Gut Microbes

Early-life gut microbiome-metabolome crosstalk has a pivotal role in the maintenance of host physiology. However, our understanding on early-life gut microbiome-metabolome maturation trajectories in humans remains limited. This study aims to explore the longitudinal patterns of gut metabolites during early life, and how they are related to gut microbiota composition in birth cohort samples of n = 670 children collected at 2.5 (n=272), 6 (n=232), 14 (n=289), and 30 months (n=157) of age. Factor analysis showed that breastfeeding has an effect on several metabolites including secondary bile acids. We found that the prevalent gut microbial abundances were associated with metabolite levels, especially in the 2.5 months-olds. We also demonstrated that the prevalent early colonizers Bacteroides, Escherichia and Bifidobacterium abundances associated with microbial metabolites bile acids especially in the breastfed infants. Taken together, our results suggests that as the microbiome matures during the early-life there is an association with the metabolome composition in an analogous fashion to how the genome information mature during early life.

Preterm infants with very low birthweight are at serious risk for necrotizing enterocolitis. To functionally analyse the principles of three successful preventive NEC regimens, we characterized faecal samples of 54 infants (< 1,500 g, n = 383) longitudinally (two weeks) with respect to gut microbiome profiles (bacteria, archaea, fungi, viruses), microbial function, virulence factors, antibiotic resistances and metabolic profiles, including human milk oligosaccharides (HMOs) and short-chain fatty acids. Probiotic Bifidobacterium longum ssp. infantis supplementation affected microbiome development globally, pointing toward the genomic potential to convert HMOs. Engraftment of Bifidobacterium substantially reduced microbiome-associated antibiotic resistance as compared to regimens using probiotic Lactobacillus rhamnosus or no supplementation. Crucially, the beneficial effects of Bifidobacterium supplementation depended on simultaneous feeding with HMOs. We demonstrate that preventive regimens have the highest impact on early maturation of the gastrointestinal microbiome, enabling the establishment of a resilient microbial ecosystem that reduces pathogenic threats in at-risk preterm infants.

Faecal incontinence (FI) is a frequent and debilitating sequela of surgical repair of anorectal malformations (ARMs). The rectoanal inhibitory reflex (RAIR), an enteric nervous system (ENS)-mediated circuit essential for continence, is often absent or impaired in these children post-surgically. However, the biological cascade linking surgery to this reflex failure remains unknown. To identify the mechanistic pathways underlying post-surgical FI, we performed a multi-omics case-control study of 31 post-ARM children (12 incontinent, 20 continent), integrating stool 16S rRNA sequencing with untargeted serum metabolomics by liquid chromatography-mass spectrometry (LC-MS). Incontinent children exhibited greater microbial richness yet distinct communities, marked by depletion of butyrate-producing Faecalibacterium and expansion of mucin-degrading Ruminococcus along with Proteobacteria. These ecological shifts coincided with signatures of impaired fatty acid oxidation, and elevated levels of neurotoxic and inflammatory compounds such as trimethylamine and kynurenines. These findings suggest that surgical trauma destabilizes microbial and metabolic homeostasis, compromising ENS circuits. These results raise the possibility that microbial and metabolic restoration could restore faecal continence after surgical repair. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/25338825v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@908faforg.highwire.dtl.DTLVardef@c9537borg.highwire.dtl.DTLVardef@187d27eorg.highwire.dtl.DTLVardef@c6692_HPS_FORMAT_FIGEXP M_FIG C_FIG

BackgroundChildhood with obesity is characterized by metabolic dysregulation and unique gut microbiota profiles. Nevertheless, the comprehensive understanding of gut microbiota and metabolic dysregulation of Childhood with obesity remains unclear. ObjectivesThis study aimed to investigate the causal relationship of gut microbiota and Childhood with obesity and identify the blood metabolites as potential mediators. MethodsThe exposure genome-wide association studies (GWAS) data were sourced from the GWAS Catalog, while the outcome GWAS data were obtained from the Early Growth Genetics (EGG) Consortium. The study used 473 types of gut microbiota, 233 types of blood metabolites, and Childhood with obesity from GWAS. We then performed two-sample Mendelian randomization (TSMR) and bidirectional Mendelian randomization (BDMR) analyses to explore the causal relationships between gut microbiota, blood metabolites, and Childhood with obesity. Additionally, we conducted multivariable Mendelian randomization (MVMR) and two-step Mendelian randomization (2SMR) to identify potential mediating blood metabolites in this process. ResultsMR analysis identified 13 types of gut microbiota and 12 types of blood metabolites that were causally associated with Childhood with obesity. Furthermore, there was no strong evidence that genetically predicted Childhood with obesity had an effect on these gut microbiota and blood metabolites. Further, 2SMR analysis revealed that the association between K10 sp001941205 and Childhood with obesity was mediated by the Total cholesterol to total lipids ratio in medium VLDL, accounting for 2.53% (95%CI; 2.14%-2.92%) of the association. Similarly, the relationship between SM23-33 and Childhood with obesity was mediated by the Ratio of 22:6 docosahexaenoic acid to total fatty acids, which accounted for 4.07% (95%CI; 2.70%-5.44%) of the association. ConclusionsThe present study is the first to investigate the causal relationships among 473 gut microbiota phenotypes, 233 blood metabolites, and Childhood with obesity through Mendelian randomization analysis, identifying 13 gut microbiota types with potential causal links to Childhood with obesity and suggesting that 2 blood metabolites may mediate these associations, thereby providing valuable insights for future intervention strategies aimed at addressing Childhood with obesity.

Background and aimsYAQ001 is a novel, highly engineered, non-absorbable, gut-restricted, multiporous, carbon bead adsorbent. Pre-clinical studies and a clinical trial confirmed its therapeutic potential and safety in patients with cirrhosis. The aims of this sub study were to evaluate the effect of YAQ001 on the gut microbiome and its association with biomarkers of gut permeability and systemic inflammation. MethodsIn total, 28-patients with cirrhosis were randomized (double-blind) to receive YAQ001 (4g once daily) or Placebo. Gut microbiome and biomarkers of inflammation and gut permeability were assessed at baseline, after 4 and 12-weeks. Changes in biomarkers and relationship with microbiome composition and gene profiling were assessed. The effect of YAQ001 on Klebsiella pneumoniae bacterial biofilms was also assessed using an in vitro gut epithelial model. ResultsAlpha and beta diversity at different time points were unaltered. YAQ001 increased the abundance of bacteria associated with improved gut health such as Adlercreutzia equolifaciens (p<0.05), a bacterium commonly depleted in liver disease, and decreased the abundance of bacteria associated with infections and poor outcomes such as Klebsiella pneumonia and Streptococcus mutans (p<0.05 each). YAQ001 impacted positively on virulence factors such as siderophores, fimbriae structures and lipopolysaccharides that are associated with inflammation and invasion (p<0.05 each). Antibiotic resistance genes, decreased significantly in the YAQ001 group. These changes were associated with reduction in markers of gut permeability and systemic inflammation with no significant effect on bile acid metabolism. YAQ001 prevented Klebsiella pneumoniae biofilms in vitro. ConclusionsThe results show that YAQ001 impacts positively on the composition of the microbiome, significantly reduces its virulence, antibiotic resistance genes and biofilm formation, which is associated with modulation of gut permeability and systemic inflammation. Impact and implicationsYAQ001 exerts its therapeutic effect by favorably modulating the gut ecosystem in cirrhosis. It selectively increases beneficial gut bacteria while suppressing pathogenic taxa linked to adverse outcomes. Beyond composition, YAQ001 reduces microbial virulence by limiting the production of invasive toxins and lowers the abundance of antibiotic-resistance genes. In vitro models also demonstrated its efficacy in inhibiting biofilm formation by key pathogens. In summary, this multifaceted modulation of the microbiome led to tangible clinical improvements, notably enhanced gut barrier function and reduced systemic inflammation. The data support further development of YAQ001 as a novel microbiome therapeutic. HighlightsO_LIIn patients with cirrhosis, YAQ001 specifically enhanced beneficial gut bacteria while suppressing pathogenic bacteria linked to adverse clinical outcomes. C_LIO_LIYAQ001 significantly reduced the genetic expression of critical virulence factors, including siderophores, fimbriae, and lipopolysaccharides, thereby diminishing the potential for microbial invasion and inflammation. C_LIO_LIYAQ001 administration led to a significant decrease in the abundance of antibiotic resistance genes within the gut microbiome, potentially restoring therapeutic efficacy of antibiotics. C_LIO_LIIn vitro studies demonstrated that YAQ001 effectively prevents the formation of Klebsiella pneumoniae biofilms, a key mechanism of bacterial persistence and chronic infection. C_LIO_LIThe beneficial microbial shifts were directly associated with clinically relevant improvements in biomarkers of gut permeability and systemic inflammation. C_LI

The gut microbiota in early life, when critical immune maturation takes place, may influence the immunogenicity of childhood vaccinations. We assessed the association between mode of delivery, gut microbiota development in the first year of life, and mucosal antigen-specific immunoglobulin G (IgG) responses against pneumococcal and meningococcal conjugate vaccination at ages 12 and 18 months, respectively, in a prospective birth cohort of 120 infants. Birth by natural delivery was associated with higher IgG responses against both vaccines, which for the anti-pneumococcal IgG response could be explained by a gut microbial community composition with high abundances of Bifidobacterium and Escherichia coli in the first weeks of life. High E. coli abundance in the same period was also associated with higher anti-meningococcal IgG responses. Our results suggest that associations between mode of delivery and antibody responses to routine childhood vaccines are mediated by gut microbiota development.

The early life gut microbiome has been suggested to be a potential driver of neurocognitive development. Evidence for this relationship in preterm children, who are at increased risk of both gut microbiome disruptions and neurodevelopmental impairment, is scarce. In a sample of 73 very preterm infants drawn from a prospective birth cohort, we assessed associations between the neonatal gut microbiome and neurodevelopment at 9 months and 2 years. The gut microbiome was profiled from stool samples collected prior to NICU discharge using shotgun metagenomics. By taking a consensus-based analytic approach, we found strong evidence for associations between the abundances of several gut bacterial species and measures related to autistic traits (e.g. Klebsiella spp.), socio-emotional development, including temperament (e.g. Enterobacter cloacae complex, Veillonella parvula), and executive functioning (Clostridium perfringens). The abundances of functional modules involved in gut-brain signalling, particularly those involved in histamine, tryptophan and quinolinic acid metabolism, were associated with measures related to executive functioning and cognitive-behavioural flexibility. This study provides evidence that the neonatal gut microbiome composition may affect longer-term neurodevelopmental profiles following preterm birth, particularly those related to socio-emotional development, autistic traits and executive functioning.

The gut microbiome is a key regulator of metabolic homeostasis and contributes to obesity progression through effects on immune signaling, gut barrier integrity, and systemic inflammation. Microbiome-targeted strategies are therefore being explored as complementary approaches to conventional weight-loss therapies. Here, we investigated the probiotic yeast Saccharomyces boulardii in a murine model of diet-induced obesity (DIO) using an integrated multi-omics framework combining metabolic phenotyping, gut microbiome profiling, cecal metabolomics, colonic transcriptomics, and portal cytokine analysis. S. boulardii reduced food intake, attenuated weight gain, and increased energy expenditure without major changes in circulating metabolic hormone levels. Microbial diversity remained largely preserved, but selective enrichment of Bacteroidales lineages, including Muribaculaceae, was observed alongside functional remodeling of microbial pathways. Cecal metabolomics revealed increased B-vitamins, betaine, and GABA, with reduced stress-associated metabolites. Colonic transcriptomics showed attenuation of TNF/NF-{kappa}B signaling and enrichment of interferon and epithelial programs, while portal cytokine profiling indicated reduced inflammatory chemokines with trends toward increased IL-17A and IL-22. Integrated multi-omics analysis identified coordinated host-microbe interactions across metabolic, transcriptional, and immune layers. Collectively, these findings demonstrate that S. boulardii modulates the gut-immune-metabolic axis in obesity, supporting microbiome-based interventions as potential adjunct strategies targeting metabolic inflammation.

Changes in microbiome composition have been associated with a wide array of human diseases, turning the human microbiota into an attractive target for therapeutic intervention. Yet clinical translation of these findings requires the establishment of causative connections between specific microbial taxa and their functional impact on host tissues. Here, we colonized gut organ cultures with longitudinal microbiota samples collected from newly-diagnosed and therapy-naive irritable bowel syndrome (IBS) patients under low-FODMAP (fermentable Oligo-, Di-, Mono- saccharides and Polyols) diet. We show that post-diet microbiota regulates intestinal expression of inflammatory and neuro-muscular gene-sets. Specifically, we identify Bifidobacterium adolescentis as a diet-sensitive pathobiont that alters tight junction integrity and disrupts gut barrier functions. Collectively, we present a unique pathway discovery approach for mechanistic dissection and identification of functional diet-host-microbiota modules. Our data support the hypothesis that the gut microbiota mediates the beneficial effects of low-FODMAP diet, and reinforce the potential feasibility of microbiome based-therapies in IBS.

BackgroundAnorectal malformations (ARMs) are rare birth defects with established maternal risk factors. However, the molecular mechanisms linking these risk factors to ARM development remain unclear. Maternal vascular dysfunction may serve as a unifying mechanistic pathway. ObjectiveTo investigate whether mothers of ARM-affected children exhibit molecular signatures of vascular dysfunction using integrated microbiome and metabolomic profiling. MethodsMothers of ARM children (cases; n = 10) and matched healthy controls (n = 10), recruited more than one year postpartum, were analyzed using 16S rRNA sequencing and untargeted LC-MS-based serum metabolomics. Microbial diversity was assessed using Shannon and Chao1 indices; compositional differences were evaluated by PERMANOVA across multiple distance metrics. Metabolites were analyzed using univariate and multivariate methods with FDR correction (q < 0.05). ResultsCases exhibited elevated Firmicutes:Bacteroidetes ratios (70.1% vs 51.6%) and significant depletion of Olsenella (6.2% vs 16.4%, p < 0.05), a genus associated with cortisol metabolism. Metabolomic profiling revealed 174 significantly altered serum metabolites (p < 0.05, fold change >1.5). Among these, reduced D-glutamic acid, elevated thromboxane A , and decreased hexacosanoic acid emerged as key discriminants, mapping to pathways involved in oxidative stress, vasoconstriction, and peroxisomal dysfunction. ConclusionsThis pilot study reveals maternal microbiome-metabolome signatures suggestive of subclinical vascular dysfunction, resembling aspects of pre-eclampsia, in mothers of children with ARMs. These findings support the hypothesis that maternal vascular health influences ARM risk and warrant validation in larger, prospective cohorts. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/25330492v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@11d2066org.highwire.dtl.DTLVardef@13a1778org.highwire.dtl.DTLVardef@dafa2corg.highwire.dtl.DTLVardef@5e9db7_HPS_FORMAT_FIGEXP M_FIG C_FIG

Group B Streptococcus (GBS) is the leading cause of neonatal invasive infections. Late-onset infections (7-89 days after birth) are caused by GBS clonal complex 17 (CC17) in 50-80% of cases, likely resulting from bacterial translocation across the intestinal barrier. However, the factors influencing GBS colonization in neonates are incompletely understood. We used shotgun metagenomics on fecal samples from 100 neonates aged 21 days and identified taxonomic signatures of GBS colonization, including decreased Enterobacter hormaechei abundance in neonates colonized by non-CC17 GBS. Using in vitro assays with representative isolates, we demonstrate that GBS CC17 competes more effectively than GBS non-CC17 against E. hormaechei, with enhanced adherence to enterocytes mediated by the CC17-specific HvgA adhesin. Our findings highlight lineage-dependent interspecies interactions of GBS that likely influence its ability to colonize the neonatal gut. These interactions must be considered when developing microbiota-based strategies to mitigate neonatal colonization and infection by GBS.

Stunting remains a major public health challenge in Indonesia and is increasingly associated with gut microbiota dysbiosis. This study examined 36 children aged 2-5 years through anthropometry, dietary assessment, and pooled fecal sampling. Full-length 16S rRNA sequencing using Oxford Nanopore Technologies revealed notable microbial alterations in the stunted group. Stunted children exhibited reduced alpha diversity and lower microbial richness, indicating a simplified gut ecosystem. Although both groups were dominated by Bacillota (>96%), stunted children showed higher proportions of Clostridia affiliated orders, including Eubacteriales, Peptostreptococcales, and Erysipelotrichaceae, along with enrichment of fermentative and dysbiosis associated genera such as Blautia, Romboutsia, and Terrisporobacter. Beneficial fiber degrading taxa, including Lachnospiraceae, were proportionally higher in normal children. Functional predictions using PICRUSt2 revealed greater microbial metabolic activity in the stunting group, particularly in carbohydrate, amino acid, and nucleotide metabolism, with elevated pathways such as starch and sucrose metabolism, glycolysis, and porphyrin and pyrimidine metabolism. Dietary assessment showed significantly lower intake of energy, protein, fat, and multiple micronutrients among stunted children, consistent with observed microbial and functional alterations. These findings indicate a distinct fermentative dysbiosis in Banyumas stunted children and highlight the need for integrated nutritional and microbiota targeted interventions.

Severe Acute Malnutrition (SAM) in early days of life has been a concerning global health challenge, contributing to high child mortality and morbidity. The mechanistic role of the gut microbiota in its pathophysiology remains incompletely understood. In this case-control study we profiled gut-microbiota using 16S-rRNA sequencing for V3-V4 region for 115 SAM children (52 SAM and 63 Healthy) aged 6-59 months. Inflammatory markers along with fecal sIgA levels were analysed and correlated with clinical parameters, and dietary intake of these children. Alpha diversity has revealed a significant difference in ChaoI index indicating reduced richness in SAM group (p<0.001). Children with SAM have also shown reduced abundance of beneficial groups such as Blautia, Akkermansia, and Ruminococcus gnavus, with an expansion of opportunistic groups like Enterococcus, Staphylococcus, and Turicibacter. Inflammatory markers show elevated levels of inflammation in SAM children when compared to healthy controls. Reduced fecal sIgA levels in SAM group have been noted, suggesting an impaired immune response. Male children were at higher risk of inflammation and immune dysfunction. Our findings delineate gut-microbial disruption as a central feature of childhood SAM. Targeting these specific taxa and their associated metabolic pathways can help in tailoring future interventions.

Early exposure to antibiotics and prolonged hospitalization in preterm infants may perturb microbiome development and contribute to adverse health outcomes. Although nasopharyngeal microbiomes are linked to respiratory infections, their early development is underexplored and often assessed with 16S rRNA sequencing, which lacks species resolution. Here, we investigated nasopharyngeal microbiota dynamics in 66 preterm infants by performing deep shotgun metagenomics on 369 nasopharyngeal aspirates collected from birth until 6 months corrected age ([~]7-10 months chronological age). The nasopharyngeal microbiota evolved dynamically, exhibiting age-structured and individualized patterns shaped by postnatal antibiotic exposure and hospitalization. Early-life antibiotic exposure (ampicillin + gentamicin) had transient but significant effects on microbial diversity, composition, stability, and community dynamics. Conversely, an unexpected NICU outbreak left a lasting signature, with persistent S. marcescens carriage observed at 6 months corrected age, which our machine learning algorithm accurately predicted based on microbiome composition in the first days of life. A S. marcescens-dominated community type was present in 45% of total samples and exhibited remarkable stability over time, with minimal transitions to other types regardless of antibiotic exposure. These findings underscore the need for deeper insight into how antibiotics and potential outbreaks can lead to alterations in microbiome trajectories, with possible long-term health implications.

BackgroundChronic liver disease (CLD) is a progressive condition that can advance to cirrhosis and acute-on-chronic liver failure (ACLF), a syndrome characterised by multi-organ dysfunction, critical illness, and high mortality. ACLF is driven by systemic inflammation, often without overt infection, suggesting alternative immune activation pathways, including microbial translocation. While intestinal perturbations, bacterial translocation, and immune dysfunction are hallmarks of ACLF, the specific microbial contributors remain unclear. ObjectiveTo investigate relationships between gut microbiome alterations, systemic inflammation, and clinical markers of disease severity across the cirrhosis spectrum. DesignThis cross-sectional, prospective study analysed faecal microbiota, plasma bile acids, urinary and plasma metabolites, gut and systemic inflammation and translocation markers, and monocyte dysfunction, in a well-phenotyped cohort of ACLF patients, decompensated and stable cirrhosis, compared to healthy individuals. ResultsAdvanced stages of cirrhosis exhibited higher Enterococcus abundance, correlating with systemic inflammation, particularly in ACLF patients. Anaerobic commensal genera (Roseburia, Ruminococcus, and Faecalibacterium) were significantly lower. Lower urinary hippurate and trimethylamine N-oxide (TMAO) levels, linked to reduced microbial metabolism, paralleled these microbiome changes. Systemic inflammatory markers suggested parallel gut barrier dysfunction and microbial translocation in advanced cirrhosis. ConclusionIntestinal Enterococcus abundance, in advanced cirrhosis with greater antibiotic exposure, is a potential driver of gut barrier inflammation and dysfunction, and systemic immune activation. Further research into tailored microbiome-targeted therapies, including prebiotics, probiotics, phages and focused antibiotic use may prevent Enterococcus dominance, restore gut-liver axis homeostasis, and mitigate disease progression in cirrhosis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/25322003v4_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@d0843borg.highwire.dtl.DTLVardef@19966f0org.highwire.dtl.DTLVardef@352be6org.highwire.dtl.DTLVardef@d5146d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LICLD can progress to ACLF, a life-threatening syndrome with high mortality rates characterised by systemic inflammation, impaired phagocytosis and immune dysfunction with associated multiple organ failure. C_LIO_LIThe gut microbiomes role in underpinning the gut-liver axis is recognised, with microbial perturbations and gut barrier dysfunction associated with CLD, yet the exact microbiome changes and their link to inflammatory pathways remain unclear. C_LI What this study addsO_LIThis study reveals that Enterococcus significantly increases with CLD severity and antibiotic use and correlates with markers of systemic inflammation and gut barrier dysfunction. C_LIO_LIReductions in obligate anaerobe commensal bacteria, such as Roseburia and Faecalibacterium, are observed, alongside depressed levels of key microbial metabolites, including hippurate and TMAO, across CLD stages. C_LIO_LIThese changes suggest that Enterococcus predominance and gut microbiome perturbations driven by factors including disease severity and antibiotic use may actively drive inflammation and impaired monocyte function in CLD. C_LI How this study might affect research, practice, or policyO_LIFindings indicate that Enterococcus and wider gut microbiome perturbations provide a rationale for targeting as therapeutic strategies to modulate the gut-liver axis in CLD. C_LIO_LIThis highlights the potential of microbiome-focused interventions, such as faecal microbial transplantation, probiotics, prebiotics or phages, to improve gut health, reduce gut and systemic inflammation, and ultimately mitigate cirrhosis-related complications. C_LIO_LIFuture research and development of targeted microbiome therapeutics and rapid infection diagnostics may positively influence CLD management, including a focus on antimicrobial stewardship and informing clinical guidelines whilst improving patient outcomes. C_LI

The early infant gut microbiota is dominated by bifidobacteria, but there is substantial variation at the (sub)species level. Patterns of postnatal Bifidobacterium subspecies colonization in low or middle-income countries have not been widely studied. We used (sub)species-specific qPCR to quantify B. infantis, B. longum, and B. breve in stool samples from 1132 infants (0-6 months) in urban Dhaka, Bangladesh. B. infantis absolute abundance started low but increased in the first two months, whereas B. longum and B. breve abundances remained comparatively low. B. infantis emerged earlier in infants delivered by C-section, but by [~]2 months of age, infants delivered by C-section or vaginally had similar B. infantis abundances. Infant antibiotic exposure, feeding patterns, and maternal stool B. infantis were not associated with infant B. infantis. In settings where B. infantis is widespread, its patterns of postnatal colonization can be used to inform the design of targeted microbiota-modifying interventions in infancy.

Evidence is emerging that microbiome-immune system crosstalk regulates the tenor of host intestinal immunity and predisposition to inflammatory bowel disease (IBD). We identified five NF-{kappa}B suppressive strains affiliated with Clostridium clusters IV, XIVa and XV that independently suppressed secretion of the chemokine IL-8 by peripheral blood mononuclear cells and gut epithelial organoids from healthy human subjects, as well as patients with the predominant IBD subtypes, Crohns disease and ulcerative colitis. The NF-{kappa}B suppressive Clostridium bolteae AHG0001, but not C. bolteae BAA-613, suppressed cytokine-driven inflammatory responses and endoplasmic reticulum stress in gut epithelial organoids derived from Winnie mice that develop spontaneous colitis. This predicted in vivo responses thereby validating a precision medicine approach to treat Winnie colitis and suggesting the microbiome may function as an extrinsic regulator of host immunity. Finally, we identified a novel molecule associated with NF-{kappa}B suppression indicating gut bacteria could be harnessed to develop new therapeutics.

Recently, an intestinal dysbiotic microbiota with enrichment in oral cavity bacteria has been described in colorectal cancer (CRC) patients. Here we characterized and investigated one of these oral pathobionts, the Gram-positive anaerobic coccus Parvimonas micra. We identified two phylotypes (A and B) exhibiting different phenotypes and adhesion capabilities. We observed a strong association of phylotype A with CRC, with its higher abundance in feces and in tumoral tissue compared with the normal homologous colonic mucosa, which was associated with a distinct methylation status of patients. By developing an in vitro hypoxic co-culture system of human primary colonic cells with anaerobic bacteria, we showed that P. micra phylotype A alters the DNA methylation profile promoters of key tumor-suppressor genes, oncogenes, and genes involved in epithelial-mesenchymal transition. In colonic mucosa of CRC patients carrying P. micra phylotype A, we found similar DNA methylations alterations, together with significant enrichment of differentially expressed genes in pathways involved in inflammation, cell adhesion, and regulation of actin cytoskeleton, providing evidence of P. micra possible role in the carcinogenic process.

ObjectiveGrowing evidence links bacterial dysbiosis with colorectal cancer (CRC) carcinogenesis, characterized by an increased presence of core pathogens such as Bacteroides fragilis and Fusobacterium nucleatum. Here, we characterized the in situ biogeography and transcriptional interactions between bacteria and the host in mucosal colon biopsies. DesignThe influence of CRC core pathogens and biofilms on the tumour microenvironment (TME) was investigated in biopsies from patients with and without CRC (paired normal tissue and healthy tissue biopsies) using fluorescence in situ hybridization and dual-RNA sequencing. ResultsTissue-invasive, mixed-species biofilms enriched for B. fragilis and F. nucleatum were observed in CRC tissue, especially in right-sided tumours. Fusobacterium spp. was associated with increased bacterial biomass and inflammatory response in CRC samples. CRC samples with high bacterial activity demonstrated increased expression of pro-inflammatory cytokines, defensins, matrix-metalloproteases, and immunomodulatory factors. In contrast, the gene expression profiles of CRC samples with low bacterial activity resembled healthy tissue samples. Moreover, immune cell profiling showed that B. fragilis and F. nucleatum modulated the TME and correlated with increased infiltration of neutrophils and CD4+ T-cells. Overall, bacterial activity was critical for the immune phenotype and correlated with the infiltration of several immune cell subtypes, including M2 macrophages and regulatory T-cells. ConclusionBiofilms and core pathogens shape the TME and immune phenotype in CRC. Our results support that Fusobacterium spp. may provide a future therapeutic target to reduce biofilms and the inflammatory response in the TME while highlighting the importance of widening the scope of bacterial pathogenesis in CRC beyond core pathogens.

Nisin Z, an antimicrobial metabolite produced by Lactococcus lactis spp., has been safely used as a food preservative for many years. Nisin Z also showed promising activity against various cancer types in vitro, and significantly reduced tumor size in an ectopic head and neck cancer model. Here, we investigate the activity of nisin Z for colorectal cancer treatment and observed an in vitro reduction in cellular proliferation, and a moderate enhancement in cell death. We next analyzed the effect of oral nisin Z administration in the Apcmin/+ intestinal adenoma mouse model. We measured tumor burden along the gastrointestinal tract and observed a decrease in tumor burden in the middle region of the small intestine, but not in the lower region or colon. Since tumor progression in the Apcmin/+ model is exacerbated by an inflammatory environment, we next determined whether nisin Z impacts this in a direct or indirect manner. We show that nisin Z can directly reduce NF-{kappa}B activation in a dose-dependent manner. In addition, nisin Z impacted the cecal microbiome composition as well as microbiota-associated plasma metabolites, causing an overall shift towards a more health-associated profile. Interestingly, the Apcmin/+ genotype differentially impacted the nisin Z-mediated differences in cecal microbiome composition and plasma metabolites compared to wildtype animals. In summary, our data suggest that the reduction in small intestinal tumor burden could be due to nisin Zs contribution to a reduced pro-inflammatory environment. Future studies will reveal whether nisins localized effect is due to degradation of the peptidic compound in more distal regions of the gastrointestinal tract and focus on development of delivery systems to increase efficacy. ImportanceWith the increased incidence of colorectal cancer, especially among younger individuals, it is critical to study approaches that help with the prevention and treatment of this debilitating disease. Our study indicates that nisin Z, a bacterially produced peptide antibiotic, decreases the growth of colorectal cancer cells and moderately increases cell death in vitro. Oral administration of nisin Z in an intestinal adenoma mouse model revealed a reduction of tumor burden in the middle region of the small intestine. This decreased tumor burden might in part be attributed to a direct anti-inflammatory effect, as well as an indirect effect on the gut microbiota and their metabolites due to nisin Zs antibacterial activity. Overall, we demonstrate a potential activity for nisin Z in the prevention or amelioration of inflammation-associated colorectal cancer, underscoring the significance of investigating the properties of bacterial natural products in human health.