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Gut Microbes 2024The gut microbiota has been implicated as a driver of irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Recently we described, mucosal biofilms,...
The gut microbiota has been implicated as a driver of irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Recently we described, mucosal biofilms, signifying alterations in microbiota composition and bile acid (BA) metabolism in IBS and ulcerative colitis (UC). Luminal oxygen concentration is a key factor in the gastrointestinal (GI) ecosystem and might be increased in IBS and UC. Here we analyzed the role of archaea as a marker for hypoxia in mucosal biofilms and GI homeostasis. The effects of archaea on microbiome composition and metabolites were analyzed via amplicon sequencing and untargeted metabolomics in 154 stool samples of IBS-, UC-patients and controls. Mucosal biofilms were collected in a subset of patients and examined for their bacterial, fungal and archaeal composition. Absence of archaea, specifically , correlated with disrupted GI homeostasis including decreased microbial diversity, overgrowth of facultative anaerobes and conjugated secondary BA. IBS-D/-M was associated with absence of archaea. Presence of correlated with and epithelial short chain fatty acid metabolism and decreased levels of . Absence of fecal may indicate a less hypoxic GI environment, reduced fatty acid oxidation, overgrowth of facultative anaerobes and disrupted BA deconjugation. Archaea and could distinguish distinct subtypes of mucosal biofilms. Further research on the connection between archaea, mucosal biofilms and small intestinal bacterial overgrowth should be performed.
Topics: Humans; Biofilms; Gastrointestinal Microbiome; Archaea; Adult; Middle Aged; Female; Male; Bacteria; Feces; Colon; Methanobrevibacter; Colitis, Ulcerative; Irritable Bowel Syndrome; Aged; Intestinal Mucosa; Ileum; Fatty Acids, Volatile; Young Adult; Bile Acids and Salts
PubMed: 38825783
DOI: 10.1080/19490976.2024.2359500 -
Frontiers in Veterinary Science 2024The present study was designed to evaluate the effect of a mixture of Chinese medicinal residues (CMRs) consisting of residues (SMR) and residues (IRR) on productive...
The present study was designed to evaluate the effect of a mixture of Chinese medicinal residues (CMRs) consisting of residues (SMR) and residues (IRR) on productive performance, egg quality, serum lipid and hormone levels, liver and blood antioxidant capacity, oviduct inflammation levels, and gut microbiota in the late-laying stage. A total of 288 fifty-four-week-old long-tailed hens were divided into four groups. The feed trial period was 8 weeks. The control group was fed the basic diet as a CCMR group, supplemented with 3, 4, and 6% for the experimental groups LCMR, MCMR, and HCMR. The egg production rate of the MCMR group was 8.1% higher than that of the CCMR group ( < 0.05). Serum triglyceride (TG) levels of hens of the CMR-supplemented group were significantly decreased than those of the CCMR group ( < 0.05). The group supplemented with different levels of CMR had significantly higher serum HDL-C levels compared with the control group ( < 0.05). Follicle-stimulating hormone (FSH) and luteinizing hormone (LH) levels were remarkably increased for the LCMR and MCMR groups and significantly decreased for the HCMR group compared to CCMR ( < 0.05). Serum and liver glutathione peroxidase (GSH-PX) activities were significantly increased, and malondialdehyde (MDA) levels were significantly decreased in the MCMR group compared to the CCMR group ( < 0.05). The expression levels of tubal inflammatory factor markers (IL-4, IL-1β, TNF-α) in the MCMR and HCMR groups were consistent with the pathological findings of the sections. As for cecal microbiota, supplementation with CMR affected the alpha diversity of the cecum microbiome at the genus level. The Shannon index was significantly higher in the MCMR group than in the CCMR and HCMR groups ( < 0.05). Supplementation with different levels of CMR mainly regulated the ratio of intestinal to and the abundance of phyla such as . In addition, CMR supplementation at different levels in the diet enriched lipid-metabolizing bacteria, such as and . Furthermore, according to linear discriminant analysis (LDA) effect size (LEfSe) analysis, the MCMR group showed an increase in the number of short-chain fatty acid-producing bacteria and fiber-degrading specialized bacteria . Therefore, supplementation of appropriate amounts of CMR to the diet of laying hens enhanced reproductive hormone levels, hepatic antioxidant capacity, and lipid metabolism, alleviated the levels of oviductal inflammatory factors, and modulated the abundance structure of bacterial flora to improve the late-laying performance and egg quality. The results of the current study showed that CMR is a beneficial feed supplement for chickens when added in moderation.
PubMed: 38764854
DOI: 10.3389/fvets.2024.1381226 -
Frontiers in Immunology 2024Previous research has partially revealed distinct gut microbiota in ankylosing spondylitis (AS). In this study, we performed non-targeted fecal metabolomics in AS in...
OBJECTIVE
Previous research has partially revealed distinct gut microbiota in ankylosing spondylitis (AS). In this study, we performed non-targeted fecal metabolomics in AS in order to discover the microbiome-metabolome interface in AS. Based on prospective cohort studies, we further explored the impact of the tumor necrosis factor inhibitor (TNFi) on the gut microbiota and metabolites in AS.
METHODS
To further understand the gut microbiota and metabolites in AS, along with the influence of TNFi, we initiated a prospective cohort study. Fecal samples were collected from 29 patients with AS before and after TNFi therapy and 31 healthy controls. Metagenomic and metabolomic experiments were performed on the fecal samples; moreover, validation experiments were conducted based on the association between the microbiota and metabolites.
RESULTS
A total of 7,703 species were annotated using the metagenomic sequencing system and by profiling the microbial community taxonomic composition, while 50,046 metabolites were identified using metabolite profiling. Differential microbials and metabolites were discovered between patients with AS and healthy controls. Moreover, TNFi was confirmed to partially restore the gut microbiota and the metabolites. Multi-omics analysis of the microbiota and metabolites was performed to determine the associations between the differential microbes and metabolites, identifying compounds such as oxypurinol and biotin, which were correlated with the inhibition of the pathogenic bacteria and the promotion of the probiotic bacteria . Through experimental studies, the relationship between microbes and metabolites was further confirmed, and the impact of these two types of microbes on the enterocytes and the inflammatory cytokine interleukin-18 (IL-18) was explored.
CONCLUSION
In summary, multi-omics exploration elucidated the impact of TNFi on the gut microbiota and metabolites and proposed a novel therapeutic perspective: supplementation of compounds to inhibit potential pathogenic bacteria and to promote potential probiotics, therefore controlling inflammation in AS.
Topics: Humans; Spondylitis, Ankylosing; Gastrointestinal Microbiome; Probiotics; Male; Female; Metabolome; Adult; Feces; Metagenomics; Middle Aged; Prospective Studies; Metabolomics; Bacteria; Tumor Necrosis Factor Inhibitors
PubMed: 38711505
DOI: 10.3389/fimmu.2024.1369116 -
Scientific Reports Apr 2024Gut microbiome dysbiosis contributes to the pathophysiology of both gestational diabetes mellitus (GDM) and its associated adverse outcomes in the woman and offspring....
Gut microbiome dysbiosis contributes to the pathophysiology of both gestational diabetes mellitus (GDM) and its associated adverse outcomes in the woman and offspring. Even though GDM prevalence, complications, and outcomes vary among different ethnic groups, limited information is available about the influence of ethnicity on gut microbiome dysbiosis in pregnancies complicated by GDM. This pilot prospective cohort study examined the impact of ethnicity on gut dysbiosis in GDM among three Asian ethnic groups (Chinese, Malay, Indian) living in Singapore, and investigated the potential modulatory roles of diet and lifestyle modifications on gut microbiome post-GDM diagnosis. Women with GDM (n = 53) and without GDM (n = 16) were recruited. Fecal samples were collected at 24-28- and 36-40-weeks' gestation and analyzed by targeted 16S rRNA gene-based amplicon sequencing. Permutational multivariate analysis of variance (PERMANOVA) analysis was performed to evaluate differences between groups. Differentially abundant taxa were identified by DeSeq2 based analysis. Functional prediction was performed using the phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2). Among women with GDM, gut microbiome from different ethnicities harbored common microbial features. However, among those without GDM, there was contrasting microbiome composition between ethnic groups. Microbial members such as Collinsella, Blautia, Ruminococcus, Ruminococcus gnavus, Ruminococcus torques, and Eubacterium hallii groups were differentially enriched (p < 0.05) in women with GDM compared to those without. Among women with GDM, no differences in alpha- and beta- diversity were observed when comparing 24-28 weeks' samples with 36-40 weeks' samples, a period covering intense dietary and lifestyle modification, suggesting an inability to modulate gut microbiota through classic GDM management. Women with GDM have a distinct gut microbiome profile which harbours common features across different Asian ethnic groups, consistent with the notion that specific microbes are involved in the pathogenesis of insulin resistance, pro-inflammatory conditions, and other metabolic dysregulation known to be present in GDM.
Topics: Humans; Female; Pregnancy; Gastrointestinal Microbiome; Diabetes, Gestational; Dysbiosis; Pilot Projects; Adult; Singapore; Prospective Studies; Asian People; RNA, Ribosomal, 16S; Diet; Ethnicity; Feces; Bacteria
PubMed: 38684759
DOI: 10.1038/s41598-024-60386-y -
Nature Communications Apr 2024The etiopathogenesis of diverticulitis, among the most common gastrointestinal diagnoses, remains largely unknown. By leveraging stool collected within a large...
The etiopathogenesis of diverticulitis, among the most common gastrointestinal diagnoses, remains largely unknown. By leveraging stool collected within a large prospective cohort, we performed shotgun metagenomic sequencing and untargeted metabolomics profiling among 121 women diagnosed with diverticulitis requiring antibiotics or hospitalizations (cases), matched to 121 women without diverticulitis (controls) according to age and race. Overall microbial community structure and metabolomic profiles differed in diverticulitis cases compared to controls, including enrichment of pro-inflammatory Ruminococcus gnavus, 1,7-dimethyluric acid, and histidine-related metabolites, and depletion of butyrate-producing bacteria and anti-inflammatory ceramides. Through integrated multi-omic analysis, we detected covarying microbial and metabolic features, such as Bilophila wadsworthia and bile acids, specific to diverticulitis. Additionally, we observed that microbial composition modulated the protective association between a prudent fiber-rich diet and diverticulitis. Our findings offer insights into the perturbations in inflammation-related microbial and metabolic signatures associated with diverticulitis, supporting the potential of microbial-based diagnostics and therapeutic targets.
Topics: Humans; Female; Gastrointestinal Microbiome; Middle Aged; Diverticulitis; Feces; Aged; Prospective Studies; Bilophila; Metabolomics; Case-Control Studies; Clostridiales; Bile Acids and Salts; Adult; Dietary Fiber; Metabolome; Metagenomics
PubMed: 38684664
DOI: 10.1038/s41467-024-47859-4 -
Frontiers in Microbiology 2024infection (CDI) is responsible for around 300,000 hospitalizations yearly in the United States, with the associated monetary cost being billions of dollars. Gut...
infection (CDI) is responsible for around 300,000 hospitalizations yearly in the United States, with the associated monetary cost being billions of dollars. Gut microbiome dysbiosis is known to be important to CDI. To the best of our knowledge, metatranscriptomics (MT) has only been used to characterize gut microbiome composition and function in one prior study involving CDI patients. Therefore, we utilized MT to investigate differences in active community diversity and composition between CDI+ ( = 20) and CDI- ( = 19) samples with respect to microbial taxa and expressed genes. No significant (Kruskal-Wallis, > 0.05) differences were detected for richness or evenness based on CDI status. However, clustering based on CDI status was significant for both active microbial taxa and expressed genes datasets (PERMANOVA, ≤ 0.05). Furthermore, differential feature analysis revealed greater expression of the opportunistic pathogens and in CDI+ compared to CDI- samples. When only fungal sequences were considered, the family Saccharomycetaceae expressed more genes in CDI-, while 31 other fungal taxa were identified as significantly (Kruskal-Wallis ≤ 0.05, log(LDA) ≥ 2) associated with CDI+. We also detected a variety of genes and pathways that differed significantly (Kruskal-Wallis ≤ 0.05, log(LDA) ≥ 2) based on CDI status. Notably, differential genes associated with biofilm formation were expressed by . This provides evidence of another possible contributor to 's resistance to antibiotics and frequent recurrence . Furthermore, the greater number of CDI+ associated fungal taxa constitute additional evidence that the mycobiome is important to CDI pathogenesis. Future work will focus on establishing if is actively producing biofilms during infection and if any specific fungal taxa are particularly influential in CDI.
PubMed: 38680911
DOI: 10.3389/fmicb.2024.1398018 -
BioRxiv : the Preprint Server For... Apr 2024There is growing appreciation that commensal bacteria impact the outcome of viral infections, though the specific bacteria and their underlying mechanisms remain poorly...
There is growing appreciation that commensal bacteria impact the outcome of viral infections, though the specific bacteria and their underlying mechanisms remain poorly understood. Studying a simian-human immunodeficiency virus (SHIV)-challenged cohort of pediatric nonhuman primates, we bioinformatically associated Lactobacillus gasseri and the bacterial family Lachnospiraceae with enhanced resistance to infection. We experimentally validated these findings by demonstrating two different Lachnospiraceae isolates, Clostridium immunis and Ruminococcus gnavus, inhibited HIV replication in vitro and ex vivo. Given the link between tryptophan catabolism and HIV disease severity, we found that an isogenic mutant of C. immunis that lacks the aromatic amino acid aminotransferase (ArAT) gene, which is key to metabolizing tryptophan into 3-indolelactic acid (ILA), no longer inhibits HIV infection. Intriguingly, we confirmed that a second commensal bacterium also inhibited HIV in an ArAT-dependent manner, thus establishing the generalizability of this finding. In addition, we found that purified ILA inhibited HIV infection by agonizing the aryl hydrocarbon receptor (AhR). Given that the AhR has been implicated in the control of multiple viral infections, we demonstrated that C. immunis also inhibited human cytomegalovirus (HCMV) infection in an ArAT-dependent manner. Importantly, metagenomic analysis of individuals at-risk for HIV revealed that those who ultimately acquired HIV had a lower fecal abundance of the bacterial ArAT gene compared to individuals who did not, which indicates our findings translate to humans. Taken together, our results provide mechanistic insights into how commensal bacteria decrease susceptibility to viral infections. Moreover, we have defined a microbiota-driven antiviral pathway that offers the potential for novel therapeutic strategies targeting a broad spectrum of viral pathogens.
PubMed: 38659737
DOI: 10.1101/2024.04.21.589969 -
Clinical and Experimental... 2024The diagnosis of irritable bowel syndrome (IBS) is based on symptom-based criteria due to lack of reliable disease-specific biomarkers. Gut microbiota is perturbed in... (Review)
Review
A Systematic Review: Fecal Bacterial Profile in Patients with Irritable Bowel Syndrome Analyzed with the GA-Map Dysbiosis Test Based on the 16S rRNA Gene of Bacterial Species or Groups.
PURPOSE
The diagnosis of irritable bowel syndrome (IBS) is based on symptom-based criteria due to lack of reliable disease-specific biomarkers. Gut microbiota is perturbed in IBS and when comparing different methods used to analyze gut microbiota, the results might be obscured. Therefore, in this systematic review we aimed to investigate the profile of fecal bacterial markers and dysbiosis index (DI) in patients with IBS and IBS subgroups compared to healthy controls (HCs) conducted by the same method (GA-map Dysbiosis Test based on16S rRNA sequencing).
MATERIAL AND METHOD
We searched PubMed, EMBASE (Ovid) and Cochrane Library for case-control studies comparing fecal gut microbiota analyzed with the GA-map Dysbiosis Test (Oslo, Norway) in patients with IBS and HCs. Our outcomes were the difference in fecal bacterial markers and DI in patients with IBS and IBS subgroups compared to HCs.
RESULTS
The search identified 28 citations; five articles were included. Most studies evaluated fecal bacterial markers and DI in patients with diarrhea-predominant IBS (IBS-D). Results of fecal bacteria profile in IBS and IBS subgroups compared to HCs are inconsistent, however, two studies showed increased levels of in IBS-D compared to HCs and results of DI indicated IBS and IBS subgroups (especially IBS-D) having higher DI compared to HCs.
CONCLUSION
This systematic review revealed inconsistent findings in respect to differences in bacterial markers between IBS and IBS subgroups with HCs in studies using the GA-map Dysbiosis Test based on 16S rRNA sequencing. However, the test is quite novel, and few studies have used the method so far. More research comparing fecal microbiota profile differences in IBS and IBS subgroups compared to HCs utilizing the same method of analysis is needed to give us further insight into the gut bacteria profile in IBS and the clinical consequences of intestinal dysbiosis.
PubMed: 38646157
DOI: 10.2147/CEG.S451675 -
Nutrients Apr 2024Exclusive enteral nutrition (EEN) is effective in inducing remission in pediatric Crohn disease (CD). EEN alters the intestinal microbiome, but precise mechanisms are...
Exclusive enteral nutrition (EEN) is effective in inducing remission in pediatric Crohn disease (CD). EEN alters the intestinal microbiome, but precise mechanisms are unknown. We hypothesized that pre-diagnosis diet establishes a baseline gut microbiome, which then mediates response to EEN. We analyzed prospectively recorded food frequency questionnaires (FFQs) for pre-diagnosis dietary patterns. Fecal microbiota were sequenced (16SrRNA) at baseline and through an 18-month follow-up period. Dietary patterns, Mediterranean diet adherence, and stool microbiota were associated with EEN treatment outcomes, disease flare, need for anti-tumor necrosis factor (TNF)-α therapy, and long-term clinical outcomes. Ninety-eight patients were included. Baseline disease severity and microbiota were associated with diet. Four dietary patterns were identified by FFQs; a "mature diet" high in fruits, vegetables, and fish was linked to increased baseline microbial diversity, which was associated with fewer disease flares ( < 0.05) and a trend towards a delayed need for anti-TNF therapy ( = 0.086). Baseline stool microbial taxa were increased ( and ) or decreased ( group) with the mature diet compared to other diets. Surprisingly, a "pre-packaged" dietary pattern (rich in processed foods) was associated with delayed flares in males ( < 0.05). Long-term pre-diagnosis diet was associated with outcomes of EEN therapy in pediatric CD; diet-microbiota and microbiota-outcome associations may mediate this relationship.
Topics: Animals; Male; Child; Humans; Enteral Nutrition; Crohn Disease; Tumor Necrosis Factor Inhibitors; Microbiota; Diet, Mediterranean
PubMed: 38613066
DOI: 10.3390/nu16071033 -
Frontiers in Cellular and Infection... 2024Children have regional dynamics in the gut microbiota development trajectory. Hitherto, the features and influencing factors of the gut microbiota and fecal and plasma...
INTRODUCTION
Children have regional dynamics in the gut microbiota development trajectory. Hitherto, the features and influencing factors of the gut microbiota and fecal and plasma metabolites in children from Northwest China remain unclear.
METHODS
Shotgun metagenomic sequencing and untargeted metabolomics were performed on 100 healthy volunteers aged 2-12 years.
RESULTS
Age, body mass index (BMI), regular physical exercise (RPE), and delivery mode (DM) significantly affect gut microbiota and metabolites. , , , , and predicted pathway propanoate production were significantly increased with age while , , and carbohydrate degradation were decreased. Fecal metabolome revealed that the metabolism of caffeine, amino acids, and lipid significantly increased with age while galactose metabolism decreased. Noticeably, BMI was positively associated with pathogens including , , , and amino acid metabolism but negatively associated with beneficial , , , and caffeine metabolism. RPE has increased probiotic and , acetate and lactate production, and major nutrient metabolism in gut and plasma, but decreased pathobiont , taurine degradation, and pentose phosphate pathway. Interestingly, DM affects the gut microbiota and metabolites throughout the whole childhood. , , , primary bile acid, and neomycin biosynthesis were enriched in eutocia, while anti-inflammatory , , , and pathogenic , , and amino acid metabolism were enriched in Cesarean section children.
DISCUSSION
Our results provided theoretical and data foundation for the gut microbiota and metabolites in preadolescent children's growth and development in Northwest China.
Topics: Pregnancy; Child; Humans; Female; Gastrointestinal Microbiome; Caffeine; Cesarean Section; Urban Population; Metabolome; Amino Acids
PubMed: 38585649
DOI: 10.3389/fcimb.2024.1374544