{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T21:31:36Z","timestamp":1792099896012,"version":"4.4.0"},"reference-count":114,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,9,8]],"date-time":"2022-09-08T00:00:00Z","timestamp":1662595200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81970494"],"award-info":[{"award-number":["81970494"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    <jats:italic>Roseburia intestinalis<\/jats:italic>\n                    is an anaerobic bacterium that produces butyric acid and belongs to the phylum Firmicutes. There is increasing evidence that this bacterium has positive effects on several diseases, including inflammatory bowel disease, atherosclerosis, alcoholic fatty liver, colorectal cancer, and metabolic syndrome, making it a potential \u201cNext Generation Probiotic.\u201d We investigated the genomic characteristics, probiotic properties, cytotoxicity, oral toxicity, colonization characteristics of the bacterium, and its effect on the gut microbiota. The genome contains few genes encoding virulence factors, three clustered regularly interspaced short palindromic repeat (CRISPR) sequences, two Cas genes, no toxic biogenic amine synthesis genes, and several essential amino acid and vitamin synthesis genes. Seven prophages and 41 genomic islands were predicted. In addition to a bacteriocin (Zoocin A), the bacterium encodes four metabolic gene clusters that synthesize short-chain fatty acids and 222 carbohydrate-active enzyme modules. This bacterium is sensitive to antibiotics specified by the European Food Safety Authority, does not exhibit hemolytic or gelatinase activity, and exhibits some acid resistance.\n                    <jats:italic>R. intestinalis<\/jats:italic>\n                    adheres to intestinal epithelial cells and inhibits the invasion of certain pathogens.\n                    <jats:italic>In vitro<\/jats:italic>\n                    experiments showed that the bacterium was not cytotoxic.\n                    <jats:italic>R. intestinalis<\/jats:italic>\n                    did not affect the diversity or abundance of the gut flora. Using the fluorescent labelling method, we discovered that\n                    <jats:italic>R. intestinalis<\/jats:italic>\n                    colonizes the cecum and mucus of the colon. An oral toxicity study did not reveal any obvious adverse effects. The lethal dose (LD)50 of\n                    <jats:italic>R. intestinalis<\/jats:italic>\n                    exceeded 1.9\u2009\u00d7\u200910\n                    <jats:sup>9<\/jats:sup>\n                    colony forming units (CFU)\/kg, whereas the no observed adverse effect level (NOAEL) derived from this study was 1.32\u2009\u00d7\u200910\n                    <jats:sup>9<\/jats:sup>\n                    \u2009CFU\/kg\/day for 28\u2009days. The current research shows that,\n                    <jats:italic>R. intestinalis<\/jats:italic>\n                    is a suitable next-generation probiotic considering its probiotic properties and safety.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2022.973046","type":"journal-article","created":{"date-parts":[[2022,9,8]],"date-time":"2022-09-08T05:51:26Z","timestamp":1662616286000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":49,"title":["Assessment of the safety and probiotic properties of Roseburia intestinalis: A potential \u201cNext Generation Probiotic\u201d"],"prefix":"10.3389","volume":"13","author":[{"given":"Chao","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kejia","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Nie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minzi","family":"Deng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiwei","family":"Luo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xing","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujun","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,9,8]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"e0235873","DOI":"10.1371\/journal.pone.0235873","article-title":"Integrated genome-based probiotic relevance and safety evaluation of lactobacillus reuteri PNW1","volume":"15","author":"Alayande","year":"2020","journal-title":"PLoS One"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"D517","DOI":"10.1093\/nar\/gkz935","article-title":"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1186\/1471-2164-12-402","article-title":"BLAST ring image generator (BRIG): simple prokaryote genome comparisons","volume":"12","author":"Alikhan","year":"2011","journal-title":"BMC Genomics"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"428","DOI":"10.1016\/j.resmic.2015.03.002","article-title":"Determining the probiotic potential of cholesterol-reducing lactobacillus and Weissella strains isolated from gherkins (fermented cucumber) and south Indian fermented koozh","volume":"166","author":"Anandharaj","year":"2015","journal-title":"Res. Microbiol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: a better, faster version of the PHAST phage search tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1038\/nature09944","article-title":"Enterotypes of the human gut microbiome","volume":"473","author":"Arumugam","year":"2011","journal-title":"Nature"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2019\/5938210","article-title":"Enterococci: Between emerging pathogens and potential probiotics","volume":"2019","author":"Ben Bra\u00efek","year":"2019","journal-title":"Biomed. Res. Int."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"W30","DOI":"10.1093\/nar\/gkx343","article-title":"IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets","volume":"45","author":"Bertelli","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"e0142038","DOI":"10.1371\/journal.pone.0142038","article-title":"Global profiling of carbohydrate active enzymes in human gut microbiome","volume":"10","author":"Bhattacharya","year":"2015","journal-title":"PLoS One"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1016\/S0968-4328(00)00030-5","article-title":"Phage-related DNA polymorphism in dairy and probiotic lactobacillus","volume":"32","author":"Brandt","year":"2001","journal-title":"Micron"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1046\/j.1365-2958.2003.03580.x","article-title":"Prophages and bacterial genomics: what have we learned so far?","volume":"49","author":"Casjens","year":"2003","journal-title":"Mol. Microbiol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1016\/j.canlet.2019.11.019","article-title":"Clostridium butyricum, a butyrate-producing probiotic, inhibits intestinal tumor development through modulating Wnt signaling and gut microbiota","volume":"469","author":"Chen","year":"2020","journal-title":"Cancer Lett."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"2264","DOI":"10.3390\/foods10102264","article-title":"Potential probiotic enterococcus faecium OV3-6 and its bioactive peptide as alternative bio-preservation","volume":"10","author":"Choeisoongnern","year":"2021","journal-title":"Foods"},{"key":"ref43","article-title":"Performance standards for antimicrobial susceptibility testing","volume-title":"CLSI Document M100S","year":"2016"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"771","DOI":"10.1038\/s41396-019-0566-x","article-title":"The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition","volume":"14","author":"Cornuault","year":"2020","journal-title":"ISME J."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1038\/nrmicro2937","article-title":"Bacteriocins - a viable alternative to antibiotics?","volume":"11","author":"Cotter","year":"2013","journal-title":"Nat. Rev. Microbiol."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"W246","DOI":"10.1093\/nar\/gky425","article-title":"CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins","volume":"46","author":"Couvin","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"189","DOI":"10.3390\/microorganisms8020189","article-title":"Preliminary evaluation of the safety and probiotic potential of Akkermansia muciniphila DSM 22959 in comparison with lactobacillus rhamnosus GG","volume":"8","author":"Cozzolino","year":"2020","journal-title":"Microorganisms"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"D777","DOI":"10.1093\/nar\/gkab1019","article-title":"GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison","volume":"50","author":"Dai","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"931","DOI":"10.1016\/j.immuni.2016.09.009","article-title":"Enterococcus hirae and Barnesiella intestinihominis facilitate cyclophosphamide-induced therapeutic Immunomodulatory effects","volume":"45","author":"Daill\u00e8re","year":"2016","journal-title":"Immunity"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"D606","DOI":"10.1093\/nar\/gkz943","article-title":"The PATRIC bioinformatics resource center: expanding data and analysis capabilities","volume":"48","author":"Davis","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.bbadis.2005.09.008","article-title":"VSL#3 probiotic preparation has the capacity to hydrolyze gliadin polypeptides responsible for celiac Sprue","volume":"1762","author":"De Angelis","year":"2006","journal-title":"Biochim. Biophys. Acta"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"538077","DOI":"10.3389\/fcimb.2020.538077","article-title":"Quorum sensing, biofilm, and intestinal mucosal barrier: involvement the role of probiotic","volume":"10","author":"Deng","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1016\/j.jbiotec.2005.02.005","article-title":"Purification and characterisation of acidocin D20079, a bacteriocin produced by lactobacillus acidophilus DSM 20079","volume":"117","author":"Deraz","year":"2005","journal-title":"J. Biotechnol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"1642","DOI":"10.3389\/fmicb.2020.01642","article-title":"The Butyrogenic and lactic bacteria of the gut microbiota determine the outcome of Allogenic hematopoietic cell transplant","volume":"11","author":"Devaux","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1007\/s00535-021-01774-3","article-title":"Lactobacillus stress protein GroEL prevents colonic inflammation","volume":"56","author":"Dias","year":"2021","journal-title":"J. Gastroenterol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1097\/QAD.0000000000001366","article-title":"Low abundance of colonic butyrate-producing bacteria in HIV infection is associated with microbial translocation and immune activation","volume":"31","author":"Dillon","year":"2017","journal-title":"AIDS"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1038\/nrmicro3552","article-title":"Gut biogeography of the bacterial microbiota","volume":"14","author":"Donaldson","year":"2016","journal-title":"Nat. Rev. Microbiol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"D571","DOI":"10.1093\/nar\/gkab1045","article-title":"The carbohydrate-active enzyme database: functions and literature","volume":"50","author":"Drula","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"1191","DOI":"10.1007\/s10482-020-01426-1","article-title":"Mucin pre-cultivated lactobacillus reuteri E shows enhanced adhesion and increases mucin expression in HT-29 cells","volume":"113","author":"Dud\u00edk","year":"2020","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"1615","DOI":"10.1099\/00207713-52-5-1615","article-title":"Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces","volume":"52","author":"Duncan","year":"2002","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref31","first-page":"183","article-title":"Intraluminal pH of the human gastrointestinal tract","volume":"46","author":"Fallingborg","year":"1999","journal-title":"Dan. Med. Bull."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1128\/mSystems.00305-19","article-title":"Bacteroides fragilis strain ZY-312 defense against Cronobacter sakazakii-induced necrotizing Enterocolitis In vitro and in a neonatal rat model","volume":"4","author":"Fan","year":"2019","journal-title":"mSystems"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1787","DOI":"10.3945\/jn.114.197723","article-title":"Modulation of fecal Clostridiales bacteria and butyrate by probiotic intervention with lactobacillus paracasei DG varies among healthy adults","volume":"144","author":"Ferrario","year":"2014","journal-title":"J. Nutr."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1128\/AEM.01647-08","article-title":"Use of 4-sulfophenyl isothiocyanate labeling and mass spectrometry to determine the site of action of the streptococcolytic peptidoglycan hydrolase zoocin A","volume":"75","author":"Gargis","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1016\/j.chom.2014.02.005","article-title":"The treatment-naive microbiome in new-onset Crohn\u2019s disease","volume":"15","author":"Gevers","year":"2014","journal-title":"Cell Host Microbe"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1126\/science.1124234","article-title":"Metagenomic analysis of the human distal gut microbiome","volume":"312","author":"Gill","year":"2006","journal-title":"Science"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"840","DOI":"10.4014\/jmb.2103.03017","article-title":"Application of the combination of soybean lecithin and whey protein concentrate 80 to improve the bile salt and acid tolerance of probiotics","volume":"31","author":"Gou","year":"2021","journal-title":"J. Microbiol. Biotechnol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"6375","DOI":"10.18632\/aging.202739","article-title":"Oral administration of Akkermansia muciniphila elevates systemic antiaging and anticancer metabolites","volume":"13","author":"Grajeda-Iglesias","year":"2021","journal-title":"Aging (Albany NY)"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1038\/nrgastro.2014.66","article-title":"Expert consensus document. The international scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic","volume":"11","author":"Hill","year":"2014","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"20","DOI":"10.3390\/foods10010020","article-title":"Molecular characterization of Cronobacter sakazakii strains isolated from powdered Milk","volume":"10","author":"Hol\u00fd","year":"2020","journal-title":"Foods"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1111\/lam.12418","article-title":"Enhancement of bile resistance in lactobacillus plantarum strains by soy lecithin","volume":"61","author":"Hu","year":"2015","journal-title":"Lett. Appl. Microbiol."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"608314","DOI":"10.3389\/fmicb.2020.608314","article-title":"Assessment of safety and probiotic traits of enterococcus durans OSY-EGY, isolated From Egyptian artisanal cheese, using comparative genomics and phenotypic analyses","volume":"11","author":"Hussein","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1111\/j.1574-6976.2008.00136.x","article-title":"Genomic islands: tools of bacterial horizontal gene transfer and evolution","volume":"33","author":"Juhas","year":"2009","journal-title":"FEMS Microbiol. Rev."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1461","DOI":"10.1038\/s41564-018-0272-x","article-title":"Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model","volume":"3","author":"Kasahara","year":"2018","journal-title":"Nat. Microbiol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1038\/s41467-019-08812-y","article-title":"The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary \u03b2-mannans","volume":"10","author":"La Rosa","year":"2019","journal-title":"Nat. Commun."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"422","DOI":"10.4093\/dmj.2018.0090","article-title":"Additional effect of dietary fiber in patients with type 2 diabetes mellitus using metformin and sulfonylurea: An open-label","volume":"43","author":"Lee","year":"2019","journal-title":"Pilot Trial. Diabetes Metab J"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"670","DOI":"10.1128\/AEM.70.2.670-674.2004","article-title":"Permanent colonization by lactobacillus casei is hindered by the low rate of cell division in mouse gut","volume":"70","author":"Lee","year":"2004","journal-title":"Appl. Environ. Microbiol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"2105","DOI":"10.1111\/febs.15117","article-title":"Molecular insight into a new low-affinity xylan binding module from the xylanolytic gut symbiont Roseburia intestinalis","volume":"287","author":"Leth","year":"2020","journal-title":"FEBS J."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"1179","DOI":"10.1053\/j.gastro.2020.09.003","article-title":"Streptococcus thermophilus inhibits colorectal tumorigenesis Through secreting \u03b2-Galactosidase","volume":"160","author":"Li","year":"2021","journal-title":"Gastroenterology"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"1943","DOI":"10.3389\/fmicb.2018.01943","article-title":"Evaluating the safety of potential probiotic enterococcus durans KLDS6.0930 using whole genome sequencing and Oral toxicity study","volume":"9","author":"Li","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"2061","DOI":"10.1158\/1078-0432.CCR-16-1599","article-title":"Fecal bacteria act as novel biomarkers for noninvasive diagnosis of colorectal cancer","volume":"23","author":"Liang","year":"2017","journal-title":"Clin. Cancer Res."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"2083","DOI":"10.1007\/s00726-017-2493-3","article-title":"A review of the relationship between the gut microbiota and amino acid metabolism","volume":"49","author":"Lin","year":"2017","journal-title":"Amino Acids"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"14166","DOI":"10.1096\/fj.202000622R","article-title":"Metagenomic analysis of the gut microbiome in atherosclerosis patients identify cross-cohort microbial signatures and potential therapeutic target","volume":"34","author":"Liu","year":"2020","journal-title":"FASEB J."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","article-title":"VFDB 2022: a general classification scheme for bacterial virulence factors","volume":"50","author":"Liu","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2019\/5037578","article-title":"Mesenchymal progenitors derived from different locations in long bones display diverse characteristics","volume":"2019","author":"Lu","year":"2019","journal-title":"Stem Cells Int."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.3892\/mmr.2019.10327","article-title":"Roseburia intestinalis supernatant ameliorates colitis induced in mice by regulating the immune response","volume":"20","author":"Luo","year":"2019","journal-title":"Mol. Med. Rep."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"109496","DOI":"10.1016\/j.foodres.2020.109496","article-title":"Differential pattern of indigenous microbiome responses to probiotic Bifidobacterium lactis V9 consumption across subjects","volume":"136","author":"Ma","year":"","journal-title":"Food Res. Int."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/19490976.2020.1832857","article-title":"Spermidine improves gut barrier integrity and gut microbiota function in diet-induced obese mice","volume":"12","author":"Ma","year":"","journal-title":"Gut Microbes"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1136\/gutjnl-2013-304833","article-title":"A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis","volume":"63","author":"Machiels","year":"2014","journal-title":"Gut"},{"key":"ref61","doi-asserted-by":"publisher","first-page":"2788","DOI":"10.1126\/science.aan2788","article-title":"Spermidine in health and disease","volume":"359","author":"Madeo","year":"2018","journal-title":"Science"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"141","DOI":"10.3390\/v9060141","article-title":"The human gut phage community and its implications for health and disease","volume":"9","author":"Manrique","year":"2017","journal-title":"Viruses"},{"key":"ref63","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1016\/j.chom.2019.08.011","article-title":"Regional diversity of the gastrointestinal microbiome","volume":"26","author":"Martinez-Guryn","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref64","doi-asserted-by":"publisher","first-page":"1957","DOI":"10.3168\/jds.2017-13919","article-title":"Short communication: lactose enhances bile tolerance of yogurt culture bacteria","volume":"101","author":"Mena","year":"2018","journal-title":"J. Dairy Sci."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"104538","DOI":"10.1016\/j.yrtph.2019.104538","article-title":"Safety evaluation of Bacillus coagulans SNZ 1969 in Wistar rats","volume":"110","author":"Metlakunta","year":"2020","journal-title":"Regul. Toxicol. Pharmacol."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1128\/mBio.00300-15","article-title":"Identification of metabolic signatures linked to anti-inflammatory effects of Faecalibacterium prausnitzii","volume":"6","author":"Miquel","year":"2015","journal-title":"MBio"},{"key":"ref67","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1111\/j.1365-2672.2010.04671.x","article-title":"Dietary fibre degradation and fermentation by two xylanolytic bacteria Bacteroides xylanisolvens XB1A and Roseburia intestinalis XB6B4 from the human intestine","volume":"109","author":"Mirande","year":"2010","journal-title":"J. Appl. Microbiol."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"1573","DOI":"10.1016\/j.chom.2021.08.001","article-title":"Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors","volume":"29","author":"Montalban-Arques","year":"2021","journal-title":"Cell Host Microbe"},{"key":"ref69","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1080\/21678421.2020.1828475","article-title":"The human gut microbiota in people with amyotrophic lateral sclerosis","volume":"22","author":"Nicholson","year":"2021","journal-title":"Amyotroph Lateral Scler Frontotemporal Degener"},{"key":"ref70","doi-asserted-by":"publisher","first-page":"757718","DOI":"10.3389\/fcimb.2021.757718","article-title":"Roseburia intestinalis: A beneficial gut organism From the discoveries in genus and species","volume":"11","author":"Nie","year":"2021","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"473","DOI":"10.4161\/viru.25730","article-title":"Common and pathogen-specific virulence factors are different in function and structure","volume":"4","author":"Niu","year":"2013","journal-title":"Virulence"},{"key":"ref72","doi-asserted-by":"publisher","first-page":"17057","DOI":"10.1038\/nmicrobiol.2017.57","article-title":"Next-generation probiotics: the spectrum from probiotics to live biotherapeutics","volume":"2","author":"O\u2019Toole","year":"2017","journal-title":"Nat. Microbiol."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"D206","DOI":"10.1093\/nar\/gkt1226","article-title":"The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST)","volume":"42","author":"Overbeek","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"683743","DOI":"10.3389\/fcimb.2021.683743","article-title":"Gut microbiota, glucose, lipid, and water-electrolyte metabolism in children With nonalcoholic fatty liver disease","volume":"11","author":"Pan","year":"2021","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"720","DOI":"10.3390\/microorganisms8050720","article-title":"Comprehensive mining and characterization of CRISPR-Cas Systems in Bifidobacterium","volume":"8","author":"Pan","year":"2020","journal-title":"Microorganisms"},{"key":"ref76","doi-asserted-by":"publisher","first-page":"W263","DOI":"10.1093\/nar\/gkab353","article-title":"The gut SMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota","volume":"49","author":"Pascal Andreu","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref77","doi-asserted-by":"publisher","first-page":"e0121120","DOI":"10.1128\/mSystems.01211-20","article-title":"Comprehensive scanning of Prophages in lactobacillus: distribution, diversity, antibiotic resistance genes, and linkages with CRISPR-Cas systems","volume":"6","author":"Pei","year":"2021","journal-title":"mSystems"},{"key":"ref78","doi-asserted-by":"publisher","first-page":"682721","DOI":"10.3389\/fmicb.2021.682721","article-title":"A Metagenome-wide association study of the gut microbiome and metabolic syndrome","volume":"12","author":"Qin","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref79","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1016\/j.bbrc.2018.05.075","article-title":"Roseburia intestinalis-derived flagellin is a negative regulator of intestinal inflammation","volume":"501","author":"Quan","year":"2018","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref80","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1007\/s12602-019-09610-0","article-title":"In vitro evaluation of probiotic potential and safety assessment of lactobacillus mucosae strains isolated from Donkey\u2019s lactation","volume":"12","author":"Rastogi","year":"2020","journal-title":"Probiotics Antimicrob Proteins"},{"key":"ref81","doi-asserted-by":"publisher","first-page":"2524","DOI":"10.3390\/microorganisms9122524","article-title":"Succession analysis of gut microbiota structure of participants from long-lived families in Hechi, Guangxi, China","volume":"9","author":"Ren","year":"2021","journal-title":"Microorganisms"},{"key":"ref82","doi-asserted-by":"publisher","first-page":"1223","DOI":"10.3168\/jds.2019-17092","article-title":"Characterization and evaluation of lactic acid bacteria from indigenous raw milk for potential probiotic properties","volume":"103","author":"Reuben","year":"2020","journal-title":"J. Dairy Sci."},{"key":"ref83","doi-asserted-by":"publisher","first-page":"7707","DOI":"10.3168\/jds.2020-18271","article-title":"Growth of lactic acid bacteria in milk phospholipids enhances their adhesion to Caco-2 cells","volume":"103","author":"Rocha-Mendoza","year":"2020","journal-title":"J. Dairy Sci."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"1975","DOI":"10.1136\/gutjnl-2019-319726","article-title":"Discovery of the gut microbial signature driving the efficacy of prebiotic intervention in obese patients","volume":"69","author":"Rodriguez","year":"2020","journal-title":"Gut"},{"key":"ref85","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1038\/s41575-021-00440-6","article-title":"The international scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics","volume":"18","author":"Salminen","year":"2021","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref86","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1111\/1751-2980.12591","article-title":"Vitamin D administration leads to a shift of the intestinal bacterial composition in Crohn\u2019s disease patients, but not in healthy controls","volume":"19","author":"Sch\u00e4ffler","year":"2018","journal-title":"J. Dig. Dis."},{"key":"ref87","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1007\/s12602-017-9264-z","article-title":"Lactobacillus plantarum and its probiotic and food potentialities","volume":"9","author":"Seddik","year":"2017","journal-title":"Probiotics Antimicrob Proteins"},{"key":"ref88","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1136\/gut.47.3.397","article-title":"Butyrate inhibits inflammatory responses through NFkappaB inhibition: implications for Crohn\u2019s disease","volume":"47","author":"Segain","year":"2000","journal-title":"Gut"},{"key":"ref89","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/j.chom.2019.11.001","article-title":"Roseburia spp. abundance associates with alcohol consumption in humans and its administration ameliorates alcoholic fatty liver in mice","volume":"27","author":"Seo","year":"2020","journal-title":"Cell Host Microbe"},{"key":"ref90","doi-asserted-by":"publisher","first-page":"774","DOI":"10.1007\/s12602-018-9466-z","article-title":"Selection and evaluation of probiotic and functional characteristics of autochthonous lactic acid bacteria isolated from fermented wheat flour dough Babroo","volume":"11","author":"Sharma","year":"2019","journal-title":"Probiotics Antimicrob Proteins"},{"key":"ref91","doi-asserted-by":"publisher","first-page":"1751","DOI":"10.1111\/jgh.14144","article-title":"Insights into Roseburia intestinalis which alleviates experimental colitis pathology by inducing anti-inflammatory responses","volume":"33","author":"Shen","year":"2018","journal-title":"J. Gastroenterol. Hepatol."},{"key":"ref92","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1016\/j.fm.2013.10.003","article-title":"Tailoring the probiotic potential of non-starter lactobacillus strains from ripened Parmigiano Reggiano cheese by in vitro screening and principal component analysis","volume":"38","author":"Solieri","year":"2014","journal-title":"Food Microbiol."},{"key":"ref93","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1038\/ni1079","article-title":"Getting a grip on things: how do communities of bacterial symbionts become established in our intestine?","volume":"5","author":"Sonnenburg","year":"2004","journal-title":"Nat. Immunol."},{"key":"ref94","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1016\/j.fct.2014.06.024","article-title":"Safety assessment of the butyrate-producing Butyricicoccus pullicaecorum strain 25-3(T), a potential probiotic for patients with inflammatory bowel disease, based on oral toxicity tests and whole genome sequencing","volume":"72","author":"Steppe","year":"2014","journal-title":"Food Chem. Toxicol."},{"key":"ref95","doi-asserted-by":"publisher","first-page":"8322","DOI":"10.1038\/ncomms9322","article-title":"Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera","volume":"6","author":"Sun","year":"2015","journal-title":"Nat. Commun."},{"key":"ref96","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/19490976.2021.1880221","article-title":"Elevated gut microbiome abundance of Christensenellaceae, Porphyromonadaceae and Rikenellaceae is associated with reduced visceral adipose tissue and healthier metabolic profile in Italian elderly","volume":"13","author":"Tavella","year":"2021","journal-title":"Gut Microbes"},{"key":"ref97","doi-asserted-by":"publisher","first-page":"965","DOI":"10.1128\/IAI.01197-12","article-title":"Intestinal microbiota containing Barnesiella species cures vancomycin-resistant enterococcus faecium colonization","volume":"81","author":"Ubeda","year":"2013","journal-title":"Infect. Immun."},{"key":"ref98","doi-asserted-by":"publisher","first-page":"949","DOI":"10.1038\/ismej.2012.158","article-title":"Butyrate-producing clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model","volume":"7","author":"Van den Abbeele","year":"2013","journal-title":"ISME J."},{"key":"ref99","doi-asserted-by":"publisher","first-page":"W278","DOI":"10.1093\/nar\/gky383","article-title":"BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins","volume":"46","author":"van Heel","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref100","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1016\/j.tifs.2007.07.013","article-title":"Biosafety assessment of probiotics used for human consumption: recommendations from the EU-PROSAFE project","volume":"19","author":"Vankerckhoven","year":"2008","journal-title":"Trends Food Sci. Technol."},{"key":"ref101","doi-asserted-by":"publisher","first-page":"2215","DOI":"10.3168\/jds.2014-8869","article-title":"Whey protein isolate improves acid and bile tolerances of Streptococcus thermophilus ST-M5 and lactobacillus delbrueckii ssp. bulgaricus LB-12","volume":"98","author":"Vargas","year":"2015","journal-title":"J. Dairy Sci."},{"key":"ref102","doi-asserted-by":"publisher","first-page":"2481","DOI":"10.1039\/D0FO02624G","article-title":"Colonisation with endogenous lactobacillus reuteri R28 and exogenous lactobacillus plantarum AR17-1 and the effects on intestinal inflammation in mice","volume":"12","author":"Wang","year":"2021","journal-title":"Food Funct."},{"key":"ref103","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1039\/C8FO01453A","article-title":"The ameliorative effect of a lactobacillus strain with good adhesion ability against dextran sulfate sodium-induced murine colitis","volume":"10","author":"Wang","year":"2019","journal-title":"Food Funct."},{"key":"ref104","doi-asserted-by":"publisher","first-page":"2731","DOI":"10.1111\/cmi.12731","article-title":"A fibronectin-binding protein (FbpA) of Weissella cibaria inhibits colonization and infection of Staphylococcus aureus in mammary glands","volume":"19","author":"Wang","year":"2017","journal-title":"Cell. Microbiol."},{"key":"ref105","doi-asserted-by":"publisher","first-page":"1602","DOI":"10.1017\/S0007114513004200","article-title":"Selective proliferation of intestinal Barnesiella under fucosyllactose supplementation in mice","volume":"111","author":"Weiss","year":"2014","journal-title":"Br. J. Nutr."},{"key":"ref106","doi-asserted-by":"publisher","first-page":"2695","DOI":"10.3892\/mmr.2020.11351","article-title":"Roseburia intestinalis-derived flagellin ameliorates colitis by targeting miR-223-3p-mediated activation of NLRP3 inflammasome and pyroptosis","volume":"22","author":"Wu","year":"2020","journal-title":"Mol. Med. Rep."},{"key":"ref107","doi-asserted-by":"publisher","first-page":"175628482110044","DOI":"10.1177\/17562848211004469","article-title":"New pathway ameliorating ulcerative colitis: focus on Roseburia intestinalis and the gut-brain axis","volume":"14","author":"Xu","year":"2021","journal-title":"Ther. Adv. Gastroenterol."},{"key":"ref108","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1007\/s11684-022-0921-6","article-title":"Integrated analysis of gut microbiome and host immune responses in COVID-19","volume":"16","author":"Xu","year":"2022","journal-title":"Front. Med."},{"key":"ref109","doi-asserted-by":"publisher","first-page":"25088","DOI":"10.1074\/jbc.M113.452516","article-title":"Beneficial metabolic effects of a probiotic via butyrate-induced GLP-1 hormone secretion","volume":"288","author":"Yadav","year":"2013","journal-title":"J. Biol. Chem."},{"key":"ref110","doi-asserted-by":"publisher","first-page":"843650","DOI":"10.3389\/fmicb.2022.843650","article-title":"Spatial and temporal persistence of fluorescent Lactiplantibacillus plantarum RS-09 in intestinal tract","volume":"13","author":"Zhao","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref111","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1186\/s12967-021-02882-7","article-title":"The fecal microbiota of patients with pancreatic ductal adenocarcinoma and autoimmune pancreatitis characterized by metagenomic sequencing","volume":"19","author":"Zhou","year":"2021","journal-title":"J. Transl. Med."},{"key":"ref112","doi-asserted-by":"publisher","first-page":"109351","DOI":"10.1016\/j.foodres.2020.109351","article-title":"Partial replacement of nitrite with a novel probiotic lactobacillus plantarum on nitrate, color, biogenic amines and gel properties of Chinese fermented sausages","volume":"137","author":"Zhu","year":"2020","journal-title":"Food Res. Int."},{"key":"ref113","doi-asserted-by":"publisher","first-page":"7567","DOI":"10.3892\/mmr.2018.8833","article-title":"Roseburia intestinalis inhibits interleukin-17 excretion and promotes regulatory T cells differentiation in colitis","volume":"17","author":"Zhu","year":"2018","journal-title":"Mol. Med. Rep."},{"key":"ref114","doi-asserted-by":"publisher","first-page":"1388","DOI":"10.1016\/j.cell.2018.08.041","article-title":"Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features","volume":"174","author":"Zmora","year":"2018","journal-title":"Cell"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.973046\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,8]],"date-time":"2022-09-08T05:51:34Z","timestamp":1662616294000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.973046\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,9,8]]},"references-count":114,"alternative-id":["10.3389\/fmicb.2022.973046"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2022.973046","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,9,8]]},"article-number":"973046"}}