Microbiome research reports最新文献

{"title":"Comparative genome analysis of microbial strains marketed for probiotic interventions: an extension of the Integrated Probiotic Database.","authors":"Silvia Petraro, Chiara Tarracchini, Gabriele Andrea Lugli, Leonardo Mancabelli, Federico Fontana, Francesca Turroni, Marco Ventura, Christian Milani","doi":"10.20517/mrr.2024.11","DOIUrl":"10.20517/mrr.2024.11","url":null,"abstract":"<p><p><b>Background:</b> Members of the <i>Bifidobacterium</i> genus and lactobacilli are the most commonly used probiotics to promote human health. In this context, genome-based <i>in silico</i> analyses have been demonstrated as a fast and reliable tool for identifying and characterizing health-promoting activities imputed to probiotics. <b>Methods:</b> This study is an extension of the Integrated Probiotic Database (IPDB) previously created on probiotics of the genus <i>Bifidobacterium</i>, facilitating a comprehensive understanding of the genetic characteristics that contribute to the diverse spectrum of beneficial effects of probiotics. The strains integrated into this new version of the IPDB, such as various lactobacilli and strains belonging to the species <i>Streptococcus thermophilus</i> (<i>S. thermophilus</i>) and <i>Heyndrickxia coagulans</i> (<i>H. coagulans</i>) (formerly <i>Bacillus coagulans</i>), were selected based on the labels of probiotic formulations currently on the market and using the bacterial strains whose genome had already been sequenced. On these bacterial strains, comparative genome analyses were performed, mainly focusing on genetic factors that confer structural, functional, and chemical characteristics predicted to be involved in microbe-host and microbe-microbe interactions. <b>Results:</b> Our investigations revealed marked inter- and intra-species variations in the genetic makeup associated with the biosynthesis of external structures and bioactive metabolites putatively associated with microbe- and host-microbe interactions. <b>Conclusion:</b> Although genetic differences need to be confirmed as functional or phenotypic differences before any probiotic intervention, we believe that considering these divergences will aid in improving effective and personalized probiotic-based interventions.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"3 4","pages":"45"},"PeriodicalIF":0.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11684986/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916782","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":"The inner elbow skin microbiome contains <i>Lactobacillus</i> among its core taxa and varies with age, season and lifestyle.","authors":"Lize Delanghe, Ilke De Boeck, Joke Van Malderen, Thies Gehrmann, Camille Nina Allonsius, Peter A Bron, Ingmar Claes, Margo Hagendorens, Julie Leysen, Stijn Wittouck, Sarah Lebeer","doi":"10.20517/mrr.2024.23","DOIUrl":"10.20517/mrr.2024.23","url":null,"abstract":"<p><p><b>Background:</b> The human skin microbiome plays an essential role in protecting against pathogens and other external substances. This open ecosystem is also influenced by personal and environmental factors, but the precise impact of these factors, such as lifestyle and season, is understudied. We focused here on the inner elbow, a skin site prone to inflammatory conditions like atopic dermatitis and psoriasis. <b>Methods:</b> We collected skin swabs from the inner elbow of 52 children and adults, with no signs of skin disorders, in the winter and summer seasons. Samples were analyzed using metagenomic shallow shotgun sequencing. In addition, metadata were collected using questionnaires on health, lifestyle, and environmental factors. <b>Results:</b> The core inner elbow community, taxa with a prevalence of 95% or higher, consisted of several well-known skin taxa, such as <i>Staphylococcus hominis</i>, <i>Staphylococcus capitis</i>, <i>Staphylococcus epidermidis</i>, and <i>Cutibacterium acnes</i>. In addition, <i>Streptococcus</i> and <i>Lactobacillus</i> species were also found to be highly prevalent members of the skin microbiota, especially in the age group up to 3 years old. Of all investigated factors, age appeared to be the major driver defining the skin microbiome composition and longitudinal stability over the seasons. Differential abundance analysis using three statistical tests also pointed out that specific skin species were significantly associated with sampling season, age, hygiene practices, vitamin D supplements, probiotics, and the number of household members. <b>Conclusion:</b> This study identifies novel factors influencing the inner elbow skin microbiome composition and paves the way for future comparative and intervention studies in skin disorders such as atopic dermatitis.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"3 4","pages":"43"},"PeriodicalIF":0.0,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11684916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916809","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":"Gut microbiota prevents small intestinal tumor formation due to bile acids in gnotobiotic mice.","authors":"Esther Wortmann, David Wylensek, Marijana Basic, Sven Hermeling, André Bleich, Dirk Haller, René Tolba, Gerhard Liebisch, Klaus-Peter Janssen, Thomas Clavel","doi":"10.20517/mrr.2024.20","DOIUrl":"10.20517/mrr.2024.20","url":null,"abstract":"<p><p><b>Aim:</b> The gut microbiota is implicated in the development of intestinal tumors. Furthermore, Western diet is a risk factor for colorectal cancer and induces alterations in both the microbiota and bile acid metabolism. Therefore, we aimed to investigate the causal role of Western diet-induced changes in the microbiota and secondary bile acid production, which were linked to disease exacerbation in <i>APC</i> ^1311/+ pigs. <b>Methods:</b> We performed fecal microbiota transfer experiments by inoculating germfree <i>Apc</i> ^1368N/+ mice with stool from genetically engineered <i>APC</i> ^1311/+ pigs. A control group of <i>Apc</i> ^1368N/+ mice stayed germfree. All mice were fed either a control diet, or the same diet supplemented with the primary bile acid cholic acid (CA) to stimulate secondary bile acid production. <b>Results:</b> Unexpectedly, the germfree mice fed CA had a high number of lesions in the upper small intestine, which was reduced by the colonization with microbes. The same mice (germfree, CA diet) were characterized by a remarkable lengthening of the small intestine (approximately +10 cm on average). Colonic lesions were rare and only observed in the mice that received stool from control pigs and fed the CA diet. Diversity and composition analyses showed that the microbiota transfer was incomplete. Nevertheless, mice receiving the Western diet-associated microbiota clustered separately from control animals. The effects of the CA diet on the microbiota were less pronounced and were observed primarily in mice that received stool from control pigs. Bile acid analysis in the recipient mice revealed associations between the phenotype and specific bile acid species in bile and cecum. <b>Conclusion:</b> This descriptive study highlights the importance of diet-microbiota-bile acid interactions in intestinal morphogenesis and tumorigenesis.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"3 4","pages":"44"},"PeriodicalIF":0.0,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11684917/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916800","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":"Secondary analysis reveals gut microbiota differences in patients with Parkinson's disease and/or cognitive impairment.","authors":"Xin Shen, Bing Leng, Shukun Zhang, Lai-Yu Kwok, Feiyan Zhao, Jia Zhao, Zhihong Sun, Jinbiao Zhang","doi":"10.20517/mrr.2024.35","DOIUrl":"10.20517/mrr.2024.35","url":null,"abstract":"<p><p><b>Background:</b> Parkinson's disease (PD) is a neurodegenerative disorder, and the main clinical characteristics are bradykinesia and muscle stiffness. Cognitive impairment (CI) is a prevalent non-motor manifestation observed in individuals with PD. According to disease severity, it can be divided into PD with mild cognitive impairment (MCI) and PD dementia. CI in PD patients may precede motor symptoms, and the gut microbiota plays an important role in PD pathogenesis. Therefore, gut microbiota may be one of the diagnostic targets for PD-CI. <b>Methods:</b> This study compared the gut microbiota of 43 PD-CI patients [Montreal Cognitive Assessment (MoCA) score < 26] and 38 PD patients without CI (MoCA ≥ 26). Patients' neuropsychological conditions, depression scale, and brain structure scanned by magnetic resonance imaging (MRI) were also recorded. The fecal metagenomic datasets of patients with PD, PD-CI, and CI only were retrieved from public databases for reanalysis to explore the relationship between PD, CI, and gut microbiota. <b>Results:</b> We found that the cortical thickness and the volume of the hippocampus, gray matter, and thalamus were significantly reduced among patients with PD-CI compared to PD without CI (<i>P</i> < 0.05). Moreover, the gut microbiome in patients with PD-CI had fewer short-chain fatty acid (SCFA) producing bacteria and more pathogenic bacteria. There were also alterations in patterns of metabolic pathway-encoding genes. Additionally, PD affected gut microbiota more than CI. <b>Conclusion:</b> CI may aggravate the severity of PD, but it did not drastically alter subjects' gut microbiota. This study reveals the relationship between gut microbiota, PD, and CI.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"3 4","pages":"42"},"PeriodicalIF":0.0,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11684920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916806","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":"Cataloging metagenome-assembled genomes and microbial genes from the athlete gut microbiome","authors":"Laura Wosinska, Liam H. Walsh, C. Walsh, P. Cotter, C. Guinane, O. O’Sullivan","doi":"10.20517/mrr.2023.69","DOIUrl":"https://doi.org/10.20517/mrr.2023.69","url":null,"abstract":"Aim: Exercise has been increasingly recognized as a potential influencer of the gut microbiome. Nevertheless, findings remain incongruous, particularly in relation to sport-specific patterns.\u0000 Methods: In this study, we harness all publicly available data from athlete gut microbiome shotgun studies to explore how exercise may influence the gut microbiota through metagenomic assembly supplemented with short read-based taxonomic profiling. Through this analysis, we provide insights into exercise-associated taxa and genes, including the identification and annotation of putative novel species from the analysis of approximately 2,000 metagenome-assembled genomes (MAGs), classified as high-quality (HQ) MAGs and assembled as part of this investigation.\u0000 Results: Our metagenomic analysis unveiled potential athlete-associated microbiome patterns at both the phylum and species levels, along with their associated microbial genes, across a diverse array of sports and individuals. Specifically, we identified 76 species linked to exercise, with a notable prevalence of the Firmicutes phylum. Furthermore, our analysis detected MAGs representing potential novel species across various phyla, including Bacteroidota , Candidatus Melainabacteria , Elusimicrobia , Firmicutes , Lentisphaerae , Proteobacteria , Tenericutes , and Verrucomicrobiota .\u0000 Conclusion: In summary, this catalog of MAGs and their corresponding genes stands as the most extensive collection yet compiled from athletes. Our analysis has discerned patterns in genes associated with exercise. This underscores the value of employing shotgun metagenomics, specifically a MAG recovery strategy, for pinpointing sport-associated microbiome signatures. Furthermore, the identification of novel MAGs holds promise for developing probiotics and deepening our comprehension of the intricate interplay between fitness and the microbiome.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"2 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141815405","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":"Host response to cholestyramine can be mediated by the gut microbiota.","authors":"Nolan K Newman, Philip M Monnier, Richard R Rodrigues, Manoj Gurung, Stephany Vasquez-Perez, Kaito A Hioki, Renee L Greer, Kevin Brown, Andrey Morgun, Natalia Shulzhenko","doi":"10.20517/mrr.2023.82","DOIUrl":"10.20517/mrr.2023.82","url":null,"abstract":"<p><p><b>Background:</b> The gut microbiota has been implicated as a major factor contributing to metabolic diseases and the response to drugs used for the treatment of such diseases. In this study, we tested the effect of cholestyramine, a bile acid sequestrant that reduces blood cholesterol, on the murine gut microbiota and metabolism. We also explored the hypothesis that some effects of this drug on systemic metabolism can be attributed to alterations in the gut microbiota. <b>Methods:</b> We used a Western diet (WD) for 8 weeks to induce metabolic disease in mice, then treated some mice with cholestyramine added to WD. Metabolic phenotyping, gene expression in liver and ileum, and microbiota 16S rRNA genes were analyzed. Then, transkingdom network analysis was used to find candidate microbes for the cholestyramine effect. <b>Results:</b> We observed that cholestyramine decreased glucose and epididymal fat levels and detected dysregulation of genes known to be regulated by cholestyramine in the liver and ileum. Analysis of gut microbiota showed increased alpha diversity in cholestyramine-treated mice, with fourteen taxa showing restoration of relative abundance to levels resembling those in mice fed a control diet. Using transkingdom network analysis, we inferred two amplicon sequence variants (ASVs), one from the <i>Lachnospiraceae</i> family (ASV49) and the other from the <i>Muribaculaceae</i> family (ASV1), as potential regulators of cholestyramine effects. ASV49 was also negatively linked with glucose levels, further indicating its beneficial role. <b>Conclusion:</b> Our results indicate that the gut microbiota has a role in the beneficial effects of cholestyramine and suggest specific microbes as targets of future investigations.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"3 4","pages":"40"},"PeriodicalIF":0.0,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11684918/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916802","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":"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}