Host-microbiota Crosstalk Research Articles

P0115 Selective immune responses to Lachnospiraceae flagellins discriminate therapy-naive pediatric Crohn’s disease patients with distinct host-microbial interaction

Abstract Background Pathogenic CD4+ T-cell responses to commensal microbial antigens drive intestinal inflammation in Crohn’s disease (CD). Both hypo- or hyperactive anti-microbial innate immunity could underlie these aberrant T-cell responses. CD patients have increased IgG and T cell responses against commensal Lachnospiraceae-derived flagellins, which associate with disease complications. We investigated whether CD patients with high anti-Lachnospiraceae flagellin responses at diagnosis have underlying innate hypo- or hyperresponsiveness and high IgG responses to other dysbiotic commensals. Methods IgG reactivity to 19 recombinant flagellins from Lachnospiraceae species colonizing mouse and human gut, was measured in plasma of therapy-naïve pediatric CD patients (n=49) and controls (n=29). In addition, we measured plasma IgG responses to 1 recombinant flagellin and 71 microbial lysates of dysbiotic commensal species in therapy-naive pediatric CD patients (n=103) and controls (n=61). IgG responses were related to immunological and clinicopathological parameters. Results CD patients had significantly higher IgG responses to 12/19 Lachnospiraceae-derived flagellins compared to controls. Multi-reactivity to more than 10 flagellins was common in CD (41%) and associated with increased circulating flagellin-specific memory CD4+ T-cell frequencies. Multi-reactivity, and even single-reactivity to recombinant flagellin, correlated with reduced immune cell infiltration and epithelial damage, and fewer calprotectin-positive neutrophils in colonic lesional tissue, based on histological severity scoring and immune histochemistry, respectively. As these data may argue that high anti-flagellin IgG reactivity relates to innate hyporesponsiveness, we next assessed whether patients had a generalized high IgG response to lysates of dysbiotic intestinal bacteria. Hierarchical clustering identified subgroups of CD patients with different patterns of significantly increased anti-commensal IgG responses. Patients with high anti-Lachnospiraceae flagellin IgG also had high IgG responses against lysate of Roseburia inulinivorans, a Lachnospiraceae species. Of these anti-flagellin high responders, two-thirds responded to many commensals while one-third did not, arguing against a generalized high anti-commensal IgG response. Conclusion In conclusion, high IgG responses to Lachnospiraceae-derived flagellins identify a subgroup of pediatric therapy-naive CD patients with features of innate hyporesponsiveness. These patients do not have uniformly high IgG responses to other dysbiotic commensals, arguing that disturbed host-microbiota responses in CD are highly personalized and do not stem from an overall failure in microbiota-host crosstalk.

P0060 GPR15L counteracts chronic colitis by shaping the intestinal microbiota

Abstract Background The G protein-coupled receptor 15 (GPR15) is expressed on gut-homing T cells and the interaction of the GPR15 ligand GPR15L with GPR15 has recently been shown to crucially control integrin-dependent adhesion to the endothelium. However, the impact of GPR15L, which is predominantly expressed by colonic epithelial cells, on experimental colitis and inflammatory bowel disease (IBD) is currently not clear. Methods We studied GPR15L in experimental colitis with Gpr15l-deficient and -overexpressing mice as well as with rectal application of recombinant GPR15L. We performed phenotypical and molecular disease characterization using endoscopy, IVIS in vivo imaging, histology, immunofluorescence, FISH, qPCR, and multiplex ELISA. We also performed bulk RNA and metagenomic sequencing. We analyzed the expression of GPR15L in samples from IBD patients and non-IBD controls using qPCR and immunofluorescence and correlated it with clinical information. We explored the function of GPR15L in vitro using radial diffusion assays and antimicrobial assays. Results Acute DSS colitis was aggravated in Gpr15l-deficient mice compared to Gpr15l-proficient mice, while it was attenuated in Gpr15l-transgenic mice. This was T cell-independent, since the phenotype was conserved in Rag-/-Gpr15l-/- mice. Moreover, it was independent of Gpr15 in T cell transfer colitis with Gpr15-deficient and -proficient donor cells. RNA sequencing of colon tissue from Gpr15l-/- and Gpr15l+/+ mice with DSS colitis showed differential regulation in genes related to mucosal barrier function and host-microbiota crosstalk. Accordingly, 16S rRNA sequencing revealed a substantial difference in the intestinal microbial diversity of Gpr15l-/- and Gpr15l+/+ mice. Shotgun metagenomics and radial diffusion assays revealed that GPR15L acts as a selective anti-microbial peptide on community and single strain level, respectively, that predominantly restrains the growth of pathogenic bacteria. Rectal supplementation of recombinant GPR15L in Gpr15l-/- mice rescued increased disease severity in acute DSS colitis and reduced bacterial abundance and translocation. Patients with IBD showed reduced expression of GPR15L compared to controls. Furthermore, the expression of GPR15L was lower in patients with high disease severity compared to those with low severity. Finally, flare-free survival in patients with high GPR15L expression was substantially longer than in patients with low GPR15L expression. Conclusion GPR15L counteracts experimental colitis and seems beneficial in human IBD. Mechanically, it acts as an anti-microbial peptide to promote the homeostasis of the intestinal microbiota. Thus, GPR15L emerges as a potential future therapeutic approach for IBD.

Insights into Microbiota-Host Crosstalk in the Intestinal Diseases Mediated by Extracellular Vesicles and Their Encapsulated MicroRNAs.

Microorganisms that colonize the intestine communicate with the host in various ways and affect gut function and health. Extracellular vesicles (EVs), especially their encapsulated microRNAs (miRNAs), participate in the complex and precise regulation of microbiota-host interactions in the gut. These roles make miRNAs critically important for the prevention, diagnosis, and treatment of intestinal diseases. Here, we review the current knowledge on how different sources of EVs and miRNAs, including those from diets, gut microbes, and hosts, maintain gut microbial homeostasis and improve the intestinal barrier and immune function. We further highlight the roles of EVs and miRNAs in intestinal diseases, including diarrhea, inflammatory bowel disease, and colorectal cancer, thus providing a perspective for the application of EVs and miRNAs in these diseases.

Dissecting causal relationships between gut microbiome, immune cells, and brain injury: A Mendelian randomization study.

Increasing literature has affirmed that changes in the gut microbiome (GM) composition were linked to distinct brain injury (BI) through the gut-brain axis, but it is uncertain if such links reflect causality. Further, the immune cell changes mediating the impact of GM on BI are not completely understood. We made use of the summary statistics of 211 GM (MiBioGen consortium), 731 immune cells, and 2 different BIs (FinnGen consortium), namely traumatic BI (TBI) and focal BI (FBI), from the extensive genome-wide association studies to date. We executed bidirectional Mendelian randomization (MR) analyses to ascertain the causal relationships between the GM and BI, and 2-step MR to validate possible mediating immune cells. Additionally, thorough sensitivity analyses verified the heterogeneity, robustness, as well as horizontal pleiotropy of the results. Based on the results of inverse-variance weighted (IVW) and sensitivity analyses, in MR analyses, 5 specific GM taxa and 6 specific GM taxa were causally associated with FBI and TBI, respectively; 27 immunophenotypes and 39 immunophenotypes were causally associated with FBI and TBI, respectively. Remarkably, Anaerofilum, LachnospiraceaeNC2004group, RuminococcaceaeUCG004, CCR2 on myeloid dendritic cell (DC), CD123 on CD62L+ plasmacytoid DC, and CD123 on plasmacytoid DC were causally associated with TBI and FBI (all P < .040). However, our reverse MR did not indicate any influence of TBI and FBI on the specific GM. In mediation analysis, we found that the associations between Escherichia.Shigella and FBI were mediated by CD123 on CD62L + plasmacytoid DC in addition to CD123 on plasmacytoid DC, each accounting for 4.21% and 4.21%; the association between FamilyXIIIAD3011group and TBI was mediated by CCR2 on myeloid DC, with mediated proportions of 5.07%. No remarkable horizontal pleiotropy or heterogeneity of instrumental variables was detected. Our comprehensive MR analysis first provides insight into potential causal links between several specific GM taxa with FBI/TBI. Additionally, CD123 on plasmacytoid DC in conjunction with CCR2 on myeloid DC may function in gut microbiota-host crosstalk in FBI and TBI, correspondingly. Further studies are critical to unravel the underlying mechanisms of the links between GM and BI.

Desaminotyrosine is a redox-active microbial metabolite that bolsters macrophage antimicrobial functions while attenuating IL-6 production.

Intestinal microbiota contributes to host defense against pathogens while avoiding the induction of inflammation in homeostatic conditions, but the mechanism is not fully understood. To investigate the potential role of the bacterial metabolite desaminotyrosine (DAT) in regulating host defense and inflammation, we pretreated mouse bone marrow-derived macrophages (BMDMs) with DAT for 12 hours and then challenged with bacterial lipopolysaccharide (LPS). We found that DAT priming-enhanced type I interferon response while selectively inhibiting proinflammatory interleukin (IL)-6 production after exposure to LPS. This is related to the fact that DAT is a natural antioxidant determined by radical scavenging assay in a cell-free system. DAT-primed cells had increased levels of the reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) upon LPS stimulation. Countering the increased NADPH by supplementing extra oxidized NADP+ to cells reversed DAT's effect on LPS-induced Il-6 and interferon-stimulated gene expressions. DAT-primed cells also were more resistant to oxidative stress-induced generation of reactive oxygen species and cell death. DAT promoted the production of antimicrobial effector nitric oxide in a cellular redox-dependent manner, leading to enhanced macrophage antimicrobial activity during Salmonella enterica infection. Our data suggest that DAT acts as a host-microbiota crosstalk signal in shaping host immune defense and inflammatory response.

Microbiota-bone axis in ageing-related bone diseases.

Bone homeostasis in physiology depends on the balance between bone formation and resorption, and in pathology, this homeostasis is susceptible to disruption by different influences, especially under ageing condition. Gut microbiota has been recognized as a crucial factor in regulating host health. Numerous studies have demonstrated a significant association between gut microbiota and bone metabolism through host-microbiota crosstalk, and gut microbiota is even an important factor in the pathogenesis of bone metabolism-related diseases that cannot be ignored. This review explores the interplay between gut microbiota and bone metabolism, focusing on the roles of gut microbiota in bone ageing and aging-related bone diseases, including osteoporosis, fragility fracture repair, osteoarthritis, and spinal degeneration from different perspectives. The impact of gut microbiota on bone metabolism during aging through modification of endocrinology system, immune system and gut microbiota metabolites are summarized, facilitating a better grasp of the pathogenesis of aging-related bone metabolic diseases. This review offers innovative insights into targeting the gut microbiota for the treatment of bone ageing-related diseases as a clinical therapeutic strategy.

O-305 Mapping the entire functionally active seminal microbiota and its association with semen quality parameters

Abstract Study question Does semen harbour functionally active microorganisms, and whether the microbial composition associate with semen quality parameters? Summary answer Seminal fluid harbours functionally alive microorganisms including bacteria, viruses, archaea, viroids and fungi whose composition and metabolic functions associate with semen quality parameters. What is known already Seminal fluid has been shown to possess different microbes, where different bacteria have been associated with spermatogenesis, seminal parameters and infertility. Nevertheless, previous results are inconclusive and the core microorganismal composition in semen is not determined and whether the identified bacterial DNA sequences refer to alive/functionally active microbes is not clear. Further, there is limited knowledge of the potential host-microbe interactions. Study design, size, duration In total 78 men with age between 18 and 45 years donated semen for the study, 59 men with good quality semen parameters and 19 men with low semen quality and diagnosed asthenospermia, oligoasthenozoospermia or oligoasthenoteratozoospermia comprised control and case groups, respectively. Participants/materials, setting, methods Semen quality parameters were analysed following WHO, 2021 guidelines. Seminal fluid underwent NextSeq total RNA sequencing, separating human and non-human sequences with Hisat2 aligner. Taxonomic classification of microorganisms was obtained using Kraken2. Microbial species and human RNA-Seq analyses, comparing control and infertility groups, utilized metagenomeSeq and edgeR R packages. Human and microbial pathways were annotated using MetaCyc, followed by GSEA analysis. The integration of metabolic pathways between host and microbes was investigated. Main results and the role of chance With our total RNAseq analysis, we mapped the entire alive microbiota composing of 6453 microorganisms within the seminal fluid samples. Microbes such as bacteria, fungi, viruses, viroids and archea were identified. When analysing microbiota associations with seminal parameters, 404 microbial species (Lactobacillus, Gardnerella, Prevotella, Atopobium, Pseudomonas among others) were significantly differently present among infertile men vs. good quality semen group. The host transcriptomic analysis identified 2569 differentially expressed genes in infertile vs. good quality semen groups, involved in sperm differentiation, spermatid development, reproduction, cilium movement and meiosis. Metabolic pathway analysis detected possible metabolic activity in the host-microbiota crosstalk in FAO-PWY: fatty acid &amp; beta-oxidation, LIPASYN-PWY: phospholipases, PWY66-429: fatty acid biosynthesis, PWY-3781: aerobic respiration I pathways. Limitations, reasons for caution Bigger sample size of infertile men would be needed to validate the study findings. Wider implications of the findings We confirm the presence of active microbes in semen with implications in seminal quality parameters such as motility, sperm count and morphology. Our results contribute to better understanding of seminal microbiota dysregulation in infertility with broader implications for reproductive health, suggesting functional links between seminal microbiota and sperm parameters. Trial registration number NA

A multi-omics dataset of the response to early plant polysaccharide ingestion in rabbits

The transition from a milk-based diet to exclusive solid feeding deeply modifies microbiota-host crosstalk. Specifically, early ingestion of plant polysaccharides would be one of the main nutritional components to drive host-microbiota-interaction. To capture the effects of polysaccharides early-life nutrition (starch vs rapidly fermentable fiber) on the holobiont development, we investigated on the one hand the gut bacteriome and metabolome and on the other hand the transcriptome of two host gut tissues. Rabbit model was used to study post-natal co-development of the gut microbiota and its host around weaning transition. The assessment of the microbial composition of the gut appendix together with the caecum was provided for the first time. Gene expression signatures were analyzed along the gut (ileum and caecum) through high-throughput qPCR. The data collected were completed by the analysis of animal growth changes and time-series assessment of blood biomarkers. Those accessible and reusable data could help highlight the gut development dynamics as well as biological adaptation processes at the onset of solid feeding.

Association between gut microbiota and acute pancreatitis: a bidirectional Mendelian randomization study.

The dysbiosis of gut microbiota has been reported in acute pancreatitis. However, the direction and magnitude between host microbiota and pancreas remains to be established. This study investigated the association between gut microbiota and acute pancreatitis using Mendelian randomization (MR) methods. Summary statistics of gut microbiota abundance and acute pancreatitis were extracted from genome-wide association studies (GWAS). The two-sample bidirectional MR design was employed to assess genetic association between the microbiota and pancreatitis, followed by a comprehensive sensitivity analysis to verify the robustness of the results. Seven microbiota taxa have been identified as significantly associated with the development of pancreatitis. Host genetic-driven order Bacteroidales and class Bacteroidia are associated with an increased risk of pancreatitis. The genera Coprococcus and Eubacterium fissicatena group also exhibit a positive effect on the development of pancreatitis, while the genera Prevotella, Ruminiclostridium, and Ruminococcaceae act as protective factors against pancreatitis. In contrast, acute pancreatitis was positively correlated with phylum Proteobacteria and genus Lachnospiraceae and negatively correlated with genus Holdemania. The bidirectional relationship between gut microbiota and acute pancreatitis suggests a critical role for host-microbiota crosstalk in the development of the disease. Targeted modulation of specific gut microbiota enables the prevention and treatment of acute pancreatitis.

Alistipes indistinctus-derived hippuric acid promotes intestinal urate excretion to alleviate hyperuricemia

Hyperuricemia induces inflammatory arthritis and accelerates the progression of renal and cardiovascular diseases. Gut microbiota has been linked to the development of hyperuricemia through unclear mechanisms. Here, we show that the abundance and centrality of Alistipes indistinctus are depleted in subjects with hyperuricemia. Integrative metagenomic and metabolomic analysis identified hippuric acid as the key microbial effector that mediates the uric-acid-lowering effect of A.indistinctus. Mechanistically, A.indistinctus-derived hippuric acid enhances the binding of peroxisome-proliferator-activated receptor γ (PPARγ) to the promoter of ATP-binding cassette subfamily G member 2 (ABCG2), which in turn boosts intestinal urate excretion. Tofacilitate this enhanced excretion, hippuric acid also promotes ABCG2 localization to the brush border membranes in a PDZ-domain-containing 1 (PDZK1)-dependent manner. These findings indicate that A.indistinctus and hippuric acid promote intestinal urate excretion and offer insights into microbiota-host crosstalk in the maintenance of uric acid homeostasis.

Lacticaseibacillus chiayiensis mediate intestinal microbiome and microbiota-derived metabolites regulating the growth and immunity of chicks

Emerging evidence confirms beneficial properties of probiotics in promoting growth and immunity of farmed chicken. However, the molecular mechanisms underlying the host-microbiome interactions mediated by probiotics are not fully understood. In this study, the internal mechanisms of Lacticaseibacillus chiayiensis-mediated host-microbiome interactions and to elucidate how it promotes host growth were investigated by additional supplementation with L. chiayiensis. We conducted experiments, including intestinal cytokines, digestive enzymes test, intestinal microbiome, metabolome and transcriptome analysis. The results showed that chickens fed L. chiayiensis exhibited higher body weight gain and digestive enzyme activity, and lower pro-inflammatory cytokines, compared to controls. Microbiota sequencing analysis showed that the gut microbiota structure was reshaped with L. chiayiensis supplementation. Specifically, Lactobacillus and Escherichia increased in abundance and Enterococcus, Lactococcus, Corynebacterium, Weissella and Gallicola decreased. In addition, the bacterial community diversity was significantly increased compared to controls. Metabolomic and transcriptomic analyses revealed that higher bile acids and N-acyl amides concentrations and lower carbohydrates concentrations in L. chiayiensis-fed chickens. Meanwhile, the expression of genes related to nutrient transport and absorption in the intestine was upregulated, which reflected the enhanced digestion and absorption of nutrients in chickens supplemented with L. chiayiensis. Moreover, supplementation of L. chiayiensis down-regulated genes involved in inflammation-related, mainly involved in NF-κB signaling pathway and MHC-II mediated antigen presentation process. Cumulatively, these findings highlight that host-microbiota crosstalk enhances the host growth phenotype in two ways: by enhancing bile acid metabolism and digestive enzyme activity, and reducing the occurrence of intestinal inflammation to promote nutrient absorption and maintain intestinal health. This provides a basis for the application of LAB as an alternative to antibiotics in animal husbandry.

Metabolomics in NEC: An Updated Review.

Necrotizing enterocolitis (NEC) represents the most common and lethal acute gastrointestinal emergency of newborns, mainly affecting those born prematurely. It can lead to severe long-term sequelae and the mortality rate is approximately 25%. Furthermore, the diagnosis is difficult, especially in the early stages, due to multifactorial pathogenesis and complex clinical pictures with mild and non-specific symptoms. In addition, the existing tests have poor diagnostic value. Thus, the scientific community has been focusing its attention on the identification of non-invasive biomarkers capable of prediction, early diagnosis and discriminating NEC from other intestinal diseases in order to intervene early and block the progression of the pathology. In this regard, the use of "omics" technologies, especially metabolomics and microbiomics, could be a fundamental synergistic strategy to study the pathophysiology of NEC. In addition, a deeper knowledge of the microbiota-host cross-talk can clarify the metabolic pathways potentially involved in the pathology, allowing for the identification of specific biomarkers. In this article, the authors analyze the state-of-the-art concerning the application of metabolomics and microbiota analysis to investigate this pathology and discuss the future possibility of the metabolomic fingerprint of patients for diagnostic purposes.

Integrated multi-omics reveals the roles of cecal microbiota and its derived bacterial consortium in promoting chicken growth.

The improvement of chicken growth performance is one of the major concerns for the poultry industry. Gut microbes are increasingly evidenced to be associated with chicken physiology and metabolism, thereby influencing chicken growth and development. Here, through integrated multi-omics analyses, we showed that chickens from the same line differing in their body weight were very different in their gut microbiota structure and host-microbiota crosstalk; microbes in high body weight (HBW) chickens contributed to chicken growth by regulating the gut function and homeostasis. We also verified that a specific bacterial consortium consisting of isolates from the HBW chickens has the potential to be used as chicken growth promoters. These findings provide new insights into the potential links between gut microbiota and chicken phenotypes, shedding light on future manipulation of chicken gut microbiota to improve chicken growth performance.

Fecal microbiota transplantation—could stool donors’ and receptors’ diet be the key to future success?

Fecal microbiota transplantation (FMT) is indicated in many countries for patients with multiple recurrences of Clostridioides difficile infection (CDI) for whom appropriate antibiotic treatments have failed. Donor selection is a demanding and rigorous process in view of the implementation of FMT programs worldwide. One of the most noteworthy factors that has been shown to affect FMT outcomes is the microbial diversity of the stool donor. A detailed assessment of the donor’s microbiota is crucial, as the microbiota is complex, dynamic, and resilient, and a healthy microbiota has several dimensions in addition to the absence of pathogens. Diet is one of the most important factors that modulates the composition and function of the gut microbiome (GM) and has a critical role in orchestrating the host–microbiota crosstalk throughout life. The diversity of the human GM seems to be related to variations in dietary patterns. Currently, the dietary patterns of stool donors and receptors are not taken into consideration in any way for FMT. In this study, we reflect on the importance of including this type of assessment in the stool donor screening process and knowing the impact of diet on the GM, as well as the importance of monitoring receptors’ diet to ensure the engraftment of the transplanted microbiota.

Microbial-host-isozyme analyses reveal microbial DPP4 as a potential antidiabetic target.

A mechanistic understanding of how microbial proteins affect the host could yield deeper insights into gut microbiota-host cross-talk. We developed an enzyme activity-screening platform to investigate how gut microbiota-derived enzymes might influence host physiology. We discovered that dipeptidyl peptidase 4 (DPP4) is expressed by specific bacterial taxa of the microbiota. Microbial DPP4 was able to decrease the active glucagon like peptide-1 (GLP-1) and disrupt glucose metabolism in mice with a leaky gut. Furthermore, the current drugs targeting human DPP4, including sitagliptin, had little effect on microbial DPP4. Using high-throughput screening, we identified daurisoline-d4 (Dau-d4) as a selective microbial DPP4 inhibitor that improves glucose tolerance in diabetic mice.

Gut barrier-microbiota imbalances in early life lead to higher sensitivity to inflammation in a murine model of C-section delivery

BackgroundMost interactions between the host and its microbiota occur at the gut barrier, and primary colonizers are essential in the gut barrier maturation in the early life. The mother–offspring transmission of microorganisms is the most important factor influencing microbial colonization in mammals, and C-section delivery (CSD) is an important disruptive factor of this transfer. Recently, the deregulation of symbiotic host-microbe interactions in early life has been shown to alter the maturation of the immune system, predisposing the host to gut barrier dysfunction and inflammation. The main goal of this study is to decipher the role of the early-life gut microbiota-barrier alterations and its links with later-life risks of intestinal inflammation in a murine model of CSD.ResultsThe higher sensitivity to chemically induced inflammation in CSD mice is related to excessive exposure to a too diverse microbiota too early in life. This early microbial stimulus has short-term consequences on the host homeostasis. It switches the pup’s immune response to an inflammatory context and alters the epithelium structure and the mucus-producing cells, disrupting gut homeostasis. This presence of a too diverse microbiota in the very early life involves a disproportionate short-chain fatty acids ratio and an excessive antigen exposure across the vulnerable gut barrier in the first days of life, before the gut closure. Besides, as shown by microbiota transfer experiments, the microbiota is causal in the high sensitivity of CSD mice to chemical-induced colitis and in most of the phenotypical parameters found altered in early life. Finally, supplementation with lactobacilli, the main bacterial group impacted by CSD in mice, reverts the higher sensitivity to inflammation in ex-germ-free mice colonized by CSD pups’ microbiota.ConclusionsEarly-life gut microbiota-host crosstalk alterations related to CSD could be the linchpin behind the phenotypic effects that lead to increased susceptibility to an induced inflammation later in life in mice.BBJL6KRzb7pAFtZtZ-zX7MVideo

Gut microbiota induced epigenetic modifications in the non-alcoholic fatty liver disease pathogenesis.

Non-alcoholic fatty liver disease (NAFLD) represents a growing global health concern that can lead to liver disease and cancer. It is characterized by an excessive accumulation of fat in the liver, unrelated to excessive alcohol consumption. Studies indicate that the gut microbiota-host crosstalk may play a causal role in NAFLD pathogenesis, with epigenetic modification serving as a key mechanism for regulating this interaction. In this review, we explore how the interplay between gut microbiota and the host epigenome impacts the development of NAFLD. Specifically, we discuss how gut microbiota-derived factors, such as lipopolysaccharides (LPS) and short-chain fatty acids (SCFAs), can modulate the DNA methylation and histone acetylation of genes associated with NAFLD, subsequently affecting lipid metabolism and immune homeostasis. Although the current literature suggests a link between gut microbiota and NAFLD development, our understanding of the molecular mechanisms and signaling pathways underlying this crosstalk remains limited. Therefore, more comprehensive epigenomic and multi-omic studies, including broader clinical and animal experiments, are needed to further explore the mechanisms linking the gut microbiota to NAFLD-associated genes. These studies are anticipated to improve microbial markers based on epigenetic strategies and provide novel insights into the pathogenesis of NAFLD, ultimately addressing a significant unmet clinical need.

Intestinal Epithelial Cell PTPN2 Restricts Intestinal Permeability and Tight-Junction Remodelling Caused by Adherent-invasive E. coli in Mice

Background: Alterations in epithelial tight junction proteins can compromise the ability of the intestinal mucosa to act as a barrier between luminal contents and underlying tissues. The resulting increase in intestinal permeability can give rise to conditions such as inflammatory bowel disease (IBD). Additionally, expansion of pathobionts, such as adherent-invasive Escherichia coli (AIEC), are associated with IBD. Mice deficient in the IBD gene candidate, Ptpn2, exhibit increased intestinal permeability and a pronounced expansion of a novel murine AIEC ( mAIEC). This study aimed to investigate how PTPN2 expression in intestinal epithelial cells protects intestinal barrier properties after mAIEC infection. Methods: Tamoxifen-inducible, intestinal epithelial cell (IEC)-specific knockout mice ( Ptpn2 ΔIEC ) and control littermates ( Ptpn2 fl/fl ) were infected with either PBS, non-invasive E. coli K12, or mcherry-tagged mAIEC ( mAIEC red ). FITC-Dextran (FD4) and Rhodamine-Dextran (RD70) permeability probes were administered by oral-gavage and serum collected after 5hrs. Results: Ptpn2 ΔIEC mice exhibited intestinal region-specific higher mAIEC red - but not K12 - bacterial load compared to Ptpn2 fl/fl mice ( P=0.038). E. coli K12 increased FD4 but not RD70 permeability in Ptpn2 ΔIEC mice compared with Ptpn2 fl/fl mice ( P=0.0025). mAIEC red also had no effect on RD70, but caused an even greater increase in FD4 permeability in Ptpn2 ΔIEC vs. Ptpn2 fl/fl mice ( P&lt; 0.0001). Ptpn2 fl/fl mice infected with mAIEC red also exhibited increased FD4 permeability compared to PBS-treated littermates ( P =0.0210). To identify if increased FD4 permeability was due to changes in expression of relevant tight-junction proteins, we performed western blot analysis on isolated IECs. Ptpn2 ΔIEC + mAIEC red mice had decreased expression of occludin ( P=0.0030) and the adherens junction protein, E-cadherin ( P=0.0142). Expression of the cation pore, claudin-2, was increased in PBS and K12-infected Ptpn2 ΔIEC vs. Ptpn2 fl/fl mice ( P=0.015). Interestingly, mAIEC red increased claudin-2 expression in Ptpn2 fl/fl mice compared to PBS controls ( P=0.0105) however, Ptpn2 ΔIEC + mAIEC red mice exhibited decreased claudin-2 levels compared to Ptpn2 fl/fl + mAIEC red mice ( P=0.0436). Immunofluorescence staining of claudin-2 confirmed reduced claudin-2 in Ptpn2 ΔIEC + mAIEC red mice. Furthermore, we observed gaps in ZO-1 membrane localization in Ptpn2 ΔIEC mice treated with PBS and K12 but not in their Ptpn2 fl/fl controls. ZO-1 membrane localization was dramatically depleted in Ptpn2 ΔIEC + mAIEC red mice compared to the Ptpn2 fl/fl + mAIEC red controls. Conclusion: Intestinal epithelial PTPN2 exhibits a major role in maintaining intestinal homeostasis by preserving intestinal barrier function and the integrity of tight-junction protein localization. Given that loss of PTPN2 in vivo also provokes expansion of adherent-invasive E. coli, these studies indicate that PTPN2 is an important mediator of host-microbiota crosstalk. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Dissecting the causal effect between gut microbiota, DHA, and urate metabolism: A large-scale bidirectional Mendelian randomization.

Our aim was to investigate the interactive causal effects between gut microbiota and host urate metabolism and explore the underlying mechanism using genetic methods. We extracted summary statistics from the abundance of 211 microbiota taxa from the MiBioGen (N =18,340), 205 microbiota metabolism pathways from the Dutch Microbiome Project (N =7738), gout from the Global Biobank Meta-analysis Initiative (N =1,448,128), urate from CKDGen (N =288,649), and replication datasets from the Global Urate Genetics Consortium (N gout =69,374; N urate =110,347). We used linkage disequilibrium score regression and bidirectional Mendelian randomization (MR) to detect genetic causality between microbiota and gout/urate. Mediation MR and colocalization were performed to investigate potential mediators in the association between microbiota and urate metabolism. Two taxa had a common causal effect on both gout and urate, whereas the Victivallaceae family was replicable. Six taxa were commonly affected by both gout and urate, whereas the Ruminococcus gnavus group genus was replicable. Genetic correlation supported significant results in MR. Two microbiota metabolic pathways were commonly affected by gout and urate. Mediation analysis indicated that the Bifidobacteriales order and Bifidobacteriaceae family had protective effects on urate mediated by increasing docosahexaenoic acid. These two bacteria shared a common causal variant rs182549 with both docosahexaenoic acid and urate, which was located within MCM6/LCT locus. Gut microbiota and host urate metabolism had a bidirectional causal association, implicating the critical role of host-microbiota crosstalk in hyperuricemic patients. Changes in gut microbiota can not only ameliorate host urate metabolism but also become a foreboding indicator of urate metabolic diseases.

Effect of environmental variance-based resilience selection on the gut metabolome of rabbits

BackgroundGut metabolites are key actors in host-microbiota crosstalk with effect on health. The study of the gut metabolome is an emerging topic in livestock, which can help understand its effect on key traits such as animal resilience and welfare. Animal resilience has now become a major trait of interest because of the high demand for more sustainable production. Composition of the gut microbiome can reveal mechanisms that underlie animal resilience because of its influence on host immunity. Environmental variance (VE), specifically the residual variance, is one measure of resilience. The aim of this study was to identify gut metabolites that underlie differences in the resilience potential of animals originating from a divergent selection for VE of litter size (LS). We performed an untargeted gut metabolome analysis in two divergent rabbit populations for low (n = 13) and high (n = 13) VE of LS. Partial least square-discriminant analysis was undertaken, and Bayesian statistics were computed to determine dissimilarities in the gut metabolites between these two rabbit populations.ResultsWe identified 15 metabolites that discriminate rabbits from the divergent populations with a prediction performance of 99.2% and 90.4% for the resilient and non-resilient populations, respectively. These metabolites were suggested to be biomarkers of animal resilience as they were the most reliable. Among these, five that derived from the microbiota metabolism (3-(4-hydroxyphenyl)lactate, 5-aminovalerate, and equol, N6-acetyllysine, and serine), were suggested to be indicators of dissimilarities in the microbiome composition between the rabbit populations. The abundances of acylcarnitines and metabolites derived from the phenylalanine, tyrosine, and tryptophan metabolism were low in the resilient population and these pathways can, therefore impact the inflammatory response and health status of animals.ConclusionsThis is the first study to identify gut metabolites that could act as potential resilience biomarkers. The results support differences in resilience between the two studied rabbit populations that were generated by selection for VE of LS. Furthermore, selection for VE of LS modified the gut metabolome, which could be another factor that modulates animal resilience. Further studies are needed to determine the causal role of these metabolites in health and disease.