Microbiome research reports最新文献

{"title":"Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry.","authors":"Angela Wang, Emily E F Fekete, Marybeth Creskey, Kai Cheng, Zhibin Ning, Annabelle Pfeifle, Xuguang Li, Daniel Figeys, Xu Zhang","doi":"10.20517/mrr.2024.21","DOIUrl":"https://doi.org/10.20517/mrr.2024.21","url":null,"abstract":"<p><p><b>Aim:</b> This study aims to evaluate the impact of experimental workflow on fecal metaproteomic observations, including the recovery of small and antimicrobial proteins often overlooked in metaproteomic studies. The overarching goal is to provide guidance for optimized metaproteomic experimental design, considering the emerging significance of the gut microbiome in human health, disease, and therapeutic interventions. <b>Methods:</b> Mouse feces were utilized as the experimental model. Fecal sample pre-processing methods (differential centrifugation and non-differential centrifugation), protein digestion techniques (in-solution and filter-aided), data acquisition modes (data-dependent and data-independent, or DDA and DIA) when combined with parallel accumulation-serial fragmentation (PASEF), and different bioinformatic workflows were assessed. <b>Results:</b> We showed that, in DIA-PASEF metaproteomics, the library-free search using protein sequence database generated from DDA-PASEF data achieved better identifications than using the generated spectral library. Compared to DDA, DIA-PASEF identified more microbial peptides, quantified more proteins with fewer missing values, and recovered more small antimicrobial proteins. We did not observe any obvious impacts of protein digestion methods on both taxonomic and functional profiles. However, differential centrifugation decreased the recovery of small and antimicrobial proteins, biased the taxonomic observation with a marked overestimation of <i>Muribaculum</i> species, and altered the measured functional compositions of metaproteome. <b>Conclusion:</b> This study underscores the critical impact of experimental choices on metaproteomic outcomes and sheds light on the potential biases introduced at different stages of the workflow. The comprehensive methodological comparisons serve as a valuable guide for researchers aiming to enhance the accuracy and completeness of metaproteomic analyses.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"3 3","pages":"39"},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of protein modification in synbiotic infant formula on probiotic metabolic activity and bacterial composition in an infant gut-model.","authors":"Eline Suzanne Klaassens, Mirna Lilian Baak, Nienke Jacobine Mekkes, Radhika Bongoni, Monika Schaubeck","doi":"10.20517/mrr.2024.13","DOIUrl":"https://doi.org/10.20517/mrr.2024.13","url":null,"abstract":"<p><p><b>Aim:</b> Microbial colonization of the neonatal gut is pivotal in priming the infant's immune system. Human milk (HM) is the best nutrition for infants and supports the development of the microbiota due to prebiotic compounds and probiotic microorganisms. When exclusive breastfeeding is not possible, infant formula (IF) with probiotics is a strategy to support the infant's microbiome development. However, knowledge about the effects of the infant gut microbiota and different compounds in IF on individual probiotic strains is limited, as strain-level detection in a complex ecosystem is challenging. The aim of the present study was to show the effects of IF with different protein forms on the metabolic activity of two probiotic strains isolated from HM in a complex ecosystem. <b>Methods:</b> By using an <i>ex-vivo</i> infant gut model containing infant donor-microbiota, the effects of IF with either intact or extensively hydrolyzed protein on the metabolic activity of the donor microbiota, as well as two probiotic strains [<i>Limosilactobacillus fermentum</i> (<i>L. fermentum</i>) CECT 5716 (Lf) and <i>Bifidobacterium breve</i> (<i>B. breve</i>) DSM 32583 (Bb)], were analyzed. A new bioinformatic pipeline combined with a specific infant microbiome database was used to explore shotgun metagenome datasets (1200 Megabases) for taxonomic identification and strain-level tracking. <b>Results:</b> Both protein forms (i.e., intact or extensively hydrolyzed protein) in IF supported infant gut microbial metabolic activity equally, as evidenced by similar levels of short-chain fatty acids (SCFAs). Interestingly, gut microbial metabolic activity was found to be differently activated in a strain-dependent manner. Taxonomic profiling of the microbiome at the strain level enabled monitoring of the prevalence and abundance of both probiotic strains, even in a complex ecosystem. <b>Conclusion:</b> Food matrix and host microbiota interactions should be considered when evaluating strain-specific probiotic effects in the future.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"3 3","pages":"38"},"PeriodicalIF":0.0,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480727/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485032","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Akkermansia</i> beyond muciniphila - emergence of new species <i>Akkermansia massiliensis</i> sp. nov.","authors":"Ritesh Kumar, Oliver Hasselwander, Helene Kane, Ashley A Hibberd","doi":"10.20517/mrr.2024.28","DOIUrl":"https://doi.org/10.20517/mrr.2024.28","url":null,"abstract":"<p><p>The human gut commensal <i>Akkermansia muciniphila</i> is the most studied bacterial species within the Verrucomicrobiota phylum. It has been proposed as a beneficial next-generation probiotic for cardiometabolic and immune health. Efforts from various research groups have resulted in the recent discovery of new species and/or phylotypes of the genus <i>Akkermansia</i>. This highlighted the genetic and phenotypic diversity among the <i>Akkermansia</i> isolates, providing an opportunity to identify novel mechanisms pertaining to health benefits. Genetic diversity between strains warrants detailed investigation to determine beneficial <i>Akkermansia</i> strains. <i>Akkermansia massiliensis</i> sp. nov. has emerged as the second most prevalent <i>Akkermansia</i> species in the human gut, with unique properties and potential relevance for human health. In addition, indications of the co-existence of more than one <i>Akkermansia</i> phylotype or species in a subject are intriguing. These new discoveries pave the way for additional developments of effective and targeted <i>Akkermansia</i> species-based interventions to provide health benefits.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"3 3","pages":"37"},"PeriodicalIF":0.0,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Omics-based analysis of <i>Akkermansia muciniphila</i> cultivation in food-grade media.","authors":"Sharon Y Geerlings, Kees van der Ark, Bart Nijsse, Sjef Boeren, Mark van Loosdrecht, Clara Belzer, Willem M de Vos","doi":"10.20517/mrr.2024.06","DOIUrl":"https://doi.org/10.20517/mrr.2024.06","url":null,"abstract":"<p><p><b>Background and Aim:</b> Over the past years, the gut microbiota and its correlation to health and disease has been studied extensively. In terms of beneficial microbes, an increased interest in <i>Akkermansia muciniphila</i> (<i>A. muciniphila</i>) has been observed since its discovery. Direct evidence for the role of <i>A. muciniphila</i> in host health has been provided in both mice and human studies. However, for human interventions with <i>A. muciniphila</i> cells, industrial-scale fermentations are needed, and hence, the used cultivation media should be free of animal-derived components, food-grade, non-allergenic and allow for efficient growth to high densities to provide cost-effective production platforms. In this study, we assessed the growth and performance of <i>A. muciniphila</i> in batch bioreactors using newly developed plant-based media. <b>Methods:</b> The bioreactors were supplemented with varying carbon sources, including different ratios of N-acetylglucosamine (GlcNAc) and glucose. We monitored the growth of <i>A. muciniphila</i> in the plant-based medium using optical density (OD600) measurements and microscopy. In addition, we used a combination of biochemical analysis as well as transcriptional and proteomics analysis to gain detailed insight into the physiology. <b>Results:</b> Comparisons between growth on these media and that on mucin revealed differences at both transcriptome and proteome levels, including differences in the expression of glycosyltransferases, signaling proteins, and stress response. Furthermore, elongated cells and higher OD600 values were observed using the plant-based media as compared to cultivation media containing mucin. <b>Conclusion:</b> These differences do not hamper growth, and therefore, our data suggest that the food-grade medium composition described here could be used to produce <i>A. muciniphila</i> with high yields for therapeutic purposes.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"3 3","pages":"36"},"PeriodicalIF":0.0,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Associations between intestinal lactic acid bacteria species and feeding habits of zoo animals.","authors":"Masanori Horie, Tomoki Ohno, Hitoshi Iwahashi, Maiko Umemura, Kazutoshi Murotomi","doi":"10.20517/mrr.2024.08","DOIUrl":"https://doi.org/10.20517/mrr.2024.08","url":null,"abstract":"<p><p><b>Aim:</b> Lactic acid bacteria are among the most important bacteria in the intestinal flora and often have beneficial effects on the host. It is known that the bacteria that compose the intestinal flora are influenced by the feeding habits of host animals, but there was a lack of knowledge about lactic acid bacteria. Therefore, also considering the use of select strains as probiotics, this study investigated the relationship between the feeding habits of zoo animals and intestinal <i>Lactobacillaceae</i> species. <b>Methods:</b> Lactic acid bacteria belonging to the family Lactobacillaceae were isolated and identified from the feces of 20 zoo animal species (5 carnivores, 4 herbivores, 7 piscivores, and 4 omnivores). Isolates were identified by the homology of the 16S rRNA gene sequence. In addition, the fecal flora of host animals was evaluated by the 16S rRNA gene amplicon sequencing. <b>Results:</b> The types of <i>Lactobacillaceae</i> species were shown to vary depending on the feeding habits of host animals. <i>Ligilactobacillus salivarius</i> (<i>L. salivarius</i>) and <i>Ligilactobacillus saerimneri</i> (<i>L. saerimneri</i>) were isolated from the feces of carnivores. Whereas <i>Ligilactobacillus equi</i> (<i>L. equi</i>), <i>Limosilactobacillus gorillae</i>, <i>Ligilactobacillus hayakitensis</i> and <i>L. salivarius</i> were isolated from the feces of herbivores. These <i>Lactobacillaceae</i> species were not found in the feces of piscivores. Instead, <i>Enterococcus</i> were frequently found in piscivores. The fecal flora also differed according to the feeding habits of host animals; at the phylum level, Bacillota was predominant in all animals; on the other hand, herbivores tended to have a higher proportion of Bacteroidota than carnivores, and piscivores tended to have a higher proportion of Proteobacteria. <b>Conclusion:</b> Lactic acid bacteria differ among animal species in a manner dependent on the hosts' feeding habits.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"3 3","pages":"35"},"PeriodicalIF":0.0,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Supplementation with a cranberry extract favors the establishment of butyrogenic guilds in the human fermentation SHIME system","authors":"Valentina Cattero, Charlène Roussel, Jacob Lessard-Lord, Denis Roy, Yves Desjardins","doi":"10.20517/mrr.2024.17","DOIUrl":"https://doi.org/10.20517/mrr.2024.17","url":null,"abstract":"Background: Proanthocyanidins (PAC) and oligosaccharides from cranberry exhibit multiple bioactive health properties and persist intact in the colon post-ingestion. They display a complex bidirectional interaction with the microbiome, which varies based on both time and specific regions of the gut; the nature of this interaction remains inadequately understood. Therefore, we aimed to investigate the impact of cranberry extract on gut microbiota ecology and function.\u0000 Methods: We studied the effect of a cranberry extract on six healthy participants over a two-week supplementation period using the ex vivo artificial fermentation system TWIN-M-SHIME to replicate luminal and mucosal niches of the ascending and transverse colon.\u0000 Results: Our findings revealed a significant influence of cranberry extract supplementation on the gut microbiota ecology under ex vivo conditions, leading to a considerable change in bacterial metabolism. Specifically, Bifidobacterium adolescentis (B. adolescentis ) flourished in the mucus of the ascending colon, accompanied by a reduced adhesion of Proteobacteria . The overall bacterial metabolism shifted from acetate to propionate and, notably, butyrate production following PAC supplementation. Although there were variations in microbiota modulation among the six donors, the butyrogenic effect induced by the supplementation remained consistent across all individuals. This metabolic shift was associated with a rise in the relative abundance of several short-chain fatty acid (SCFA)-producing bacterial genera and the formation of a consortium of key butyrogenic bacteria in the mucus of the transverse colon.\u0000 Conclusions: These observations suggest that cranberry extract supplementation has the potential to modulate the gut microbiota in a manner that may promote overall gut health.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"55 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141343988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pangenomic analysis identifies correlations between Akkermansia species and subspecies and human health outcomes","authors":"Katherine D. Mueller, M. E. Panzetta, Lauren Davey, Jessica R. McCann, John F. Rawls, Gilberto E. Flores, Raphael H. Valdivia","doi":"10.20517/mrr.2024.09","DOIUrl":"https://doi.org/10.20517/mrr.2024.09","url":null,"abstract":"Aim: Akkermansia are common members of the human gastrointestinal microbiota. The prevalence of these mucophilic bacteria, especially Akkermansia muciniphila (A. muciniphila ), correlates with immunological and metabolic health. The genus Akkermansia in humans includes species with significantly larger genomes than A. muciniphila , leading us to postulate that this added genetic content may influence how they impact human metabolic and immunological health.\u0000 Methods: We conducted a pangenomic analysis of 234 Akkermansia complete or near-complete genomes. We also used high-resolution species and subspecies assignments to reanalyze publicly available metagenomic datasets to determine if there are relationships between Akkermansia species and A. muciniphila clades with various disease outcomes.\u0000 Results: Analysis of genome-wide average nucleotide identity, 16S rRNA gene identity, conservation of core Akkermansia genes, and analysis of the fatty acid composition of representative isolates support the partitioning of the genus Akkermansia into several species. In addition, A. muciniphila sensu stricto , the most prevalent Akkermansia species in humans, should be subdivided into two subspecies. For a pediatric cohort, we observed species-specific correlations between Akkermansia abundance with baseline obesity or after various interventions. For inflammatory bowel disease cohorts, we identified a decreased abundance of Akkermansia in patients with ulcerative colitis or Crohn’s disease, which was species and subspecies-dependent. In patients undergoing immune checkpoint inhibitor therapies for non-small cell lung carcinoma, we observed a significant association between one A. muciniphila subspecies and survival outcomes.\u0000 Conclusion: Our findings suggest that the prevalence of specific Akkermansia species and/or subspecies can be crucial in evaluating their association with human health, particularly in different disease contexts, and is an important consideration for their use as probiotics.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"78 20","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141359740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A pilot case-control study on the fecal microbiota of pediatric functional abdominal pain-not otherwise specified and the role of early life stress","authors":"Nize Otaru, Benoît Pugin, Serafina Plüss, I. Hojsak, Christian Braegger, Christophe Lacroix","doi":"10.20517/mrr.2023.75","DOIUrl":"https://doi.org/10.20517/mrr.2023.75","url":null,"abstract":"Background: Gut microbial features and the role of early life stress in pediatric functional abdominal pain-not otherwise specified (FAP-NOS) have never been investigated before. Here, we hypothesize that early life stress is more prevalent in FAP-NOS compared to healthy controls and that fecal microbial profiles and related metabolites differ between groups.\u0000 Methods: In an international multicenter case-control study, FAP-NOS patients (n = 40) were compared to healthy controls (n = 55). Stool samples and demographic and clinical data including early life traumatic events and antibiotics treatments were collected from children aged four to twelve years. Fecal microbial profiles were assessed with 16S rRNA gene amplicon sequencing. Microbial metabolite concentrations in fecal supernatant, including short-chain fatty acids and amino acids, were detected via liquid chromatography.\u0000 Results: Microbial richness was increased in FAP-NOS compared to healthy controls and microbial composition (unweighted UniFrac) differed between groups. Three distinct amplicon sequencing variants and two distinct species were enriched in FAP-NOS compared to controls, with no observed changes at higher taxonomic levels. No differences in microbial metabolites and early life stress were observed between groups.\u0000 Conclusion: The presented hypothesis could not be proven, with no observed differences in occurrence of early life stress, and fecal microbial metabolic profiles between pediatric FAP-NOS and healthy controls. Pediatric FAP-NOS patients exhibited mild differences in the fecal microbial community compared with controls. Further large-scale studies with high-resolution techniques are warranted to address the biological relevance of present observations.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"269 40‐45","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141386720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling.","authors":"Kiumars Badr, Q Peter He, Jin Wang","doi":"10.20517/mrr.2023.70","DOIUrl":"https://doi.org/10.20517/mrr.2023.70","url":null,"abstract":"<p><p><b>Aim:</b> Metabolic interactions within a microbial community play a key role in determining the structure, function, and composition of the community. However, due to the complexity and intractability of natural microbiomes, limited knowledge is available on interspecies interactions within a community. In this work, using a binary synthetic microbiome, a methanotroph-photoautotroph (M-P) coculture, as the model system, we examined different genome-scale metabolic modeling (GEM) approaches to gain a better understanding of the metabolic interactions within the coculture, how they contribute to the enhanced growth observed in the coculture, and how they evolve over time. <b>Methods:</b> Using batch growth data of the model M-P coculture, we compared three GEM approaches for microbial communities. Two of the methods are existing approaches: SteadyCom, a steady state GEM, and dynamic flux balance analysis (DFBA) Lab, a dynamic GEM. We also proposed an improved dynamic GEM approach, DynamiCom, for the M-P coculture. <b>Results:</b> SteadyCom can predict the metabolic interactions within the coculture but not their dynamic evolutions; DFBA Lab can predict the dynamics of the coculture but cannot identify interspecies interactions. DynamiCom was able to identify the cross-fed metabolite within the coculture, as well as predict the evolution of the interspecies interactions over time. <b>Conclusion:</b> A new dynamic GEM approach, DynamiCom, was developed for a model M-P coculture. Constrained by the predictions from a validated kinetic model, DynamiCom consistently predicted the top metabolites being exchanged in the M-P coculture, as well as the establishment of the mutualistic N-exchange between the methanotroph and cyanobacteria. The interspecies interactions and their dynamic evolution predicted by DynamiCom are supported by ample evidence in the literature on methanotroph, cyanobacteria, and other cyanobacteria-heterotroph cocultures.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"3 3","pages":"31"},"PeriodicalIF":0.0,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480724/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Faecalibacterium prausnitzii A2-165 metabolizes host- and media-derived chemicals and induces transcriptional changes in colonic epithelium in GuMI human gut microphysiological system","authors":"Yu-Ja Huang, Caroline A. Lewis, Charles W. Wright, Kirsten Schneider, John Kemmitt, David L. Trumper, David T Breault, Omer Yilmaz, L. Griffith, Jianbo Zhang","doi":"10.20517/mrr.2024.14","DOIUrl":"https://doi.org/10.20517/mrr.2024.14","url":null,"abstract":"Aim: Recently, a GuMI gut microphysiological system has been established to coculture oxygen-intolerant Faecalibacterium prausnitzii (F. prausnitzii ) A2-165 with organoids-derived primary human colonic epithelium. This study aims to test if this GuMI system applies to different donors with different healthy states and uses metabolomics to reveal the role of gut microbes in modulating host- and diet-derived molecules in the gut lumen.\u0000 Methods: Organoids-derived colonic monolayers were generated from an uninflamed region of diverticulitis, ulcerative colitis, and Crohn’s disease patients and then integrated into the GuMI system to coculture with F. prausnitzii A2-165 for 2 to 4 days. Apical media was collected for metabolomic analysis. Targeted metabolomics was performed to profile 169 polar chemicals under three conditions: conventional static culture without bacteria, GuMI without bacteria, and GuMI with F. prausnitzii . The barrier function of monolayers was measured using transepithelial resistance.\u0000 Results: GuMI successfully cocultured patient-derived monolayers and F. prausnitzii for up to 4 days, with active bacterial growth. Introducing flow and oxygen gradient significantly increases the barrier function, while exposure to F. prausnitzii slightly increases the barrier function. Targeted metabolomics screened 169 compounds and detected 76 metabolites, of which 70 significantly differed between at least two conditions. F. prausnitzii significantly modulates the levels of nucleosides, nucleobases, and amino acids on the apical side. Further analysis suggests that F. prausnitzii changes the mRNA level of 260 transcription factor genes in colonic epithelial cells.\u0000 Conclusion: The GuMI physiomimetic system can maintain the coculture of F. prausnitzii and colonic epithelium from different donors. Together with metabolomics, we identified the modulation of F. prausnitzii in extracellular chemicals and colonic epithelial cell transcription in coculture with human colonic epithelium, which may reflect its function in gut lumen in vivo .","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"30 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141118018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}