Microbiome Signatures Research Articles

Erratum for Guo et al., "Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis".

Erratum for Guo et al., "Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis".

Comparison of different microbiome analysis pipelines to validate their reproducibility of gastric mucosal microbiome composition.

Microbiome analysis has become a crucial tool for basic and translational research due to its potential for translation into clinical practice. However, there is ongoing controversy regarding the comparability of different bioinformatic analysis platforms and a lack of recognized standards, which might have an impact on the translational potential of results. This study investigates how the performance of different microbiome analysis platforms impacts the final results of mucosal microbiome signatures. Across five independent research groups, we compared three distinct and frequently used microbiome analysis bioinformatic packages (DADA2, MOTHUR, and QIIME2) on the same subset of fastQ files. The source data set encompassed 16S rRNA gene raw sequencing data (V1-V2) from gastric biopsy samples of clinically well-defined gastric cancer (GC) patients (n = 40; with and without Helicobacter pylori [H. pylori] infection) and controls (n = 39, with and without H. pylori infection). Independent of the applied protocol, H. pylori status, microbial diversity and relative bacterial abundance were reproducible across all platforms, although differences in performance were detected. Furthermore, alignment of the filtered sequences to the old and new taxonomic databases (i.e., Ribosomal Database Project, Greengenes, and SILVA) had only a limited impact on the taxonomic assignment and thus on global analytical outcomes. Taken together, our results clearly demonstrate that different microbiome analysis approaches from independent expert groups generate comparable results when applied to the same data set. This is crucial for interpreting respective studies and underscores the broader applicability of microbiome analysis in clinical research, provided that robust pipelines are utilized and thoroughly documented to ensure reproducibility.IMPORTANCEMicrobiome analysis is one of the most important tools for basic and translational research due to its potential for translation into clinical practice. However, there is an ongoing controversy about the comparability of different bioinformatic analysis platforms and a lack of recognized standards. In this study, we investigate how the performance of different microbiome analysis platforms affects the final results of mucosal microbiome signatures. Five independent research groups used three different and commonly used bioinformatics packages for microbiome analysis on the same data set and compared the results. This data set included microbiome sequencing data from gastric biopsy samples of GC patients. Regardless of the protocol used, Helicobacter pylori status, microbial diversity, and relative bacterial abundance were reproducible across all platforms. The results show that different microbiome analysis approaches provide comparable results. This is crucial for the interpretation of corresponding studies and underlines the broader applicability of microbiome analysis.

Distinct Ocular Surface Microbiome in Keratoconus Patients Correlate With Local Immune Dysregulation.

Keratoconus (KC) is characterized by irregular astigmatism along with corneal stromal weakness and is associated with altered immune status. Tissue resident microbiomes are known to influence the immune status in other organs, but such a nexus has not been described in ocular conditions. Therefore, we examined the ocular surface microbiome of patients with KC and correlated it to the immune cell and tear molecular factor profiles. Sixty-two patients with KC and 21 healthy controls underwent corneal topography analysis and eye examination followed by a collection of Schirmer's strip, ocular surface wash, and ocular surface swabs. Microbiomes were analyzed by extracting DNA from the swabs followed by 16S rRNA gene V3-V4 amplicon sequencing and analyzed using QIIME. Fifty-two molecular factors from Schirmer's strip tear extracts and 11 immune cells from ocular wash were measured using multiplex ELISA and flow cytometry. Alpha diversity, linear discriminant analysis effect size (LEfSe), relative abundance and receiver operating characteristic - area under the curve (ROC-AUC) analysis were performed. Unsupervised clustering at the genus level with clinical parameters, soluble factors, and immune cells was performed. Fifty-two phyla/class, 132 order, 283 family, and 718 genera were identified in our cohort. Alpha diversity indices were comparable between patients with KC and the healthy controls. Dominant phyla across groups were Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes. Alphaproteobacteria increased in KC eyes whereas Actinobacteria, Firmicutes_Bacilli reduced compared with the healthy controls. We found a significant positive correlation of Microbacterium, Cutibacterium, and Brevundimonas genera abundance with keratometry and corneal thickness. Levels of IL-21, IL-9, Fractalkine, and VEGF positively correlated with Tetrasphaera (P < 0.05). β2-microglobulin and CD66bhigh cells correlated with Bacteroides (P < 0.05). CD45+ cells correlated with Escherichia_Shigella (P < 0.02). We discovered a unique microbiome signature of KC which correlated to disease grades and secreted molecular factors and immune cells. Therefore, the altered microbiome on the ocular surface may drive immune dysregulation in KC and provide scope for potential interventions in the future.

P1314 Multi-omics analysis of Crohn’s Disease trajectory from active to remission reveals that the altered ileal anti-bacterial epithelial signals and pathogenic microbial composition and metabolomics persist despite normalizing ileal immune signals during remission

Abstract Background Characterizing gut factors that improve or persist during Crohn’s disease (CD) trajectory from active to remission to healthy-normal states is crucial for defining treatment targets and CD cure. Methods Using multi-omics (ileal transcriptomics, microbiome, and metabolomics), we aimed to compare active, mostly treatment naïve newly diagnosed CD to patients in remission, using controls as a reference Results 193 subjects were included (median age 32 years, 60% male); 78 CD in remission, 38 active and mostly (80%) treatment naïve newly diagnosed CD patients, and 77 non-IBD controls (Table 1). Controls and CD remission groups had significantly lower and mostly normal CRP, with significantly lower fecal calprotectin in the remission than in the active group (Table 1). Most patients (79%) in remission were on biologics (58% on anti-TNF and 21% on vedolizumab/Stelara). Ileal transcriptomics (Fig. 1A-B) highlighted a significant reduction of genes and pathways related to adaptive T cell activation in treated patients in remission compared to active treatment naïve patients. This decrease was significantly lower than in controls, suggesting some immune compromise likely secondary to CD therapy. There were no differences between the levels of S1008/9 genes encoding for fecal calprotectin and OSM and TREM1 genes related to the anti-TNF response in patients in remission on treatment, compared to controls. Despite that, patients in remission still showed persistent signals of elevated expression of epithelial antimicrobial pathways and genes, including DUOX2, CEACAM5/6, REG4, and DMBT1, and more novel increased goblet cells and mucin glycosylated genes and signals (Fig. 1A-B). Interestingly, these epithelial antimicrobial signals during remission were coupled with persistent pathogenic gut microbial composition, as indicated by several microbial measurements, including the published Gevers et al index (PMID:24629344), our general health and specific IBD indexes (PMID:35197084), and alpha diversity (Fig. 1C), with significant enrichment of oral bacteria that dislocated to the gut in the CD groups. Similarly, 39 of 43 (91%) of the gut metabolites (Fig. 1D) that were significantly different between CD in remission vs. controls showed similar altered directionally in active treatment naïve CD patients vs. controls, suggesting persistent metabolic alterations during remission Conclusion Multi-omics analysis shows that despite normalizing ileal immune signals and genes encoding calprotectin during remission, the altered anti-bacterial epithelial signal and pathogenic microbiome and metabolome signatures persist. This highlights the need to directly target the epithelia-microbes axis, in addition to immune suppression, to improve CD outcomes.

P1351 Microbiome Diversity and Taxonomic Differences in Quiescent Ulcerative Colitis: A Comparative Study of Proximal Extension

Abstract Background The gut microbiome plays a significant role in ulcerative colitis (UC) pathogenesis, but its contributions during clinical remission and in relation to disease extent remain underexplored. This study investigates the microbiome profiles of quiescent UC patients with proximal extension (Y) and those without proximal extension (N), aiming to identify microbiome-based differences and potential biomarkers for disease stratification. Methods Fecal microbiome samples were obtained from 30 quiescent UC patients: 17 without proximal extension (N) and 13 with proximal extension (Y). Sequencing data were processed to exclude human genome reads, and rarefaction curves were used to ensure data quality. Alpha- and beta-diversity metrics assessed microbial diversity within and between groups. Differentially abundant taxa were identified, and a random forest model was employed to classify patients based on microbial composition. Results: Diversity Analysis Alpha-diversity showed no significant differences between the N and Y groups.Beta-diversity analysis revealed no distinct clustering between groups (P = 0.44), indicating shared microbial community structures. Taxonomic Composition The Y group (proximal extension) showed higher abundances of taxa such as Bartonella birtlesii, Lactobacillus salivarius, Klebsiella sp. M5al, and Proteus vulgaris. The N group (no proximal extension) was enriched with taxa like Lactococcus lactis and Pediococcus acidilactici. Machine Learning Classification The random forest model successfully classified patients into N and Y groups based on microbial features. Key predictive taxa aligned with findings from differential abundance analyses, reinforcing their potential as biomarkers. Conclusion This study highlights distinct microbiome signatures between UC patients with and without proximal extension during remission. While diversity metrics were similar, specific taxa showed significant differences in abundance. These findings may inform microbiome-based diagnostic and therapeutic approaches tailored to disease extent. Further research is required to validate these results and explore the underlying mechanisms driving microbiome-disease interactions.

P1311 Mucosal Microbiome Signatures Associated with Postoperative Endoscopic Recurrence in Paediatric Crohn’s Disease

Abstract Background Following ileocecal resection (ICR) for Crohn’s disease (CD), recurrence is frequent even in the biologic era. Gut microbiota is involved in this setting and a few adult studies have suggested that bacterial recolonization after surgery may predict recurrence. Given the inherent risk of postoperative recurrence associated with age and disease duration, studies investigating the role of the gut microbiota in predicting relapse in children undergoing ICR appears critical. We aimed to identify changes in the mucosal microbiome associated with, and predictive of, endoscopic CD recurrence within the first year post-ICR in a paediatric population. Methods Microbiota composition (16S rDNA sequencing) was assessed from ileal and colonic mucosa at the time of ICR and later during endoscopic evaluation from above and below the surgical anastomosis in 33 patients (26 with paired samples) prospectively recruited at a tertiary care paediatric IBD center. Results The study included 33 children (mean age 16±2.7 years) undergoing ICR. At the time of ileo-colonoscopy, 9 (35%) patients had endoscopic recurrence (Rutgeerts’ score≥ i2). ICR strongly modified the gut mucosal microbiota composition with significant changes in β-diversity (R2= 0.03, PERMANOVA test, p=0.01). Bacterial recolonization post-ICR differed according to recurrence status (Figure 1). Post-operatively, recurrence was associated with an increase in Fusobacterium, Dialister genera and in members of the Lachnospiraceae family, and a decrease in Faecalibacterium, Lactobacillus genera and members of the Streptococcaceae family. Microbiota colonizing the neoterminal ileum and subanastomotic colon differed in children with recurrence and showed, compared to remission, elevated and reduced bacterial abundance of the Enterobacter (q=0.1) and Ruminococcaceae (q=0.05) families in colonic samples respectively while the ileal mucosa exhibited profound depletion in Faecalibacterium (q=0.01). Postoperative colonic mucosal relative abundance of Enterobacteriaceae (q=0.06) and Ruminococcaceae (q=0.06) correlated positively and negatively with length of intestinal resection. At the time of surgery, several bacterial taxa able to predict relapse were identified (Figure 2). Conclusion Predicting postoperative CD relapse remains challenging, although several clinical risk factors of recurrence have been identified. Our study demonstrates that bacterial recolonization following ICR might pave the way towards remission or recurrence. Our results highlight, for the first time in a paediatric population, target species that may help clinicians to better define patients at risk of relapse and allow precise modulations of the overall microbial ecosystem towards remission pattern.

P0203 Unique faecal &amp; oral microbiota signatures in first degree relatives of inflammatory bowel disease patients

Abstract Background While the aetiology of IBD is unknown, a range of genetic and environmental risk factors have been described. First-degree relatives (FDRs; siblings, parents and children) of IBD patients share many of these factors. To better understand the interplay between environmental and genetic risk factors, we evaluated the gut microbial profiles of an FDR cohort, their IBD probands and healthy controls (HC). The aim was to identify whether FDRs of IBD patients have healthy or IBD-like microbial features. Methods All participants were recruited as part of the Australian IBD Microbiome (AIM) study. Participants were selected based on self-reported first-degree relative status (n=68) and, where possible, affected IBD relatives (n=24) were included for comparison. All participants were antibiotic free for 3-months prior to baseline sampling. Oral and faecal samples underwent 16S rRNA sequencing. The Microbiome Research Centre 16S analysis pipeline and R studio were used for statistical analysis and data visualisation. Results The FDR group was predominantly female (63%) with a mean age of 49.7 years and BMI of 25.5 kg/m2. The IBD cohort was significantly different in age to FDR (mean 36.7; p &amp;lt; 0.05) but not controls (mean 40.4 years) and BMI was comparable between groups. European Australians were the most represented ethnic group (47.6%) and 98.6% of participants were non-smokers. Oral microbiota profiles showed no significant difference in alpha diversity across FDR, IBD and HC groups. Differential abundance analysis of the oral microbiota revealed FDRs had increased abundance of Oribacterium, Granulicatella, Lachnoanaerobaculum and Rothia compared to HC, and increased levels of Capnocytophaga, Tannerella and Abiotrophia compared to the IBD group. In agreement with other studies, faecal microbial profiles in the IBD group had significantly reduced alpha diversity compared to both FDR and HC groups. All groups were compositionally different by Bray-Curtis beta dissimilarity analysis (p&amp;lt;0.018). FDRs had higher abundance of Akkermansia, Alistipes and Monoglobus compared to IBD and HC groups. FDRs and IBD shared similar abundance of Butyricicoccus which was lower than the HCs. Conclusion FDR oral microbiome signatures had greater variance from HC than IBD groups. Faecal microbial analysis showed distinct differences with enrichment of key beneficial genera in the FDR group. FDR profiles however still shared significant gut microbial features with the IBD group, remaining distinct from healthy controls. FDRs oral microbiome was higher in opportunistic pathogens and IBD-like whereas faecal composition was protective, rich in beneficial metabolite producing genera.

DOP022 Shared and Distinct Features of the Gut Microbiome in Immune-mediated Inflammatory Diseases: Initial Analysis from the INTEGRATE Cohort Study

Abstract Background Inflammatory bowel disease (IBD) and ankylosing spondylitis (AS) share overlapping pathophysiological mechanisms as immune-mediated inflammatory diseases. While gut microbial dysbiosis has been implicated in both conditions, the shared and distinct features of the oral-gut microbiome axis remain poorly understood. This study aims to characterize the oral and gut microbial signatures and their relationship with environmental factors in IBD and AS to identify common pathogenic pathways and disease-specific patterns. Methods The INTEGRATE study is a nationwide prospective observational study in Korea targeting recruitment of 1,100 IBD patients, 700 AS patients, and 2,244 healthy controls over five years (Table 1). Systematic collection includes clinical data and biological samples (saliva, stool, blood, intestinal tissues) for multi-omics analyses. Microbial characterization employs full-length 16S rRNA gene sequencing and shotgun metagenomics for saliva and stool samples, complemented by metabolomic analyses of saliva, stool, and plasma. This initial analysis includes gut microbiome data from 254 IBD patients, 156 AS patients, and 194 healthy controls. Results Alpha diversity analysis revealed a gradient pattern, with IBD patients showing lowest gut microbiome diversity, AS patients intermediate, and healthy controls highest (p&amp;lt;1.0e-12 for all indices, Fig. 1). In IBD patients, alpha diversity significantly correlated with disease activity indices (Harvey-Bradshaw Index score in Crohn's disease, total Mayo score in ulcerative colitis) and inflammatory markers (CRP, r=-0.13, p=0.042). Blood urea nitrogen levels showed positive correlation with alpha diversity in both IBD (r=0.21, p=0.00062) and AS cohorts (r=0.20, p=0.015). Beta diversity analysis demonstrated distinct clustering patterns (UniFrac distance), with AS patients positioned intermediately between IBD patients and healthy controls (Healthy vs IBD: R²=0.0502, Healthy vs AS: R²=0.0148, IBD vs AS: R²=0.0198; all p=0.001). Species-level analysis through full-length 16S rRNA sequencing identified specific taxa (Clostridium bolteae, Blautia hansenii) significantly enriched in both IBD and AS patients compared to controls. Conclusion Our initial analysis demonstrates distinct gut microbiome signatures across IMIDs, with a clear diversity gradient and shared taxonomic features between IBD and AS. These findings, coupled with specific clinical correlations, provide a foundation for understanding common pathogenic pathways. Ongoing multi-omics analyses and quantitative microbiome profiling will further elucidate the role of the oral-gut microbiome axis in these IMIDs, potentially identifying novel microbial biomarkers for precision medicine.

Protocol for identifying Mycobacterium tuberculosis infection status through airway microbiome profiling.

This protocol describes the steps to determine an airway microbiome signature for identifying Mycobacterium tuberculosis infection status. We outline procedures for processing microbiome data, calculating diversity measures, and fitting Dirichlet multinomial mixture models. Additionally, we provide steps for analyzing taxonomic relative and differential abundances, as well as identifying potential biomarkers associated with infection status. For complete details on the use and execution of this protocol, please refer to Kayongo etal.1.

Intratumor microbiome-derived butyrate promotes chemo-resistance in colorectal cancer

IntroductionColorectal cancer (CRC) is a leading cause of cancer-related mortality globally. Although tumor immunotherapy is widely recognized for treating unresectable CRC, challenges such as ineffective immunotherapy and drug resistance remain prevalent. While intratumor microbiome-derived butyrate has been implicated in promoting lung cancer metastasis, its role in CRC chemoresistance is not well understood. This study aimed to explore the relationship between intratumor butyrate and chemoresistance in CRC.MethodsWe performed a comprehensive analysis of the microbiome composition in CRC patients with varying resistance-free survival (RFS) durations, utilizing 16S rRNA sequencing. Furthermore, we assessed the prognostic significance of circulating microbiome DNA (cmDNA) and examined the effects of exogenous butyrate supplementation on the chemosensitivity of CRC cell lines.ResultsOur 16S sequencing analysis revealed a reduction in microbial diversity within tumor samples of patients with resistance, as indicated by metrics such as observed taxonomic units, Shannon, and Simpson indices. Notably, Roseburia and Fusobacteria emerged as prominent biomarkers for the resistance group, whereas Bifidobacterium, Helicobacter, and Akkermansia were identified as biomarkers for the non-resistant group. Utilizing a Lasso regression model, we identified six genera-Roseburia, Helicobacter, Gardnerella, Flavonifractor, Coprococcus, and Anaerostipes-that significantly correlated with recurrence-free survival. Furthermore, both the intratumor microbiome signature and circulating microbiome DNA were effective in accurately predicting CRC resistance. Experimental assays, including CCK8 and wound-healing, demonstrated that intratumor microbiome-derived butyrate enhances the proliferation and migration of HCT15 cells in a time- and concentration-dependent manner. Cell survival analysis further indicated that butyrate treatment significantly increased the IC50 value, suggesting heightened drug resistance in HCT15 cells. Mechanistically, this resistance was attributed to butyrate’s activation of the PI3K-AKT signaling pathway.ConclusionOur results suggest that intratumor microbiome-derived butyrate contributes to chemoresistance in colorectal cancer, highlighting the potential prognostic and therapeutic significance of the intratumor microbiome.

Discovery of robust and highly specific microbiome signatures of non-alcoholic fatty liver disease

BackgroundThe pathogenesis of non-alcoholic fatty liver disease (NAFLD) with a global prevalence of 30% is multifactorial and the involvement of gut bacteria has been recently proposed. However, finding robust bacterial signatures of NAFLD has been a great challenge, mainly due to its co-occurrence with other metabolic diseases.ResultsHere, we collected public metagenomic data and integrated the taxonomy profiles with in silico generated community metabolic outputs, and detailed clinical data, of 1206 Chinese subjects w/wo metabolic diseases, including NAFLD (obese and lean), obesity, T2D, hypertension, and atherosclerosis. We identified highly specific microbiome signatures through building accurate machine learning models (accuracy = 0.845–0.917) for NAFLD with high portability (generalizable) and low prediction rate (specific) when applied to other metabolic diseases, as well as through a community approach involving differential co-abundance ecological networks. Moreover, using these signatures coupled with further mediation analysis and metabolic dependency modeling, we propose synergistic defined microbial consortia associated with NAFLD phenotype in overweight and lean individuals, respectively.ConclusionOur study reveals robust and highly specific NAFLD signatures and offers a more realistic microbiome-therapeutics approach over individual species for this complex disease.E4koFqVmYng21Zwjp47efAVideo

Landscapes of gut microbiome and blood metabolomic signatures in relapsing remitting multiple sclerosis.

Although disturbances in the gut microbiome have been implicated in multiple sclerosis (MS), little is known about the changes and interactions between the gut microbiome and blood metabolome, and how these changes affect disease-modifying therapy (DMT) in preventing the progression of MS. In this study, the structure and composition of the gut microbiota were evaluated using 16S rRNA gene sequencing and an untargeted metabolomics approach was used to compare the serum metabolite profiles from patients with relapsing-remitting MS (RRMS) and healthy controls (HCs). Results indicated that RRMS was characterized by phase-dependent α-phylogenetic diversity and significant disturbances in serum glycerophospholipid metabolism. Notably, α-phylogenetic diversity was significantly decreased in RRMS patients during the chronic phase (CMS) compared with those in the acute phase (AMS). A distinctive combination of two elevated genera (Slackia, Lactobacillus) and five glycerophospholipid metabolism-associated metabolites (four increased: GPCho(22:5/20:3), PC(18:2(9Z,12Z)/16:0), PE(16:0/18:2(9Z,12Z)), PE(18:1(11Z)/18:2(9Z,12Z)); one decreased: PS(15:0/22:1(13Z))) in RRMS patients when comparing to HCs. Moreover, a biomarker panel consisting of four microbial genera (three decreased: Lysinibacillus, Parabacteroides, UBA1819; one increased: Lachnoanaerobaculum) and two glycerophospholipid metabolism-associated metabolites (one increased: PE(P-16:0/22:6); one decreased: CL(i-12:0/i-16:0/i-17:0/i-12:0)) effectively discriminated CMS patients from AMS patients, which indicate correlation with higher disability. Additionally, DMTs appeared to attenuate MS progression by reducing UBA1819 and upregulating CL(i-12:0/i-16:0/i-17:0/i-12:0). These findings expand our understanding of the microbiome and metabolome roles in RRMS and may contribute to identifying novel diagnostic biomarkers and promising therapeutic targets.

Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations.

Gut bacteria from the Enterobacteriaceae family are a major cause of opportunistic infections worldwide. Given their prevalence among healthy human gut microbiomes, interspecies interactions may play a role in modulating infection resistance. Here we uncover global ecological patterns linked to Enterobacteriaceae colonization and abundance by leveraging a large-scale dataset of 12,238 public human gut metagenomes spanning 45 countries. Machine learning analyses identified a robust gut microbiome signature associated with Enterobacteriaceae colonization status, consistent across health states and geographic locations. We classified 172 gut microbial species as co-colonizers and 135 as co-excluders, revealing a genus-wide signal of colonization resistance within Faecalibacterium and strain-specific co-colonization patterns of the underexplored Faecalimonas phoceensis. Co-exclusion is linked to functions involved in short-chain fatty acid production, iron metabolism and quorum sensing, while co-colonization is linked to greater functional diversity and metabolic resemblance to Enterobacteriaceae. Our work underscores the critical role of the intestinal environment in the colonization success of gut-associated opportunistic pathogens with implications for developing non-antibiotic therapeutic strategies.

Microdose Cocktail Study Reveals the Activity and Key Influencing Factors of OATP1B, P-Gp, BCRP, and CYP3A in End-Stage Renal Disease Patients.

OATP1B, P-gp, BCRP, and CYP3A are the most contributing drug-metabolizing enzymes or transporters (DMETs) for commonly prescribed medication. Their activities may change in end-stage renal disease (ESRD) patients with large inter-individual variabilities (IIVs), leading to altered substrate drug exposure and ultimately elevated safety risk. However, the changing extent and indictive influencing factors are not quantified so far. Here, a microdose cocktail regimen containing five sensitive substrate drugs (pitavastatin, dabigatran etexilate, rosuvastatin, midazolam, and atorvastatin) for these DMETs was administrated to Chinese healthy volunteers and ESRD patients. Drug pharmacokinetics profiles were determined, together with physiological, pharmacogenetic, and gut microbiome signature. Population pharmacokinetic and machine learning model were established to identify key influencing factors and quantify their contribution to drug exposure change. The exposure of pitavastatin, dabigatran, rosuvastatin, and atorvastatin increased to 1.8-, 3.1-, 1.1-, and 1.3-fold, respectively, whereas midazolam exposure decreased by 72% in ESRD patients. Notably, in addition to disease state, the relative abundance of genus Veillonella and Clostridium_XIVb were firstly identified as significant influencing factors for PTV and RSV apparent clearance, respectively, suggesting their indicative role for OATP and BCRP activity evaluation. Moreover, several genera were found to strongly associate with drug clearance and reduce unexplained IIVs. Accordingly, it was estimated that OATP1B and intestine P-gp activity decreased by 35-75% and 29-44%, respectively, whereas BCRP and CYP3A4 activity may upregulate to some extent. Our study provides a quantitative and mechanistic understanding of individual DMET activity and could support precision medicine of substrate drugs in ESRD patients.

Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals

As plant-based diets gain traction, interest in their impacts on the gut microbiome is growing. However, little is known about diet-pattern-specific metagenomic profiles across populations. Here we considered 21,561 individuals spanning 5 independent, multinational, human cohorts to map how differences in diet pattern (omnivore, vegetarian and vegan) are reflected in gut microbiomes. Microbial profiles distinguished these common diet patterns well (mean AUC = 0.85). Red meat was a strong driver of omnivore microbiomes, with corresponding signature microbes (for example, Ruminococcus torques, Bilophila wadsworthia and Alistipes putredinis) negatively correlated with host cardiometabolic health. Conversely, vegan signature microbes were correlated with favourable cardiometabolic markers and were enriched in omnivores consuming more plant-based foods. Diet-specific gut microbes partially overlapped with food microbiomes, especially with dairy microbes, for example, Streptococcus thermophilus, and typical soil microbes in vegans. The signatures of common western diet patterns can support future nutritional interventions and epidemiology.

Spatial heterogeneity determines the gastrointestinal microbiome signatures and ecological processes that govern bacterial community assembly in sheep.

Sheep's gastrointestinal tract harbors a diverse microbial community crucial for immune system balance, nutrient digestion, and overall health. We explored the microbial community composition, community types (enterotypes), bacterial interactions, and ecological processes in 10 gastrointestinal regions of 36 six-month-old Hu sheep raised under same diets and environmental conditions. Our findings revealed a unique U-shaped pattern of bacterial diversity from the rumen to the rectum, with the lowest diversity in the jejunum. The composition and enterotypes of bacterial communities varied spatially along the gastrointestinal tract, primarily categorized into three distinct groups. The rumen exhibited the highest abundance of bacterial taxa, unique taxa, and unique functions, while the enterotypes in the three regions of the large intestine were consistent. We explored the assembly processes of bacterial communities, elucidating how they find their ecological niches based on their characteristics and environmental demands. The assembly processes in the four-chambered stomach and small intestine resembled random selection, where bacterial positioning depended on luck and chance, while in the large intestine, it appeared more deterministic, with specific bacteria likely selected based on their unique skills and environmental requirements. This study enhances our understanding of microbial coexistence and interactions in complex ecosystems, with implications for improving animal productivity, disease treatment, and the development of novel microbial formulations.

Altered Microbiome Signature in Cushing's Syndrome Persists Beyond Remission

Abstract Context Patients with Cushing's syndrome (CS) suffer from metabolic and cardiovascular comorbidities caused by hypercortisolism. The human gut microbiome responds to different pathological conditions. Objective The aim of our study was to analyze the effect of chronic endogenous cortisol excess on the gut microbiome. Methods We prospectively recruited 18 patients with endogenous CS of different etiologies (mainly pituitary CS, n = 13). Patients provided a stool sample during active CS and 1 to 2 years after successful surgical treatment being in biochemical remission. In addition, 36 patients, in whom CS was excluded, served as an obese control group and 108 samples from healthy lean students were used as a reference group. Amplicons of the V3/V4 region of the 16S ribosomal RNA gene, from every sample, were sequenced and clustered into operational taxonomic units. The microbial profiles of CS patients were then compared to the control and reference groups using R scripts. Results In comparison to lean references, the gut microbiome of patients with florid CS demonstrated a disturbed microbial profile. Microbial dysbiosis of patients with CS was maintained even after biochemical remission following curative surgery. Conclusion Patients with CS have a distinct and disturbed gut microbiome that persists even after surgery, indicating a possible target for additional probiotic interventions to accelerate convergence to a healthy microbiome.

Differential Gut Microbiome Profiles in Long-Distance Endurance Cyclists and Runners.

We recently have shown that the gut microbiota composition in female and male runners positively correlates with sports, and female runners show similar gut microbiome diversity to male runners. However, gut microbiota composition has not yet been fully investigated in other endurance athletes, such as cyclists. Therefore, in the current study, we investigated the gut microbiome profiles in competitive, non-professional female and male cyclists compared to what we have shown in runners. We aim to understand (1) whether the gut microbiome signature is sport-specific; (2) whether there is a microbiome difference between female and male cyclists and runners; and (3) whether the gut bacteria expressed in cyclists and runners correlates with exercise performance. Our study included 58 subjects: 18 cyclists (9 males), 22 runners (13 males), and 18 control subjects (9 males). Fecal samples were obtained and subjected to taxonomic analysis to assess the relative abundances of species across subjects based on 16S rRNA sequencing results. Both alpha and beta diversity of the bacterial communities were evaluated to identify compositional variations between the groups. Each participant completed a maximal oxygen consumption test and a time-to-exhaustion test at 85% of the measured VO2max. Cyclists performed the test on an SRM ergometer, while runners used a motorized treadmill. Blood lactate levels were measured at 5 min intervals throughout the time-to-exhaustion trials. Alpha diversity demonstrated a significant difference (p-adj < 0.001) between cyclists and runners. Male cyclists showed significantly lower alpha diversity than runners (p-adj < 0.001). The taxonomic analysis of gut microbiota composition between cyclists, runners, and controls showed a lower or higher abundance of fifteen different bacteria. In cyclists, there was a significant positive correlation between six bacteria, and in runners, there was a significant positive correlation between eight bacteria, with weekly training volume, time-to-exhaustion, VO2max, and blood lactate levels. This study suggests potential sport-specific characteristics in long-distance cyclists' and runners' gut microbiome signatures. These findings emphasize the differences in gut microbiota between cyclists and runners, probably due to the difference in physiological and biomechanical conditions related to the activity mode during each sport.

Maternal Gut Microbiome-Mediated Epigenetic Modifications in Cognitive Development and Impairments: A New Frontier for Therapeutic Innovation.

Cognitive impairment in various mental illnesses, particularly neuropsychiatric disorders, has adverse functional and clinical consequences. While genetic mutations and epigenetic dysregulations of several genes during embryonic and adult periods are linked to cognitive impairment in mental disorders, the composition and diversity of resident bacteria in the gastrointestinal tract-shaped by environmental factors-also influence the brain epigenome, affecting behavior and cognitive functions. Accordingly, many recent studies have provided evidence that human gut microbiota may offer a potential avenue for improving cognitive deficits. In this review, we provide an overview of the relationship between cognitive impairment, alterations in the gut microbiome, and epigenetic alterations during embryonic and adult periods. We examine how various factors beyond genetics-such as lifestyle, age, and maternal diet-impact the composition, diversity, and epigenetic functionality of the gut microbiome, consequently influencing cognitive performance. Additionally, we explore the potential of maternal gut microbiome signatures and epigenetic biomarkers for predicting cognitive impairment risk in older adults. This article also explores the potential roles of nutritional deficiencies in programming cognitive disorders during the perinatal period in offspring, as well as the promise of gut microbiome-targeted therapeutics with epigenetic effects to prevent or alleviate cognitive dysfunctions in infants, middle-aged adults, and older adults. Unsolved challenges of gut microbiome-targeted therapeutics in mitigating cognitive dysfunctions for translation into clinical practice are discussed, lastly.

Colonization of stenotrophomonas and its associated microbiome between paired primary colorectal cancers and their lung metastatic tumors (experimental studies).

The role of gut microbiome in colorectal cancer (CRC) lung metastases is still unclear. Herein, we collected primary colorectal tumors, matched lung metastasis, and adjacent normal colon from seven patients for 16S rRNA sequencing to evaluate microbiome signature in distant site metastasis and analyze prognosis. Fecal samples from 19 non-metastases CRC patients and 11 CRC lung metastases patients were analyzed for validation. Our efforts led to a discovery of comprehensive microbiome in CRC lung metastatic tumors, characterized by a decreased microbial diversity and an increase bacterial interaction between gram-negative bacteria Stenotrophomonas and Brevundimonas . The primary-metastatic tumor pairs harbored highly similar microbial composition in both genus and species level, especially the high level of Stenotrophomonas maltophilia . Correspondingly, the S. maltophilia levels were positively associated with poor prognosis and cancer progression. Our work highlights the great potential of S. maltophilia and its associated microbiome as biomarkers in pathogenesis and prognosis of CRC lung metastases.