although comorbidities are risk factors for recurrent Clostridioides difficile infection (rCDI), many clinical trials exclude patients with medical conditions such as malignancy or immunosuppression. In a phase 3, double-blind, placebo-controlled, randomized trial (ECOSPOR III), fecal microbiota spores, live (VOWST, Seres Therapeutics; hereafter "VOS," formerly SER-109), an oral microbiota therapeutic, significantly reduced the risk of rCDI at week 8. We evaluated the efficacy of VOS compared with placebo in patients with comorbidities and other risk factors for rCDI.

METHODS: Adults with rCDI were randomized to receive VOS or placebo (4 capsules daily for 3 days) following standard-of-care antibiotics. In this post hoc analysis, the rate of rCDI through week 8 was assessed in VOS-treated participants compared with placebo for subgroups including (i) Charlson comorbidity index (CCI) score category (0, 1-2, 3-4, ≥5); (ii) baseline creatinine clearance (<30, 30-50, >50 to 80, or >80 mL/minute); (iii) number of CDI episodes, inclusive of the qualifying episode (3 and ≥4); (iv) exposure to non-CDI-targeted antibiotics after dosing; and (v) acid-suppressing medication use at baseline.

RESULTS: Of 281 participants screened, 182 were randomized (59.9% female; mean age, 65.5 years). Comorbidities were common with a mean overall baseline age-adjusted CCI score of 4.1 (4.1 in the VOS arm and 4.2 in the placebo arm). Across all subgroups analyzed, VOS-treated participants had a lower relative risk of recurrence compared with placebo.

CONCLUSIONS: In this post hoc analysis, VOS reduced the risk of rCDI compared with placebo, regardless of baseline characteristics, concomitant medications, or comorbidities.},
}

@article {pmid38029086,
year = {2023},
author = {Yang, J and He, Y and Liao, X and Hu, J and Li, K},
title = {Does postoperative pulmonary infection correlate with intestinal flora following gastric cancer surgery? - a nested case-control study.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1267750},
doi = {10.3389/fmicb.2023.1267750},
pmid = {38029086},
issn = {1664-302X},
abstract = {INTRODUCTION: The primary objective of this study was to investigate the potential correlation between gut microbes and postoperative pulmonary infection in gastric cancer patients. Additionally, we aimed to deduce the mechanism of differential functional genes in disease progression to gain a better understanding of the underlying pathophysiology.

METHODS: A nested case-control study design was utilized to enroll patients with gastric cancer scheduled for surgery at West China Hospital of Sichuan University. Patients were categorized into two groups, namely, the pulmonary infection group and the control group, based on the development of postoperative pulmonary infection. Both groups were subjected to identical perioperative management protocols. Fecal samples were collected 24 h postoperatively and upon pulmonary infection diagnosis, along with matched controls. The collected samples were subjected to 16S rDNA and metagenomic analyses, and clinical data and blood samples were obtained for further analysis.

RESULTS: A total of 180 fecal specimens were collected from 30 patients in both the pulmonary infection and control groups for 16S rDNA analysis, and 3 fecal samples from each group were selected for metagenomic analysis. The study revealed significant alterations in the functional genes of the intestinal microbiome in patients with postoperative pulmonary infection in gastric cancer, primarily involving Klebsiella, Enterobacter, Ruminococcus, and Collinsella. During postoperative pulmonary infection, gut flora and inflammatory factors were found to be associated with the lipopolysaccharide synthesis pathway and short-chain fatty acid (SCFA) synthesis pathway.

DISCUSSION: The study identified enriched populations of Klebsiella, Escherella, and intestinal bacteria during pulmonary infection following gastric cancer surgery. These bacteria were found to regulate the lipopolysaccharide synthesis pathway, contributing to the initiation and progression of pulmonary infections. Inflammation modulation in patients with postoperative pulmonary infection may be mediated by short-chain fatty acids. The study also revealed that SCFA synthesis pathways were disrupted, affecting inflammation-related immunosuppression pathways. By controlling and maintaining intestinal barrier function, SCFAs may potentially reduce the occurrence of pulmonary infections after gastric cancer surgery. These findings suggest that targeting the gut microbiome and SCFA synthesis pathways may be a promising approach for preventing postoperative pulmonary infections in gastric cancer patients.},
}

@article {pmid38029085,
year = {2023},
author = {Cronin, P and McCarthy, S and Hurley, C and Ghosh, TS and Cooney, JC and Tobin, AM and Murphy, M and O'Connor, EM and Shanahan, F and O'Toole, PW},
title = {Comparative diet-gut microbiome analysis in Crohn's disease and Hidradenitis suppurativa.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1289374},
doi = {10.3389/fmicb.2023.1289374},
pmid = {38029085},
issn = {1664-302X},
abstract = {INTRODUCTION: The chronic inflammatory skin disease Hidradenitis suppurativa (HS) is strongly associated with Crohn's Disease (CD). HS and CD share clinical similarities and similar inflammatory pathways are upregulated in both conditions. Increased prevalence of inflammatory disease in industrialised nations has been linked to the Western diet. However, gut microbiota composition and diet interaction have not been compared in HS and CD.

METHODS: Here we compared the fecal microbiota (16S rRNA gene amplicon sequencing) and habitual diet of previously reported subjects with HS (n = 55), patients with CD (n = 102) and controls (n = 95).

RESULTS AND DISCUSSION: Patients with HS consumed a Western diet similar to patients with CD. Meanwhile, habitual diet in HS and CD was significantly different to controls. Previously, we detected differences in microbiota composition among patients with HS from that of controls. We now show that 40% of patients with HS had a microbiota configuration similar to that of CD, characterised by the enrichment of pathogenic genera (Enterococcus, Veillonella and Escherichia_Shigella) and the depletion of putatively beneficial genera (Faecalibacterium). The remaining 60% of patients with HS harboured a normal microbiota similar to that of controls. Antibiotics, which are commonly used to treat HS, were identified as a co-varying with differences in microbiota composition. We examined the levels of several inflammatory markers highlighting that growth-arrest specific 6 (Gas6), which has anti-inflammatory potential, were significantly lower in the 40% of patients with HS who had a CD microbiota configuration. Levels of the pro-inflammatory cytokine IL-12, which is a modulator of intestinal inflammation in CD, were negatively correlated with the abundance of health-associated genera in patients with HS. In conclusion, the fecal microbiota may help identify patients with HS who are at greater risk for development of CD.},
}

@article {pmid38029083,
year = {2023},
author = {Khairunisa, BH and Heryakusuma, C and Ike, K and Mukhopadhyay, B and Susanti, D},
title = {Evolving understanding of rumen methanogen ecophysiology.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1296008},
doi = {10.3389/fmicb.2023.1296008},
pmid = {38029083},
issn = {1664-302X},
abstract = {Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.},
}

@article {pmid38029079,
year = {2023},
author = {Koepper, S and Clark, KF and McClure, JT and Revie, CW and Stryhn, H and Thakur, KK},
title = {Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1245818},
doi = {10.3389/fmicb.2023.1245818},
pmid = {38029079},
issn = {1664-302X},
abstract = {The shell microbial community of lobsters-a key factor in the development of epizootic shell disease (ESD)-is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently healthy lobsters from four locations in the region. More than 180 lobster shell swab samples were collected from New Brunswick, Nova Scotia and Prince Edward Island (PEI). PacBio long-read 16S rDNA sequencing and bioinformatic analyses in QIIME2 identified the shell-associated bacteria. The shell microbiome of healthy lobsters consisted mainly of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia. The microbial composition differed regionally and seasonally, with some classes showing decreased or increased relative abundances in the PEI samples as well as in the winter and spring samples in Nova Scotia. The core shell microbiome included potentially pathogenic as well as beneficial bacterial taxa, of which some were present only in certain regions. Bacterial taxa that have previously been associated with ESD were present on healthy lobsters in Atlantic Canada, but their frequency differed by location, sampling time, and moult stage. This study indicated that geographical and seasonal factors influenced the shell microbiome of apparently healthy lobsters more than host factors such as sex, size, and moult stage. Our results provide valuable reference microbial data from lobsters in a disease-free state.},
}

@article {pmid38029074,
year = {2023},
author = {Frąszczak, K and Barczyński, B and Siwiec, R and Kondracka, A and Malm, A and Kotarski, J and Witt, E and Korona-Głowniak, I},
title = {The analysis of Lactobacillus spp. distribution in the vaginal microbiota of Polish women with abnormal Pap smear result.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1257587},
doi = {10.3389/fmicb.2023.1257587},
pmid = {38029074},
issn = {1664-302X},
abstract = {INTRODUCTION: A healthy vaginal microbiota is represented mainly by Lactobacillus spp. and plays a vital role in maintaining the functional balance in the vaginal environment. Scientists have drawn attention to possible correlations between the vaginal microbiome and gynecological neoplasms. Several recent studies have shown a potential link between the vaginal microbiome and the risk of developing cervical cancer from human papillomavirus (HPV) infection. This study aimed to compare the prevalence and abundance of various lactic acid bacteria species (LABs) in vaginal swabs from healthy controls and patients with abnormal Pap smear results.

METHODS: The study included 100 women (79 patients with abnormal cervical Pap smear results and 21 controls) from whom vaginal swabs were collected. Real-time quantitative PCR was used to determine seven lactic acid bacteria (LAB) species and their quantities.

RESULTS: Most patients were colonized by two Lactobacillus species, primarily Lactobacillus gasseri (93%) and L. crispatus (83%). Patient age and place of residence were associated with the diversity of LAB in the vaginal microbiota. The abundance of L. delbrueckii in the vaginal microbiota increased, whereas the abundance of L. gasseri abundance decreased, with patient age. Lactobacillus acidophilus and Limosilactobacillus fermentum were significantly more often detected in patients living in rural versus urban areas. Statistical analysis did not show any significant differences in LAB between groups of patients with various changes on smear tests.

DISCUSSION: The degree of dysplastic changes in the endothelium or the presence of a group of atypical cervical stratified epithelial cells was not associated with significant changes in the studied vaginal bacteria.},
}

@article {pmid38029073,
year = {2023},
author = {Xie, Q and Hu, B},
title = {Effects of gut microbiota on prostatic cancer: a two-sample Mendelian randomization study.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1250369},
doi = {10.3389/fmicb.2023.1250369},
pmid = {38029073},
issn = {1664-302X},
abstract = {AIM: Recent observational and small-sample case-control studies have shown a relationship between gut microbiota composition and prostatic cancer (PCa). Nevertheless, the causal association between gut microbiota and PCa is still unclear. Herein, we used the Mendelian randomization (MR) method to explore the potential causal relationship between gut microbiota and PCa.

METHODS: In this two-sample MR study, data were extracted from the summary statistics of gut microbiota from the largest available genome-wide association study meta-analysis conducted by the MiBioGen consortium (n = 14,306) and the Dutch Microbiome Project (n = 8,208). Summary statistics for PCa were obtained from the FinnGen consortium release data (n = 95,213). Inverse variance weighted (IVW), MR-Egger, strength test (F), and MR-PRESSO were used to examine the potential causal association between gut microbiota and PCa. Cochran's Q statistics were used to quantify the heterogeneity of instrumental variables.

RESULTS: IVW estimates suggested that the relative abundance of Akkermansia muciniphila (odds ratio [OR] = 0.7926, 95% confidence interval [CI]: 0.6655-0.9440) and Bacteroides salyersiae (OR = 0.9023, 95% CI: 0.8262-0.9853) were negatively associated with the odds of PCa, while that of Eubacterium biforme (OR = 1.1629, 95% CI: 1.0110-1.3376) was positively associated with the odds of PCa. In addition, we explored these relationships among patients without other cancers and similarly found that the relative abundance of Akkermansia muciniphila, Bacteroides salyersiae, and Eubacterium biforme were linked to PCa (all P < 0.05).

CONCLUSION: Gut microbiota potentially influenced the occurrence of PCa. Our findings may provide some new ideas for researching the methods of PCa prevention. In addition, further studies are needed to explore the causal association and specific underlying mechanisms between gut microbiota and PCa.},
}

@article {pmid38029072,
year = {2023},
author = {Dreyer, A and Lenz, C and Groß, U and Bohne, W and Zautner, AE},
title = {Characterization of Campylobacter jejuni proteome profiles in co-incubation scenarios.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1247211},
doi = {10.3389/fmicb.2023.1247211},
pmid = {38029072},
issn = {1664-302X},
abstract = {In dynamic microbial ecosystems, bacterial communication is a relevant mechanism for interactions between different microbial species. When C. jejuni resides in the intestine of either avian or human hosts, it is exposed to diverse bacteria from the microbiome. This study aimed to reveal the influence of co-incubation with Enterococcus faecalis, Enterococcus faecium, or Staphylococcus aureus on the proteome of C. jejuni 81-176 using data-independent-acquisition mass spectrometry (DIA-MS). We compared the proteome profiles during co-incubation with the proteome profile in response to the bile acid deoxycholate (DCA) and investigated the impact of DCA on proteomic changes during co-incubation, as C. jejuni is exposed to both factors during colonization. We identified 1,375 proteins by DIA-MS, which is notably high, approaching the theoretical maximum of 1,645 proteins. S. aureus had the highest impact on the proteome of C. jejuni with 215 up-regulated and 230 down-regulated proteins. However, these numbers are still markedly lower than the 526 up-regulated and 516 down-regulated proteins during DCA exposure. We identified a subset of 54 significantly differentially expressed proteins that are shared after co-incubation with all three microbial species. These proteins were indicative of a common co-incubation response of C. jejuni. This common proteomic response partly overlapped with the DCA response; however, several proteins were specific to the co-incubation response. In the co-incubation experiment, we identified three membrane-interactive proteins among the top 20 up-regulated proteins. This finding suggests that the presence of other bacteria may contribute to increased adherence, e.g., to other bacteria but eventually also epithelial cells or abiotic surfaces. Furthermore, a conjugative transfer regulon protein was typically up-expressed during co-incubation. Exposure to both, co-incubation and DCA, demonstrated that the two stressors influenced each other, resulting in a unique synergistic proteomic response that differed from the response to each stimulus alone. Data are available via ProteomeXchange with identifier PXD046477.},
}

@article {pmid38028745,
year = {2023},
author = {Kural-Rendon, C and Ford, NE and Wagner, MR},
title = {Interactions with fungi vary among Tripsacum dactyloides genotypes from across a precipitation gradient.},
journal = {AoB PLANTS},
volume = {15},
number = {6},
pages = {plad072},
doi = {10.1093/aobpla/plad072},
pmid = {38028745},
issn = {2041-2851},
abstract = {Plant-associated microbes, specifically fungal endophytes, augment the ability of many grasses to adapt to extreme environmental conditions. Tripsacum dactyloides (Eastern gamagrass) is a perennial, drought-tolerant grass native to the tallgrass prairies of the central USA. The extent to which the microbiome of T. dactyloides contributes to its drought tolerance is unknown. Ninety-seven genotypes of T. dactyloides were collected from native populations across an east-west precipitation gradient in Kansas, Oklahoma and Texas, and then grown together in a common garden for over 20 years. Root and leaf samples were visually examined for fungal density. Because fungal endophytes confer drought-tolerant capabilities to their host plants, we expected to find higher densities of fungal endophytes in plants from western, drier regions, compared to plants from eastern, wetter regions. Results confirmed a negative correlation between endophyte densities in roots and precipitation at the genotype's original location (r = -0.21 P = 0.04). Our analyses reveal that the host genotype's origin along the precipitation gradient predicts the absolute abundance of symbionts in the root, but not the relative abundances of particular organisms or the overall community composition. Overall, these results demonstrate that genetic variation for plant-microbe interactions can reflect historical environment, and reinforce the importance of considering plant genotype in conservation and restoration work in tallgrass prairie ecosystems.},
}

@article {pmid38028558,
year = {2023},
author = {O'Shaughnessy, R and Common, J and Gutowska-Owsiak, D},
title = {Editorial: Novel aspects of the immunological and structural barrier of the epidermis.},
journal = {Frontiers in molecular biosciences},
volume = {10},
number = {},
pages = {1324920},
doi = {10.3389/fmolb.2023.1324920},
pmid = {38028558},
issn = {2296-889X},
}

@article {pmid38028206,
year = {2023},
author = {Chai, J and Long, X and Wu, P and Wang, J and Wu, X and Tu, Z and Wei, M and Guo, Z and Zhang, T and Chen, L},
title = {Lactobacillus sp. participated in the adaptation of Rongchang piglets to cold stress.},
journal = {Veterinarni medicina},
volume = {68},
number = {10},
pages = {392-402},
doi = {10.17221/54/2023-VETMED},
pmid = {38028206},
issn = {0375-8427},
abstract = {Rongchang piglets were easily induced to cold stress and diarrhoea in the winter when raised in an open hog house. However, they also gradually recovered under mid-cold stress. Other studies have suggested gut microbiome might be involved in the host energy metabolism to relieve stress. To study how to adapt Rongchang piglets to cold stress by gut microbiome, thirty Rongchang piglets were randomly divided into a mild cold stress group and a control group for 30 consecutive days. The findings revealed that the piglets had low growth performance and a high diarrhoea rate and mortality rate during the first half of the cold treatment, but subsequently stabilised. The level of cortisol (COR) also displayed a similar trend. In the mild cold stress group, the relative abundance of Muribaculaceae significantly increased on day 15, and the predominant bacterial on day 30 was Lactobacillus sp. Our results indicated that the Rongchang piglet's production performance and health were impaired at the start of the mild cold stress. However, as time passed, the body could progressively adapt to the low temperature, and Lactobacillus sp. participated in this process. This study provides new insight into how to alleviate health damage caused by cold stress.},
}

@article {pmid38028014,
year = {2023},
author = {Liu, W and Peng, L and Chen, L and Wan, J and Lou, S and Yang, T and Shen, Z},
title = {Skin microbial dysbiosis is a characteristic of systemic drug-related intertriginous and flexural exanthema-like lesions induced by EGFR inhibitor.},
journal = {Heliyon},
volume = {9},
number = {11},
pages = {e21690},
doi = {10.1016/j.heliyon.2023.e21690},
pmid = {38028014},
issn = {2405-8440},
abstract = {OBJECTIVES: To investigate the characteristics of the skin microbiome in severe afatinib-induced skin toxicity.

METHODS: Body site-matched skin surface samples were collected from the lesions on seven flexural sites of one lung cancer (Patient 1) with serious systemic drug-related intertriginous and flexural exanthema (SDRIFE)-like toxicity induced by EGFR-TKI and three healthy age/sex matched controls for whole metagenomics sequencing analysis. Lung cancer Patient 1 and Patient 2 were prescribed minocycline and followed up.

RESULTS: In SDRIFE-like toxicities induced by afatinib, lesion microbiota richness (ACE and Chao1 index: p < 0.001) and diversity (Shannon's and Simpson's diversity indices: p < 0.01) were reduced. Similarly, the beta diversity analysis (R = 1, p = 0.002 for ANOSIM) showed that the apparent difference in the microbiota composition was statistically significant. The microbial taxa composition in the patient showed an increased abundance of pathogenic bacteria and a decreased abundance of commensal bacteria. LEfSe analysis identified strong bacterial pathogenicity in the patient, while healthy controls exhibited enrichment in several pathways that are beneficial for skin commensal bacteria and skin physiology, including key amino acid metabolism, energy/lipid/glycan biosynthesis/metabolism, and cofactors/vitamins biosynthesis. Ultimately, the patients experienced significant improvement with minocycline.

CONCLUSION: Microbial dysbiosis is a characteristic of severe SDRIFE-like toxicity induced by afatinib.},
}

@article {pmid38027512,
year = {2023},
author = {Barton, JR and Londregan, AK and Alexander, TD and Entezari, AA and Covarrubias, M and Waldman, SA},
title = {Enteroendocrine cell regulation of the gut-brain axis.},
journal = {Frontiers in neuroscience},
volume = {17},
number = {},
pages = {1272955},
doi = {10.3389/fnins.2023.1272955},
pmid = {38027512},
issn = {1662-4548},
abstract = {Enteroendocrine cells (EECs) are an essential interface between the gut and brain that communicate signals about nutrients, pain, and even information from our microbiome. EECs are hormone-producing cells expressed throughout the gastrointestinal epithelium and have been leveraged by pharmaceuticals like semaglutide (Ozempic, Wegovy), terzepatide (Mounjaro), and retatrutide (Phase 2) for diabetes and weight control, and linaclotide (Linzess) to treat irritable bowel syndrome (IBS) and visceral pain. This review focuses on role of intestinal EECs to communicate signals from the gut lumen to the brain. Canonically, EECs communicate information about the intestinal environment through a variety of hormones, dividing EECs into separate classes based on the hormone each cell type secretes. Recent studies have revealed more diverse hormone profiles and communication modalities for EECs including direct synaptic communication with peripheral neurons. EECs known as neuropod cells rapidly relay signals from gut to brain via a direct communication with vagal and primary sensory neurons. Further, this review discusses the complex information processing machinery within EECs, including receptors that transduce intraluminal signals and the ion channel complement that govern initiation and propagation of these signals. Deeper understanding of EEC physiology is necessary to safely treat devastating and pervasive conditions like irritable bowel syndrome and obesity.},
}

@article {pmid38027267,
year = {2023},
author = {Francis, D and Chawla, A and LaComb, JF and Markarian, K and Robertson, CE and Frank, DN and Gathungu, GN},
title = {Gastroesophageal reflux and PPI exposure alter gut microbiota in very young infants.},
journal = {Frontiers in pediatrics},
volume = {11},
number = {},
pages = {1254329},
doi = {10.3389/fped.2023.1254329},
pmid = {38027267},
issn = {2296-2360},
abstract = {IMPORTANCE: Infants with symptomatic Gastroesophageal reflux are treated with pharmacological therapy that includes proton pump inhibitors (PPI) with clinical improvement. The alterations to gut microbiome profiles in comparison to infants without reflux is not known.

OBJECTIVE: To determine the effect of PPI therapy on gut bacterial richness, diversity, and proportions of specific taxa in infants when compared to infants not exposed to acid suppressive therapy.

This cohort study was conducted at the Stony Brook Hospital in Stony Brook, NY between February 2016, and June 2019. Infants meeting inclusion criteria were enrolled in a consecutive fashion.

RESULTS: A total of 76 Infants were recruited and 60 were enrolled in the study, Twenty nine infants met clinical criteria for reflux and were treated with PPI therapy: median [IQR] gestation: 38.0 weeks [34.7-39.6 weeks]; median [IQR] birthweight: 2.95 Kg [2.2-3.4]; 14 [46.7%] male) and 29 infant were healthy controls median [IQR] gestation: 39.1 weeks [38-40 weeks]; median [IQR] birthweight: 3.3 Kg [2.2-3.4]; 17 [58.6%] male); 58 stool samples from 58 infants were analyzed. There were differences in Shannon diversity between the reflux and control groups. The reflux group that was exposed to PPI therapy had increased relative abundance of a diverse set of genera belonging to the phylum Firmicutes. On the other hand, the control group microbiota was dominated by Bifidobacterium, and a comparatively lower level of enrichment and abundance of microbial taxa was observed in this group of infants.

CONCLUSIONS AND RELEVANCE: We observed significant differences in both α- and β-diversity of the microbiome, when the two groups of infants were compared. The microbiome in the reflux group had more bacterial taxa and the duration of PPIs exposure was clearly associated with the diversity and abundance of gut microbes. These findings suggest that PPI exposure among infants results in early enrichment of the intestinal microbiome.},
}

@article {pmid38027226,
year = {2023},
author = {Tang, J and Han, Y and Pei, L and Gu, W and Qiu, R and Wang, S and Ma, Q and Gan, Y and Tang, M},
title = {Comparative analysis of the rhizosphere microbiome and medicinally active ingredients of Atractylodes lancea from different geographical origins.},
journal = {Open life sciences},
volume = {18},
number = {1},
pages = {20220769},
doi = {10.1515/biol-2022-0769},
pmid = {38027226},
issn = {2391-5412},
abstract = {This study aimed to explore the important role of the rhizosphere microbiome in the quality of Atractylodes lancea (Thunb.) DC. (A. lancea). The rhizosphere microbial community of A. lancea at two sampling sites was studied using metagenomic technology. The results of α-diversity analysis showed that the rhizosphere microbial richness and diversity were higher in the Maoshan area. The higher abundance of core microorganisms of the rhizosphere, especially Penicillium and Streptomyces, in the Maoshan area compared with those in the Yingshan area might be an important factor affecting the yield of A. lancea. Redundancy analysis illustrated that the available phosphorus had a significant effect on the rhizosphere microbial community structure of A. lancea. We also showed that the plant-microbe and microbe-microbe interactions were closer in the Maoshan area than in the Yingshan area, and Streptomyces were the main contributors to the potential functional difference between the two regions. A. lancea in the Maoshan area had a high content of atractylodin and atractylon, which might be related to the enhanced abundance of Streptomyces, Candidatus-Solibacter, and Frankia. Taken together, this study provided theoretical insights into the interaction between medicinal plants and the rhizosphere microbiome and provides a valuable reference for studying beneficial microbes of A. lancea.},
}

@article {pmid38027221,
year = {2023},
author = {Nie, D and Li, C and Zhang, Y},
title = {PitNETs and the gut microbiota: potential connections, future directions.},
journal = {Frontiers in endocrinology},
volume = {14},
number = {},
pages = {1255911},
doi = {10.3389/fendo.2023.1255911},
pmid = {38027221},
issn = {1664-2392},
abstract = {The role of the gut microbiome has been widely discussed in numerous works of literature. The biggest concern is the association of the gut microbiome with the central nervous system through the microbiome-brain-gut axis in the past ten years. As more and more research has been done on the relationship between the disease of the central nervous system and gut microbes. This fact is being revealed that gut microbes seem to play an important role from the onset and progression of the disease to clinical symptoms, and new treatments. As a special tumor of the central nervous system, pituitary neuroendocrine tumors (PitNETs)are closely related to metabolism, endocrinology, and immunity. These factors are the vectors through which intestinal microbes interact with the central nervous system. However, little is known about the effects of gut microbes on the PitNET. In this review, the relationship of gut microbiota in PitNETs is introduced, the potential effects of the gut-brain axis in this relationship are analyzed, and future research directions are presented.},
}

@article {pmid38027173,
year = {2023},
author = {Aghajanova, L and Altmäe, S and Sokalska, A},
title = {Editorial: Uterine factors associated with fertility impairment.},
journal = {Frontiers in endocrinology},
volume = {14},
number = {},
pages = {1307237},
doi = {10.3389/fendo.2023.1307237},
pmid = {38027173},
issn = {1664-2392},
}

@article {pmid38027009,
year = {2023},
author = {Feng, Y and Xu, D},
title = {Short-chain fatty acids are potential goalkeepers of atherosclerosis.},
journal = {Frontiers in pharmacology},
volume = {14},
number = {},
pages = {1271001},
doi = {10.3389/fphar.2023.1271001},
pmid = {38027009},
issn = {1663-9812},
abstract = {Short-chain fatty acids (SCFAs) are metabolites produced by gut bacteria and play a crucial role in various inflammatory diseases. Increasing evidence suggests that SCFAs can improve the occurrence and progression of atherosclerosis. However, the molecular mechanisms through which SCFAs regulate the development of atherosclerosis have not been fully elucidated. This review provides an overview of the research progress on SCFAs regarding their impact on the risk factors and pathogenesis associated with atherosclerosis, with a specific focus on their interactions with the endothelium and immune cells. These interactions encompass the inflammation and oxidative stress of endothelial cells, the migration of monocytes/macrophages, the lipid metabolism of macrophages, the proliferation and migration of smooth muscle cells, and the proliferation and differentiation of Treg cells. Nevertheless, the current body of research is insufficient to comprehensively understand the full spectrum of SCFAs' mechanisms of action. Therefore, further in-depth investigations are imperative to establish a solid theoretical foundation for the development of clinical therapeutics in this context.},
}

@article {pmid38026977,
year = {2023},
author = {Zhou, J and Liu, J and Lin, Q and Shi, L and Zeng, Z and Guan, L and Ma, Y and Zeng, Y and Zhong, S and Xu, L},
title = {Characteristics of the gut microbiome and metabolic profile in elderly patients with sarcopenia.},
journal = {Frontiers in pharmacology},
volume = {14},
number = {},
pages = {1279448},
doi = {10.3389/fphar.2023.1279448},
pmid = {38026977},
issn = {1663-9812},
abstract = {Introduction: There is growing evidence of research indicating that the gut microbiota is involved in the development of sarcopenia. Nevertheless, there exists a notable deficiency in comprehension concerning the connection between irregularities in the intestinal microbiome and metabolic processes in older individuals suffering from sarcopenia. Methods: To analyze fecal samples obtained from a cohort of 30 older patients diagnosed with sarcopenia as well as 30 older patients without sarcopenia, this study employed 16S rDNA sequencing and liquid chromatography-mass spectrometry (LC-MS)-based non-targeted metabolomics profiling techniques. Results: As a result, we found that 29 genera and 172 metabolites were significantly altered in the sarcopenic patients. Among them, Blautia, Lachnospiraceae_unclassified, and Subdoligranulum were the bacteria with a potential diagnostic value for sarcopenia diagnosis. Correlation analysis between clinical indices and these gut bacteria suggested that the IL-6 level was negatively correlated with Blautia. Function prediction analysis demonstrated that 17 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways differ significantly between sarcopenic and non-sarcopenic patients. The primary classes of metabolites identified in the study included lipids and lipid-like molecules, organic acids and derivatives, and organoheterocyclic compounds. KEGG enrichment analysis showed that purine metabolism, arginine and proline metabolism, alanine, aspartate, and glutamate metabolism, butanoate metabolism, and histidine metabolism may contribute to the development of sarcopenia. The correlation study on gut microbiota and metabolites found that Lachnospiraceae_unclassified was positively associated with seven metabolites that were more abundant in the non-sarcopenia group and negatively correlated with three metabolites that were more abundant in the sarcopenia group. In addition, Subdoligranulum was positively correlated with seven metabolites that were lacking in sarcopenia and negatively correlated with two metabolites that were enriching in sarcopenia. Moreover, Blautia was positively associated with xanthosine. Discussion: We conducted a study on the intestinal microbiota and metabolic profile of elderly individuals with sarcopenia, offering a comprehensive analysis of the overall ecosystem. Through this investigation, we were able to validate existing research on the gut-muscle axis and further investigate potential pathogenic processes and treatment options for sarcopenia.},
}

@article {pmid38026796,
year = {2023},
author = {Pohlin, F and Frei, C and Meyer, LCR and Roch, FF and Quijada, NM and Conrady, B and Neubauer, V and Hofmeyr, M and Cooper, D and Stalder, G and Wetzels, SU},
title = {Capture and transport of white rhinoceroses (Ceratotherium simum) cause shifts in their fecal microbiota composition towards dysbiosis.},
journal = {Conservation physiology},
volume = {11},
number = {1},
pages = {coad089},
doi = {10.1093/conphys/coad089},
pmid = {38026796},
issn = {2051-1434},
abstract = {Translocations of Rhinocerotidae are commonly performed for conservation purposes but expose the animals to a variety of stressors (e.g. prolonged fasting, confinement, novel environment, etc.). Stress may change the composition of gut microbiota, which can impact animal health and welfare. White rhinoceroses in particular can develop anorexia, diarrhea and enterocolitis after translocation. The aim of this study was to investigate the associations of age, sex and translocation on the rhinoceros' fecal bacterial microbiota composition. fecal samples were collected from rhinoceroses at capture (n = 16) and after a >30-hour road transport (n = 7). DNA was isolated from these samples and submitted for 16S rRNA V3-V4 phylotyping. Alpha diversity indices of the rhinoceros' fecal microbiota composition of different age, sex and before and after transport were compared using non-parametric statistical tests and beta diversity indices using Permutational Multivariate Analysis Of Variance (PERMANOVA). Resulting P-values were alpha-corrected (Padj.). Alpha and beta diversity did not differ between rhinoceroses of different age and sex. However, there was a significant difference in beta diversity between fecal samples collected from adult animals at capture and after transport. The most abundant bacterial phyla in samples collected at capture were Firmicutes and Bacteroidetes (85.76%), represented by Lachnospiraceae, Ruminococcaceae and Prevotellaceae families. The phyla Proteobacteria (Padj. = 0.009) and Actinobacteria (Padj. = 0.012), amongst others, increased in relative abundance from capture to after transport encompassing potentially pathogenic bacterial families such as Enterobacteriaceae (Padj. = 0.018) and Pseudomonadaceae (Padj. = 0.022). Important commensals such as Spirochaetes (Padj. = 0.009), Fibrobacteres (Padj. = 0.018) and Lachnospiraceae (Padj. = 0.021) decreased in relative abundance. These results indicate that the stressors associated with capture and transport cause an imbalanced fecal microbiota composition in white rhinoceroses that may lead to potentially infectious intestinal disorders. This imbalance may result from recrudescence of normally innocuous pathogens, increased shedding of pathogens or increased vulnerability to new pathogens.},
}

@article {pmid38026235,
year = {2023},
author = {McCall, KD and Walter, D and Patton, A and Thuma, JR and Courreges, MC and Palczewski, G and Goetz, DJ and Bergmeier, S and Schwartz, FL},
title = {Anti-Inflammatory and Therapeutic Effects of a Novel Small-Molecule Inhibitor of Inflammation in a Male C57BL/6J Mouse Model of Obesity-Induced NAFLD/MAFLD.},
journal = {Journal of inflammation research},
volume = {16},
number = {},
pages = {5339-5366},
doi = {10.2147/JIR.S413565},
pmid = {38026235},
issn = {1178-7031},
abstract = {PURPOSE: Non-alcoholic fatty liver disease (NAFLD), recently renamed metabolic (dysfunction) associated fatty liver disease (MAFLD), is the most common chronic liver disease in the United States. Presently, there is an intense and ongoing effort to identify and develop novel therapeutics for this disease. In this study, we explored the anti-inflammatory activity of a new compound, termed IOI-214, and its therapeutic potential to ameliorate NAFLD/MAFLD in male C57BL/6J mice fed a high fat (HF) diet.

METHODS: Murine macrophages and hepatocytes in culture were treated with lipopolysaccharide (LPS) ± IOI-214 or DMSO (vehicle), and RT-qPCR analyses of inflammatory cytokine gene expression were used to assess IOI-214's anti-inflammatory properties in vitro. Male C57BL/6J mice were also placed on a HF diet and treated once daily with IOI-214 or DMSO for 16 weeks. Tissues were collected and analyzed to determine the effects of IOI-214 on HF diet-induced NAFL D/MAFLD. Measurements such as weight, blood glucose, serum cholesterol, liver/serum triglyceride, insulin, and glucose tolerance tests, ELISAs, metabolomics, Western blots, histology, gut microbiome, and serum LPS binding protein analyses were conducted.

RESULTS: IOI-214 inhibited LPS-induced inflammation in macrophages and hepatocytes in culture and abrogated HF diet-induced mesenteric fat accumulation, hepatic inflammation and steatosis/hepatocellular ballooning, as well as fasting hyperglycemia without affecting insulin resistance or fasting insulin, cholesterol or TG levels despite overall obesity in vivo in male C57BL/6J mice. IOI-214 also decreased systemic inflammation in vivo and improved gut microbiota dysbiosis and leaky gut.

CONCLUSION: Combined, these data indicate that IOI-214 works at multiple levels in parallel to inhibit the inflammation that drives HF diet-induced NAFLD/MAFLD, suggesting that it may have therapeutic potential for NAFLD/MAFLD.},
}

@article {pmid38026003,
year = {2023},
author = {Beretta, S and Apparicio, M and Toniollo, GH and Cardozo, MV},
title = {The importance of the intestinal microbiota in humans and dogs in the neonatal period.},
journal = {Animal reproduction},
volume = {20},
number = {3},
pages = {e20230082},
doi = {10.1590/1984-3143-AR2023-0082},
pmid = {38026003},
issn = {1984-3143},
abstract = {The neonatal period represents a critical stage for the establishment and development of the gut microbiota, which profoundly influences the future health trajectory of individuals. This review examines the importance of intestinal microbiota in humans and dogs, aiming to elucidate the distinct characteristics and variations in the composition between these two species. In humans, the intestinal microbiota contributes to several crucial physiological processes, including digestion, nutrient absorption, immune system development, and modulation of host metabolism. Dysbiosis, an imbalance or disruption of the gut microbial community, has been linked to various disorders, such as inflammatory bowel disease, obesity, and even neurological conditions. Furthermore, recent research has unveiled the profound influence of the gut-brain axis, emphasizing the bidirectional communication between the gut microbiota and the central nervous system, impacting cognitive function and mental health. Similarly, alterations in the canine intestinal microbiota have been associated with gastrointestinal disorders, including chronic enteropathy, such as inflammatory bowel disease, food allergies, and ulcerative histiocytic colitis. However, our understanding of the intricacies and functional significance of the intestinal microbiota in dogs remains limited. Understanding the complex dynamics of the intestinal microbiota in both humans and dogs is crucial for devising effective strategies to promote health and manage disease. Moreover, exploring the similarities and differences in the gut microbial composition between these two species can facilitate translational research, potentially leading to innovative therapeutic interventions and strategies to enhance the well-being of both humans and dogs.},
}

@article {pmid38025771,
year = {2023},
author = {Shadid, ILC and Lee-Sarwar, K and Lu, Z and Yadama, A and Laranjo, N and Carey, V and O'Connor, GT and Zeiger, RS and Bacharier, L and Guchelaar, HJ and Liu, YY and Litonjua, AA and Weiss, ST and Mirzakhani, H},
title = {Early life gut microbiome in children following spontaneous preterm birth and maternal preeclampsia.},
journal = {iScience},
volume = {26},
number = {12},
pages = {108311},
doi = {10.1016/j.isci.2023.108311},
pmid = {38025771},
issn = {2589-0042},
abstract = {The early life microbiome plays an important role in developmental and long-term health outcomes. However, it is unknown whether adverse pregnancy complications affect the offspring's gut microbiome postnatally and in early years. In a longitudinal cohort with a five-year follow-up of mother-child pairs affected by preeclampsia (PE) or spontaneous preterm birth (sPTB), we evaluated offspring gut alpha and beta diversity as well as taxa abundances considering factors like breastfeeding and mode of delivery. Our study highlights a trend where microbiome diversity exhibits comparable development across adverse and normal pregnancies. However, specific taxa at genus level emerge with distinctive abundances, showing enrichment and/or depletion over time in relation to PE or sPTB. These findings underscore the potential for certain adverse pregnancy complications to induce alterations in the offspring's microbiome over the course of early life. The implications of these findings on the immediate and long-term health of offspring should be investigated in future studies.},
}

@article {pmid38025767,
year = {2023},
author = {Sun, H and Su, X and Liu, Y and Li, G and Du, Q},
title = {Roseburia intestinalis relieves intrahepatic cholestasis of pregnancy through bile acid/FXR-FGF15 in rats.},
journal = {iScience},
volume = {26},
number = {12},
pages = {108392},
doi = {10.1016/j.isci.2023.108392},
pmid = {38025767},
issn = {2589-0042},
abstract = {Previous research has demonstrated significant differences in intestinal flora between pregnant women with intrahepatic cholestasis of pregnancy (ICP) and healthy pregnant women. The objective of our study is to identify the key bacteria involved in ICP rats and explore the underlying mechanism. We established an ICP rat model and collected rat feces for metagenomic sequencing and found that Roseburia intestinalis (R.I) is the key bacteria in ICP. Transplantation of R.I improved phenotypes associated with ICP through the bile acid/farnesoid X receptor-fibroblast growth factor 15 (FXR-FGF15) signaling pathway. We used the FXR antagonist Z-Guggulsterone (Z-Gu) to verify the key role of FXR in ICP and found that Z-Gu reversed the benefits of R.I on ICP rats. Our research highlights the important role of intestinal flora in the pathogenesis of ICP and provides a novel approach for its treatment.},
}

@article {pmid38025669,
year = {2023},
author = {Kim, HY and Kim, TH and Shin, JH and Cho, K and Ha, HK and Lee, A and Kim, YJ},
title = {Navigating the microbial community in the trachea-oropharynx of breast cancer patients with or without neoadjuvant chemotherapy (NAC) via endotracheal tube: has NAC caused any change?.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16366},
doi = {10.7717/peerj.16366},
pmid = {38025669},
issn = {2167-8359},
abstract = {BACKGROUND: We compare the diversity and niche specificity of the microbiome in the trachea-oropharynx microbiome of malignant breast neoplasm with or without neoadjuvant chemotherapy (NAC) via NGS analysis.

METHODS: We prospectively collected a total of 40 endotracheal tubes intubated from subjects, of whom 20 with NAC treated breast cancer (NAC group) and 20 with breast cancer without NAC (Non-NAC group). We generated 16S rRNA-based microbial profiles in IlluminaTM platform and alpha diversity indices were compared between groups. For the comparison of taxa abundance, linear discriminant analysis effect size method with Kruskal-Wallis test was used. The distribution of variables between the two groups was compared using the Mann-Whitney test. For beta diversity analysis, PERMANOVA was used.

RESULTS: Among the diversity indices, the NAC group showed significantly lower Chao1, Inverse Simpson, and Shannon indices than the Non-NAC group. The three most frequent taxa of all two groups were Streptococcus (20.4%), followed by Veillonella (11.9%), and Prevorella (10.4%). This order was the same in NAC and non-NAC groups.

CONCLUSION: Here, we provide the first comparison data of the respiratory tract microbiome of breast cancer patients with or without NAC via NGS analysis. This study ultimately seeks to contribute to future studies on the lower respiratory tract in cancer patients with cytotoxic chemotherapy by establishing reliable control data.},
}

@article {pmid38025434,
year = {2023},
author = {Hall, CV and Radford-Smith, G and Savage, E and Robinson, C and Cocchi, L and Moran, RJ},
title = {Brain signatures of chronic gut inflammation.},
journal = {Frontiers in psychiatry},
volume = {14},
number = {},
pages = {1250268},
doi = {10.3389/fpsyt.2023.1250268},
pmid = {38025434},
issn = {1664-0640},
abstract = {Gut inflammation is thought to modify brain activity and behaviour via modulation of the gut-brain axis. However, how relapsing and remitting exposure to peripheral inflammation over the natural history of inflammatory bowel disease (IBD) contributes to altered brain dynamics is poorly understood. Here, we used electroencephalography (EEG) to characterise changes in spontaneous spatiotemporal brain states in Crohn's Disease (CD) (n = 40) and Ulcerative Colitis (UC) (n = 30), compared to healthy individuals (n = 28). We first provide evidence of a significantly perturbed and heterogeneous microbial profile in CD, consistent with previous work showing enduring and long-standing dysbiosis in clinical remission. Results from our brain state assessment show that CD and UC exhibit alterations in the temporal properties of states implicating default-mode network, parietal, and visual regions, reflecting a shift in the predominance from externally to internally-oriented attentional modes. We investigated these dynamics at a finer sub-network resolution, showing a CD-specific and highly selective enhancement of connectivity between the insula and medial prefrontal cortex (mPFC), regions implicated in cognitive-interoceptive appraisal mechanisms. Alongside overall higher anxiety scores in CD, we also provide preliminary support to suggest that the strength of chronic interoceptive hyper-signalling in the brain co-occurs with disease duration. Together, our results demonstrate that a long-standing diagnosis of CD is, in itself, a key factor in determining the risk of developing altered brain network signatures.},
}

@article {pmid38025161,
year = {2023},
author = {Chowdhary, A and Van Gelder, RN and Sundararajan, M},
title = {Methodologic Considerations for Studying the Ocular Surface Microbiome.},
journal = {Ophthalmology science},
volume = {3},
number = {4},
pages = {100408},
doi = {10.1016/j.xops.2023.100408},
pmid = {38025161},
issn = {2666-9145},
abstract = {UNLABELLED: The ocular surface microbiome, unlike that of the skin or gut, has not been well characterized. Culture experiments historically suggested a nearly sterile ocular surface, but initial application of molecular methods such as 16S ribosomal RNA and high-throughput sequencing demonstrated a surprisingly rich ocular surface microbiome. However, a major limitation in studying such a low-biomass niche is the potential for artifactual results when amplification-based techniques such as ribosomal polymerase chain reaction and shotgun sequencing are used. It will be essential to establish standards across the field for sample collection, positive and negative controls, and limitation of contamination in both the laboratory setting and computational analysis. New developments in ocular microbiome research, including the generation of reference reagents and fluoroscopic imaging techniques, provide improved means to validate sequencing results and to visualize complex interactions between host cells and bacteria. Through more thorough characterization of the ocular surface microbiome, the connections between a dysregulated surface and ophthalmic disease may be better understood.

FINANCIAL DISCLOSURES: Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.},
}

@article {pmid38024855,
year = {2023},
author = {Mao, Z and Hui, H and Zhao, X and Xu, L and Qi, Y and Yin, L and Qu, L and Han, L and Peng, J},
title = {Protective effects of dioscin against Parkinson's disease via regulating bile acid metabolism through remodeling gut microbiome/GLP-1 signaling.},
journal = {Journal of pharmaceutical analysis},
volume = {13},
number = {10},
pages = {1153-1167},
doi = {10.1016/j.jpha.2023.06.007},
pmid = {38024855},
issn = {2214-0883},
abstract = {It is necessary to explore potent therapeutic agents via regulating gut microbiota and metabolism to combat Parkinson's disease (PD). Dioscin, a bioactive steroidal saponin, shows various activities. However, its effects and mechanisms against PD are limited. In this study, dioscin dramatically alleviated neuroinflammation and oxidative stress, and restored the disorders of mice induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). 16 S rDNA sequencing assay demonstrated that dioscin reversed MPTP-induced gut dysbiosis to decrease Firmicutes-to-Bacteroidetes ratio and the abundances of Enterococcus, Streptococcus, Bacteroides and Lactobacillus genera, which further inhibited bile salt hydrolase (BSH) activity and blocked bile acid (BA) deconjugation. Fecal microbiome transplantation test showed that the anti-PD effect of dioscin was gut microbiota-dependent. In addition, non-targeted fecal metabolomics assays revealed many differential metabolites in adjusting steroid biosynthesis and primary bile acid biosynthesis. Moreover, targeted bile acid metabolomics assay indicated that dioscin increased the levels of ursodeoxycholic acid, tauroursodeoxycholic acid, taurodeoxycholic acid and β-muricholic acid in feces and serum. In addition, ursodeoxycholic acid administration markedly improved the protective effects of dioscin against PD in mice. Mechanistic test indicated that dioscin significantly up-regulated the levels of takeda G protein-coupled receptor 5 (TGR5), glucagon-like peptide-1 receptor (GLP-1R), GLP-1, superoxide dismutase (SOD), and down-regulated NADPH oxidases 2 (NOX2) and nuclear factor-kappaB (NF-κB) levels. Our data indicated that dioscin ameliorated PD phenotype by restoring gut dysbiosis and regulating bile acid-mediated oxidative stress and neuroinflammation via targeting GLP-1 signal in MPTP-induced PD mice, suggesting that the compound should be considered as a prebiotic agent to treat PD in the future.},
}

@article {pmid38024851,
year = {2023},
author = {Ravi, A and Marietta, EV and Alexander, JA and Murray, JA and Katzka, DA},
title = {H influenzae LPS colocalization with Toll-like receptor 4 in eosinophilic esophagitis.},
journal = {The journal of allergy and clinical immunology. Global},
volume = {2},
number = {4},
pages = {100151},
doi = {10.1016/j.jacig.2023.100151},
pmid = {38024851},
issn = {2772-8293},
abstract = {BACKGROUND: Patients with eosinophilic esophagitis (EoE) have a unique esophageal microbiome with increased presence of Haemophilus influenzae, but its role in the disease is unclear.

OBJECTIVE: Microbiome-derived bacterial LPS activation of Toll-like receptors (TLR) is a potential mechanism for inducing inflammation in other chronic inflammatory diseases, but it has not been studied in EoE. Our aim was therefore to study microbiome-derived bacterial LPS activation of TLRs in EoE.

METHODS: We studied 10 patients with active EoE, 9 patients with inactive EoE, and 10 control patients. Esophageal biopsy samples from the controls, patients with active EoE (>15 eosinophils/hpf), and patients with inactive EoE were immunostained for the presence of H influenzae LPS, presence of TLR4, and colocalization of LPS and TLR4. Staining intensity was measured by using confocal laser microscopy and scored on a scale from 0 to 3 as the average score assigned by 2 blinded observers.

RESULTS: H influenzae LPS was detected by positive staining in 20 of the 29 patients (69.0%), including 9 of the 10 patients with active EoE (90.0%), 8 of the 9 patients with inactive EoE (89.9%), and 3 of the 10 controls (30%); its level was greater in the patients with active EoE than in the controls (P = .063). TLR4 was detected by positive staining in 19 of the 29 patients (65.5%), including 9 of the 10 patients with active EoE (90.0%), 4 of the 9 patients with inactive EoE (44.4%), and 6 of the 10 controls (60.0%); its level was higher in the patients with active EoE than in those with inactive EoE (P = .096). The result of testing for colocalization of LPS and TLR4 was positive in 8 of 10 patients with active EoE (80.0%), 1 of 9 patients with inactive EoE (11.1%), and 1 of 10 control patients (10.0%), with greater colocalization of H influenzae LPS and TLR4 staining density in the samples from patients with active EoE than in the controls or the patients with inactive EoE (P = .009 and P = .018, respectively).

CONCLUSION: Esophageal microbiome-rich H influenzae LPS colocalizes to TLR4 in active EoE. These data lend further support to a role for the esophageal microbiome in modulating the activity of EoE.},
}

@article {pmid38024475,
year = {2023},
author = {Zhao, W and Lei, J and Ke, S and Chen, Y and Xiao, J and Tang, Z and Wang, L and Ren, Y and Alnaggar, M and Qiu, H and Shi, W and Yin, L and Chen, Y},
title = {Fecal microbiota transplantation plus tislelizumab and fruquintinib in refractory microsatellite stable metastatic colorectal cancer: an open-label, single-arm, phase II trial (RENMIN-215).},
journal = {EClinicalMedicine},
volume = {66},
number = {},
pages = {102315},
doi = {10.1016/j.eclinm.2023.102315},
pmid = {38024475},
issn = {2589-5370},
abstract = {BACKGROUND: Immunotherapy has revolutionized the treatment of cancer. However, microsatellite stable (MSS) metastatic colorectal cancer (mCRC) shows a low response to PD-1 inhibitors. Antiangiogenic therapy can enhance anti-PD-1 efficacy, but it still cannot meet clinical needs. Increasing evidence supported a close relationship between gut microbiome and anti-PD-1 efficacy. This study aimed to explore the efficacy and safety of the combination of fecal microbiota transplantation (FMT) and tislelizumab and fruquintinib in refractory MSS mCRC.

METHODS: In the phase II trial, MSS mCRC patients were administered FMT plus tislelizumab and fruquintinib as a third-line or above treatment. The primary endpoint was progression-free survival (PFS). Secondary endpoints were overall survival (OS), objective response rate (ORR), disease control rate (DCR), duration of response (DoR), clinical benefit rate (CBR), safety and quality of life. Feces and peripheral blood were collected for exploratory biomarker analysis. This study is registered with Chictr.org.cn, identifier ChiCTR2100046768.

FINDINGS: From May 10, 2021 to January 17, 2022, 20 patients were enrolled. Median follow-up was 13.7 months. Median PFS was 9.6 months (95% CI 4.1-15.1). Median OS was 13.7 months (95% CI 9.3-17.7). Median DoR was 8.1 months (95% CI 1.7-10.6). ORR was 20% (95% CI 5.7-43.7). DCR was 95% (95% CI 75.1-99.9). CBR was 60% (95% CI 36.1-80.9). Nineteen patients (95%) experienced at least one treatment-related adverse event (TRAE). Six patients (30%) had grade 3-4 TRAEs, with the most common being albuminuria (10%), urine occult blood (10%), fecal occult blood (10%), hypertension (5%), hyperglycemia (5%), liver dysfunction (5%), hand-foot skin reaction (5%), and hypothyroidism (5%). No treatment-related deaths occurred. Responders had a high-abundance of Proteobacteria and Lachnospiraceae family and a low-abundance of Actinobacteriota and Bifidobacterium. The treatment did not change the structure of peripheral blood TCR repertoire. However, the expanded TCRs exhibited the characteristics of antigen-driven responses in responders.

INTERPRETATION: FMT plus tislelizumab and fruquintinib as third-line or above treatment showed improved survival and manageable safety in refractory MSS mCRC, suggesting a valuable new treatment option for this patient population.

FUNDING: This study was supported by the National Natural Science Foundation of China (82102954 to Wensi Zhao) and the Special Project of Central Government for Local Science and Technology Development of Hubei Province (ZYYD2020000169 to Yongshun Chen).},
}