Gut Microbiome In Subjects Research Articles

Machine learning and network analysis of the gut microbiome from patients with schizophrenia and non-psychiatric subject controls reveal behavioral risk factors and bacterial interactions

Recent findings have supported an association between deviations in gut microbiome composition and schizophrenia. However, the extent to which the gut microbiota contributes to schizophrenia remains unclear. Moreover, studies have yet to explore variations in ecological associations among bacterial types in subjects with schizophrenia, which can reveal differences in community interactions and gut stability. We examined the dataset collected by Nguyen et al. (2021) to investigate the similarities and differences in gut microbial constituents between 48 subjects with schizophrenia and 48 matched non-psychiatric comparison cases. We re-analyzed alpha- and beta-diversity differences and completed modified differential abundance analyses and confirmed the findings of Nguyen et al. (2021) that there was little variation in alpha-diversity but significant differences in beta-diversity between individuals with schizophrenia and non-psychiatric subjects. We also conducted mediation analysis, developed a machine learning (ML) model to predict schizophrenia, and completed network analysis to examine community-level interactions among bacterial taxa. Our study offers new insights, suggesting that the gut microbiome mediates the effects between schizophrenia and smoking status, BMI, anxiety score, and depression score. Our differential abundance and network analysis findings suggest that the differential abundance of Lachnospiraceae and Ruminococcaceae taxa fosters a decrease in stabilizing competitive interactions in the gut microbiome of subjects with schizophrenia. Loss of this competition may promote ecological instability and dysbiosis, altering gut-brain axis interactions in these subjects.

Gut microbiome features associated with liver fibrosis in Hispanics, a population at high risk for fatty liver disease.

Hispanics are disproportionately affected by NAFLD, liver fibrosis, cirrhosis, and HCC. Preventive strategies and noninvasive means to identify those in this population at high risk for liver fibrosis, are urgently needed. We aimed to characterize the gut microbiome signatures and related biological functions associated with liver fibrosis in Hispanics and identify environmental and genetic factors affecting them. Subjects of the population-based Cameron County Hispanic Cohort (CCHC; n = 217) were screened by vibration-controlled transient elastography (FibroScan). Among them, 144 (66.7%) had steatosis and 28 (13.0%) had liver fibrosis. The gut microbiome of subjects with liver fibrosis was enriched with immunogenic commensals (e.g., Prevotella copri, Holdemanella, Clostridiaceae 1) and depleted of Bacteroides caccae, Parabacteroides distasonis, Enterobacter, and Marinifilaceae. The liver fibrosis-associated metagenome was characterized by changes in the urea cycle, L-citrulline biosynthesis and creatinine degradation pathways, and altered synthesis of B vitamins and lipoic acid. These metagenomic changes strongly correlated with the depletion of Parabacteroides distasonis and enrichment of Prevotella and Holdemanella. Liver fibrosis was also associated with depletion of bacterial pathways related to L-fucose biosynthesis. Alcohol consumption, even moderate, was associated with high Prevotella abundance. The single-nucleotide polymorphisms rs3769502 and rs7573751 in the NCK adaptor protein 2 (NCK2) gene positively associated with high Prevotella abundance. Hispanics with liver fibrosis display microbiome profiles and associated functional changes that may promote oxidative stress and a proinflammatory environment. These microbiome signatures, together with NCK2 polymorphisms, may have utility in risk modeling and disease prevention in this high-risk population.

An alcohol-free beer enriched with isomaltulose and a resistant dextrin modulates gut microbiome in subjects with type 2 diabetes mellitus and overweight or obesity: a pilot study.

We aimed to study the effect of consuming an alcohol-free beer with modified carbohydrates composition (almost completely eliminating maltose and adding isomaltulose (16.5 g day-1) and resistant maltodextrin (5.28 g day-1)) in gut microbiome, compared to regular alcohol-free beer in subjects with T2DM or prediabetes and overweight/obesity. This is a pilot, randomized, double-blinded, crossover study including a sub-sample of a global study with 14 subjects: (a) consuming 66 cl day-1 of regular alcohol-free beer for the first 10 weeks and 66 cl day-1 of modified alcohol-free beer for the next 10 weeks; (b) the same described intervention in opposite order. BMI homogeneously decreased after both interventions. Glucose and HOMA-IR significantly decreased just after the participants consumed modified alcohol-free beer. These findings were in the same line as those reported in the global study. Dominant bacteria at baseline were Bacteroidetes, Firmicutes, Proteobacteria and Tenericutes. Parabacteroides, from the Porphymonadaceae family, resulted as the feature with the greatest difference between beers (ANCOM analysis, W = 15). Feature-volatility analysis confirmed the importance of Parabacteroides within the model. Alcohol-free beers consumption resulted in an enhancement of pathways related to metabolism according to PICRUSt analysis, including terpenoid-quinone, lipopolysaccharides and N-glycan biosynthesis. Thus, an alcohol-free beer including the substitution of regular carbohydrates for low doses of isomaltulose and the addition of maltodextrin within meals significantly impacts gut microbiota in diabetic subjects with overweight or obesity. This could, at least partially, explain the improvement in insulin resistance previously found after taking modified alcohol-free alcohol.Clinical Trial Registration: Registered under ClinicalTrials.gov identifier no. NCT03337828.

Characterization of TMAO productivity from carnitine challenge facilitates personalized nutrition and microbiome signatures discovery

The capability of gut microbiota in degrading foods and drugs administered orally can result in diversified efficacies and toxicity interpersonally and cause significant impact on human health. Production of atherogenic trimethylamine N-oxide (TMAO) from carnitine is a gut microbiota-directed pathway and varies widely among individuals. Here, we demonstrated a personalized TMAO formation and carnitine bioavailability from carnitine supplements by differentiating individual TMAO productivities with a recently developed oral carnitine challenge test (OCCT). By exploring gut microbiome in subjects characterized by TMAO producer phenotypes, we identified 39 operational taxonomy units that were highly correlated to TMAO productivity, including Emergencia timonensis, which has been recently discovered to convert γ-butyrobetaine to TMA in vitro. A microbiome-based random forest classifier was therefore constructed to predict the TMAO producer phenotype (AUROC = 0.81) which was then validated with an external cohort (AUROC = 0.80). A novel bacterium called Ihubacter massiliensis was also discovered to be a key microbe for TMA/TMAO production by using an OCCT-based humanized gnotobiotic mice model. Simply combining the presence of E. timonensis and I. massiliensis could account for 43% of high TMAO producers with 97% specificity. Collectively, this human gut microbiota phenotype-directed approach offers potential for developing precision medicine and provides insights into translational research.Abqg1iGcSpwVpbLcjp9EmdVideo

MP78-09 THE ASSOCIATION BETWEEN GUT MICROBIOME AND ERECTILE DYSFUNCTION

You have accessJournal of UrologySexual Function/Dysfunction: Evaluation II (MP78)1 Apr 2020MP78-09 THE ASSOCIATION BETWEEN GUT MICROBIOME AND ERECTILE DYSFUNCTION Teppei Okamoto*, Shingo Hatakeyama, Atsushi Imai, Hayato Yamamoto, Tohru Yoneyama, Kazuyuki Mori, Takahiro Yoneyama, Yasuhiro Hashimoto, Shigeyuki Nakaji, and Chikara Ohyama Teppei Okamoto*Teppei Okamoto* More articles by this author , Shingo HatakeyamaShingo Hatakeyama More articles by this author , Atsushi ImaiAtsushi Imai More articles by this author , Hayato YamamotoHayato Yamamoto More articles by this author , Tohru YoneyamaTohru Yoneyama More articles by this author , Kazuyuki MoriKazuyuki Mori More articles by this author , Takahiro YoneyamaTakahiro Yoneyama More articles by this author , Yasuhiro HashimotoYasuhiro Hashimoto More articles by this author , Shigeyuki NakajiShigeyuki Nakaji More articles by this author , and Chikara OhyamaChikara Ohyama More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000000964.09AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Erectiledysfunction (ED) is associated with aging and lifestyle diseases.Dysbiosis (decreased diversity and change in gut microbiome) are observed inaging and several lifestyle diseases, such as, diabetic mellitus (DM), chronickidney disease (CKD), and cardiovascular disease (CVD). However, theassociation between the ED and dysbiosis remains unclear. We investigated gutmicrobiome in subjects with ED in a community-dwelling population. METHODS: This cross-sectional study analyzed 408 men who participated in the health promotion roject in Japan. We assessed participants’ backgrounds and laboratory data. The gut microbiome composition was assessed by tag sequencing of the 16S rRNA gene extracted from fecal samples. Erectile function was assessed with the 5-item International Index of Erectile Function (IIEF-5) and the age adjusted participants were divided into two groups: the low-IIEF-5 (≤16) and high-IIEF-5 (>16). The diversity and dissimilarity of gut microbiome in each group were analyzed. The association of gut microbiome and a low-IIEF-5 was analyzed by multivariate logistic regression analysis. RESULTS: Of 408, age adjusted 192 men were selected. No significant differences in backgrounds were observed in the presence of hypertension, DM, CKD, and CVD between the low-IIEF-5 (n = 96) and high-IIEF-5 (n = 96). There were no significant differences in the diversity and dissimilarity of gut microbiome between the two groups. However, the relative abundance of Odoribacter and Alistipes genera, which are thought to produce anti-inflammatory substances, were significantly lower in the low-IIEF-5 groups. Multivariate analysis showed that the relative abundance of Odoribacter + Alistipes genera (odds ratio = 0.81, P = 0.032) were independently associated with a low-IIEF-5. CONCLUSIONS: Odoribacter and Alistipes genera were significantly lower in subjects with low-IIEF-5. Further study is warranted to clarify a possible causal relationship between gut microbiome and ED. Source of Funding: none © 2020 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 203Issue Supplement 4April 2020Page: e1176-e1176 Advertisement Copyright & Permissions© 2020 by American Urological Association Education and Research, Inc.MetricsAuthor Information Teppei Okamoto* More articles by this author Shingo Hatakeyama More articles by this author Atsushi Imai More articles by this author Hayato Yamamoto More articles by this author Tohru Yoneyama More articles by this author Kazuyuki Mori More articles by this author Takahiro Yoneyama More articles by this author Yasuhiro Hashimoto More articles by this author Shigeyuki Nakaji More articles by this author Chikara Ohyama More articles by this author Expand All Advertisement PDF downloadLoading ...

The association between gut microbiome and erectile dysfunction: a community-based cross-sectional study in Japan.

We investigated the gut microbiome in subjects with erectile dysfunction (ED) in a community-based population. This cross-sectional study surveyed comprehensive health status in 408 men who participated in the Iwaki Health Promotion Project in 2015 in Hirosaki, Japan. The gut microbiome was assessed by tag sequencing of the 16S rRNA gene, which we extracted from fecal samples. Erectile function was evaluated with the five-item International Index of Erectile Function (IIEF-5), and the men were divided into two groups: low-IIEF-5 (≤ 16) and high-IIEF-5 (> 16). Of those, we selected age-adjusted 192 men (96 each) for analysis. We investigated the association of gut microbiome with IIEF-5 between the two groups. Median age was 50years. No significant difference was seen in the history of hypertension, DM, CKD, and CVD between the low-IIEF-5 and high-IIEF-5 groups. However, the relative abundance of Alistipes (related with anti-inflammation) and Clostoridium XVIII (related with bowel movement) was significantly different between the two groups. Multivariate logistic analysis demonstrated that the relative abundance of Clostridium XVIII (OR, 2.06; 95% CI, 1.20-3.55, P=0.009) and Alistipes (OR, 0.81; 95% CI, 0.66-0.99, P=0.040) and, with an IPSS≥8, were independent factors for low IIEF-5. We observed significant association between the low-IIEF-5 and high-IIEF-5 groups in Alistipes and Clostoridium XVIII. Further study is necessary to access the causal relationship between the gut microbiome and ED.

VITORA: Clinical Study to Evaluate the Effect of KB109 on the Gut Microbiome in Subjects Whose Gastrointestinal Tracts Are Colonized With Multiple Drug-resistant Organisms

VITORA: Clinical Study to Evaluate the Effect of KB109 on the Gut Microbiome in Subjects Whose Gastrointestinal Tracts Are Colonized With Multiple Drug-resistant Organisms

Gut microbiome identifies risk for colorectal polyps

ObjectiveTo characterise the gut microbiome in subjects with and without polyps and evaluate the potential of the microbiome as a non-invasive biomarker to screen for risk of colorectal cancer (CRC).DesignPresurgery...

Clinical Food Study to Evaluate the Effect of KB174 on the Gut Microbiome in Subjects With Well-compensated Cirrhosis

Clinical Food Study to Evaluate the Effect of KB174 on the Gut Microbiome in Subjects With Well-compensated Cirrhosis

Low nadir CD4+ T-cell counts predict gut dysbiosis in HIV-1 infection

Human immunodeficiency virus (HIV)-1 infection causes severe gut and systemic immune damage, but its effects on the gut microbiome remain unclear. Previous shotgun metagenomic studies in HIV-negative subjects linked low-microbial gene counts (LGC) to gut dysbiosis in diseases featuring intestinal inflammation. Using a similar approach in 156 subjects with different HIV-1 phenotypes, we found a strong, independent, dose–effect association between nadir CD4+ T-cell counts and LGC. As in other diseases involving intestinal inflammation, the gut microbiomes of subjects with LGC were enriched in gram-negative Bacteroides, acetogenic bacteria and Proteobacteria, which are able to metabolize reactive oxygen and nitrogen species; and were depleted in oxygen-sensitive methanogenic archaea and sulfate-reducing bacteria. Interestingly, subjects with LGC also showed increased butyrate levels in direct fecal measurements, consistent with enrichment in Roseburia intestinalis despite reductions in other butyrate producers. The microbiomes of subjects with LGC were also enriched in bacterial virulence factors, as well as in genes associated with beta-lactam, lincosamide, tetracycline, and macrolide resistance. Thus, low nadir CD4+ T-cell counts, rather than HIV-1 serostatus per se, predict the presence of gut dysbiosis in HIV-1 infected subjects. Such dysbiosis does not display obvious HIV-specific features; instead, it shares many similarities with other diseases featuring gut inflammation.

Alterations of the human gut microbiome in multiple sclerosis.

The gut microbiome plays an important role in immune function and has been implicated in several autoimmune disorders. Here we use 16S rRNA sequencing to investigate the gut microbiome in subjects with multiple sclerosis (MS, n=60) and healthy controls (n=43). Microbiome alterations in MS include increases in Methanobrevibacter and Akkermansia and decreases in Butyricimonas, and correlate with variations in the expression of genes involved in dendritic cell maturation, interferon signalling and NF-kB signalling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased abundances of Prevotella and Sutterella, and decreased Sarcina, compared with untreated patients. MS patients of a second cohort show elevated breath methane compared with controls, consistent with our observation of increased gut Methanobrevibacter in MS in the first cohort. Further study is required to assess whether the observed alterations in the gut microbiome play a role in, or are a consequence of, MS pathogenesis.