{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T19:42:50Z","timestamp":1790192570284,"version":"4.1.0"},"reference-count":83,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T00:00:00Z","timestamp":1776384000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    <jats:italic>Limosilactobacillus reuteri<\/jats:italic>\n                    , formerly\n                    <jats:italic>Lactobacillus reuteri<\/jats:italic>\n                    , is a rod-shaped, Gram-positive, facultative anaerobe that colonizes the gastrointestinal tract of most vertebrates, including humans. We report the first isolation of\n                    <jats:italic>L. reuteri<\/jats:italic>\n                    strain HDB from the stool of a healthy Indian infant. Species assignment using the Type (Strain) Genome Server (TYGS) placed HDB within the\n                    <jats:italic>L. reuteri<\/jats:italic>\n                    clade, showing closest affinity to\n                    <jats:italic>L. reuteri<\/jats:italic>\n                    subspecies\n                    <jats:italic>porcinus<\/jats:italic>\n                    (dDDH 69.7%) yet clustering phylogenomically with\n                    <jats:italic>L. reuteri<\/jats:italic>\n                    DSM 17938. Hybrid\n                    <jats:italic>de novo<\/jats:italic>\n                    assembly (Illumina + Oxford Nanopore GridION MK1) generated a single circular 2,226,956 bp chromosome (GC 39.04%) encoding 2,160 CDS. Functional annotation identified genes involved in vitamin B\n                    <jats:sub>12<\/jats:sub>\n                    biosynthesis, reuterin production, and probiotic functions, along with enriched carbohydrate and cofactor metabolic pathways. Comparative analysis with 59\n                    <jats:italic>L. reuteri<\/jats:italic>\n                    genomes revealed a pangenome of 11,725 gene families, including 944 core gene families, 171 soft-core gene families, 1912 shell gene families, and 8698 cloud gene families, highlighting notable diversity. Core-genome phylogeny aligns HDB closely with the reference strain DSM 17938, confirming its identity as a human-associated lineage. dN\/dS analysis indicated strong purifying selection across host niches, with no evidence of widespread positive selection. Genome-scale modeling predicts expanded carbohydrate flux in HDB against global references. The genetic background, along with its conserved metabolic features, suggests that HDB carries genomic characteristics commonly associated with human-derived\n                    <jats:italic>L. reuteri<\/jats:italic>\n                    strains. These observations support its consideration for further evaluation as a regionally sourced probiotic candidate. These conclusions are based on genomic and computational predictions and require experimental validation through adhesion, colonization, and safety studies.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1780782","type":"journal-article","created":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T05:19:48Z","timestamp":1776403188000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Genome characterization and comparative genomics of Limosilactobacillus reuteri HDB isolated from the gut of an Indian infant"],"prefix":"10.3389","volume":"17","author":[{"given":"Hemang D.","family":"Brahmbhatt","sequence":"first","affiliation":[{"name":"Department of Science and Technology, Gujarat Biotechnology Research Centre, Government of Gujarat","place":["Gandhinagar, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Priyank","family":"Chavda","sequence":"additional","affiliation":[{"name":"Department of Science and Technology, Gujarat Biotechnology Research Centre, Government of Gujarat","place":["Gandhinagar, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dhruvinkumar","family":"Vadee","sequence":"additional","affiliation":[{"name":"Department of Science and Technology, Gujarat Biotechnology Research Centre, Government of Gujarat","place":["Gandhinagar, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amrutlal K.","family":"Patel","sequence":"additional","affiliation":[{"name":"Department of Science and Technology, Gujarat Biotechnology Research Centre, Government of Gujarat","place":["Gandhinagar, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Snehal","family":"Bagatharia","sequence":"additional","affiliation":[{"name":"Department of Science and Technology, Gujarat Biotechnology Research Centre, Government of Gujarat","place":["Gandhinagar, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,4,17]]},"reference":[{"key":"B1","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":"B2","doi-asserted-by":"publisher","first-page":"105548","DOI":"10.1016\/j.phrs.2021.105548","article-title":"Resveratrol-mediated attenuation of superantigen-driven acute respiratory distress syndrome is mediated by microbiota in the lungs and gut","volume":"167","author":"Alghetaa","year":"2021","journal-title":"Pharmacol. Res."},{"key":"B3","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST server: Rapid annotations using subsystems technology.","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"B4","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1016\/j.chom.2015.04.004","article-title":"Dynamics and stabilization of the human gut microbiome during the first year of life.","volume":"17","author":"B\u00e4ckhed","year":"2015","journal-title":"Cell. Host Microbe"},{"key":"B5","first-page":"109734","article-title":"The role of intestinal microbiota in the maintenance of immune homeostasis and prevention of inflammatory diseases.","volume":"374","author":"Bell","year":"2022","journal-title":"Int. J. Food Microbiol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"W29","DOI":"10.1093\/nar\/gkab335","article-title":"antiSMASH 6.0: Improving cluster detection and comparison capabilities.","volume":"49","author":"Blin","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B7","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data.","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"B8","doi-asserted-by":"publisher","first-page":"vbac085","DOI":"10.1093\/bioadv\/vbac085","article-title":"Porechop_ABI: Discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming.","volume":"3","author":"Bonenfant","year":"2022","journal-title":"Bioinform. Adv."},{"key":"B9","first-page":"132","article-title":"Emerging molecular insights into surface-layer protein function and assembly.","volume":"15","author":"Bron","year":"2012","journal-title":"Curr. Opin. Microbiol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"8344","DOI":"10.1128\/AEM.71.12.8344-8351.2005","article-title":"Functional analysis of putative adhesion factors in Lactobacillus acidophilus NCFM.","volume":"71","author":"Buck","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale.","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing.","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B13","doi-asserted-by":"publisher","first-page":"D325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: A reference database for bacterial virulence factors.","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"B14","first-page":"3820","article-title":"Alleviation effect and mechanism of Lactobacillus plantarum YS-3 on allergic asthma in BALB\/c mice.","volume":"12","author":"Chen","year":"2021","journal-title":"Food Funct."},{"key":"B15","first-page":"1146","article-title":"Amelioration of estrogen deficiency-induced obesity by colonic delivery of live Lactobacillus reuteri GMNL-263.","volume":"9","author":"Chiang","year":"2021","journal-title":"Microorganisms"},{"key":"B16","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":"B17","doi-asserted-by":"publisher","first-page":"e000294","DOI":"10.1099\/mgen.0.000294","article-title":"Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes.","volume":"5","author":"De Maio","year":"2019","journal-title":"Microb. Genom."},{"key":"B18","doi-asserted-by":"publisher","first-page":"1230","DOI":"10.1111\/j.1365-2672.2009.04306.x","article-title":"Effect of growth time on the surface and adhesion properties of Lactobacillus rhamnosus GG.","volume":"107","author":"Deepika","year":"2009","journal-title":"J. Appl. Microbiol."},{"key":"B19","first-page":"884","article-title":"Comparative genome analysis of Lactobacillus reuteri from different hosts reveals host-adaptive traits.","volume":"8","author":"Duar","year":"2017","journal-title":"Front. Microbiol."},{"key":"B20","first-page":"131","article-title":"Gut microbiome analysis using 16S rRNA sequencing and prediction of pathogenic bacteria.","volume":"84","author":"Dubey","year":"2016","journal-title":"Biomed. Pharmacother."},{"key":"B21","doi-asserted-by":"publisher","first-page":"e483","DOI":"10.1128\/AAC.00483-19","article-title":"Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates.","volume":"63","author":"Feldgarden","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"B22","doi-asserted-by":"publisher","first-page":"S35","DOI":"10.1017\/S0007114512004011","article-title":"Sources, isolation, characterisation and evaluation of probiotics.","volume":"109","author":"Fontana","year":"2013","journal-title":"Br. J. Nutr."},{"key":"B23","doi-asserted-by":"publisher","first-page":"e1001314","DOI":"10.1371\/journal.pgen.1001314","article-title":"The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri.","volume":"7","author":"Frese","year":"2011","journal-title":"PLoS Genet."},{"key":"B24","doi-asserted-by":"publisher","first-page":"e1004057","DOI":"10.1371\/journal.pgen.1004057","article-title":"Molecular characterization of host-specific biofilm formation in a vertebrate gut symbiont.","volume":"9","author":"Frese","year":"2013","journal-title":"PLoS Genet."},{"key":"B25","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.cofs.2015.03.001","article-title":"Lactic metabolism revisited: Metabolism of lactic acid bacteria in food fermentations and gut ecosystems.","volume":"2","author":"G\u00e4nzle","year":"2015","journal-title":"Curr Opin Food Sci."},{"key":"B26","doi-asserted-by":"publisher","first-page":"e01358-15","DOI":"10.1128\/mBio.01358-15","article-title":"Histamine H2 receptor-mediated suppression of intestinal inflammation by probiotic Lactobacillus reuteri.","volume":"6","author":"Gao","year":"2015","journal-title":"mBio"},{"key":"B27","doi-asserted-by":"publisher","first-page":"3420","DOI":"10.1093\/nar\/gkn176","article-title":"High-throughput functional annotation and data mining with the Blast2GO suite.","volume":"36","author":"G\u00f6tz","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"B28","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: Quality assessment tool for genome assemblies.","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"B29","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1084\/jem.20160961","article-title":"Resetting microbiota by Lactobacillus reuteri inhibits T reg deficiency-induced autoimmunity via adenosine A2A receptors.","volume":"214","author":"He","year":"2017","journal-title":"J. Exp. Med."},{"key":"B30","doi-asserted-by":"publisher","first-page":"1504","DOI":"10.1136\/gutjnl-2018-317232","article-title":"Bacteria engineered to produce IL-22 in intestine induce expression of REG3G to reduce ethanol-induced liver disease in mice.","volume":"68","author":"Hendrikx","year":"2019","journal-title":"Gut"},{"key":"B31","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":"B32","doi-asserted-by":"publisher","first-page":"382","DOI":"10.2174\/0929866524666170223143615","article-title":"Dietary additive probiotics modulation of the intestinal microbiota.","volume":"24","author":"Hu","year":"2017","journal-title":"Protein Pept. Lett."},{"key":"B33","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1186\/1471-2431-12-142","article-title":"Effect of routine probiotic, Lactobacillus reuteri DSM 17938, use on rates of necrotizing enterocolitis in neonates with birthweight < 1000 grams: A sequential analysis.","volume":"12","author":"Hunter","year":"2012","journal-title":"BMC Pediatr."},{"key":"B34","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1016\/j.jpeds.2007.11.005","article-title":"The effects of probiotics on feeding tolerance, bowel habits, and gastrointestinal motility in preterm newborns.","volume":"152","author":"Indrio","year":"2008","journal-title":"J. Pediatr."},{"key":"B35","doi-asserted-by":"publisher","first-page":"126","DOI":"10.3390\/nu8030126","article-title":"Apple-derived pectin modulates gut microbiota, improves gut barrier function, and attenuates metabolic endotoxemia in rats with diet-induced obesity.","volume":"8","author":"Jiang","year":"2016","journal-title":"Nutrients"},{"key":"B36","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1186\/1471-230X-13-20","article-title":"Clostridium leptum group bacteria abundance and diversity in the fecal microbiota of patients with inflammatory bowel disease: A case-control study in India.","volume":"13","author":"Kabeerdoss","year":"2013","journal-title":"BMC Gastroenterol."},{"key":"B37","first-page":"4146","article-title":"Genetic and phenotypic analysis of Lactobacillus acidophilus strains as a basis for probiotic evaluation.","volume":"65","author":"Kullen","year":"1999","journal-title":"Appl. Environ. Microbiol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.phrs.2012.09.010","article-title":"The quest for probiotic stress tolerance mechanisms.","volume":"4","author":"Lee","year":"2013","journal-title":"Front. Microbiol."},{"key":"B39","first-page":"7","article-title":"Analysis of the gut microbiota in the mouse and human gut: Potential of omics approaches.","volume":"9","author":"Lee","year":"2021","journal-title":"Microbiome"},{"key":"B40","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree of life (iTOL) v5: An online tool for phylogenetic tree display and annotation.","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B41","doi-asserted-by":"publisher","first-page":"522","DOI":"10.1016\/j.cmet.2017.02.001","article-title":"Integrative physiology: At the crossroads of nutrition, microbiota, animal physiology, and human Health.","volume":"25","author":"Leulier","year":"2017","journal-title":"Cell. Metab."},{"key":"B42","doi-asserted-by":"publisher","first-page":"1079","DOI":"10.1101\/gr.230615.117","article-title":"Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.","volume":"28","author":"Lomsadze","year":"2018","journal-title":"Genome Res."},{"key":"B43","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1038\/s41398-018-0240-5","article-title":"Gut microbiota regulates mouse behaviors through glucocorticoid receptor pathway genes in the hippocampus.","volume":"8","author":"Luo","year":"2018","journal-title":"Transl. Psychiatry"},{"key":"B44","first-page":"162","article-title":"Generation of genome-scale metabolic reconstructions for 773 human gut microbes identifies species-specific and community-wide metabolic capabilities.","volume":"2","author":"Magn\u00fasd\u00f3ttir","year":"2017","journal-title":"Nat. Microbiol."},{"key":"B45","doi-asserted-by":"publisher","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes.","volume":"38","author":"Manni","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"B46","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1016\/j.copbio.2006.02.005","article-title":"Towards understanding molecular modes of probiotic action.","volume":"17","author":"Marco","year":"2006","journal-title":"Curr. Opin. Biotechnol."},{"key":"B47","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1007\/s11914-015-0292-x","article-title":"Prebiotic and probiotic regulation of bone health: Role of the intestine and its microbiome.","volume":"13","author":"McCabe","year":"2015","journal-title":"Curr. Osteoporos Rep."},{"key":"B48","doi-asserted-by":"publisher","first-page":"e00036-e17","DOI":"10.1128\/MMBR.00036-17","article-title":"The first microbial colonizers of the human gut: Composition, activities, and health implications of the infant gut microbiota.","volume":"81","author":"Milani","year":"2017","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"B49","doi-asserted-by":"publisher","first-page":"W182","DOI":"10.1093\/nar\/gkm321","article-title":"KAAS: An automatic genome annotation and pathway reconstruction server.","volume":"35","author":"Moriya","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"B50","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1016\/j.cmet.2018.07.001","article-title":"Impaired Aryl hydrocarbon receptor ligand production by the gut microbiota is a key factor in metabolic syndrome.","volume":"28","author":"Natividad","year":"2018","journal-title":"Cell Metab."},{"key":"B51","doi-asserted-by":"publisher","first-page":"eaah6888","DOI":"10.1126\/scitranslmed.aah6888","article-title":"A role for bacterial urease in gut dysbiosis and Crohn\u2019s disease.","volume":"9","author":"Ni","year":"2017","journal-title":"Sci. Transl. Med."},{"key":"B52","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1038\/ismej.2009.123","article-title":"Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution.","volume":"4","author":"Oh","year":"2010","journal-title":"ISME J."},{"key":"B53","doi-asserted-by":"publisher","first-page":"D678","DOI":"10.1093\/nar\/gkac1003","article-title":"Introducing the bacterial and viral bioinformatics resource center (BV-BRC): A resource combining PATRIC, IRD and ViPR.","volume":"51","author":"Olson","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B54","doi-asserted-by":"publisher","first-page":"R545","DOI":"10.1016\/j.cub.2019.04.00","article-title":"Commensal interactions in the gut microbiome: Cooperative metabolism and community assembly.","volume":"29","author":"Pacheco","year":"2019","journal-title":"Curr. Biol."},{"key":"B55","first-page":"W1","article-title":"gutSMASH: Automated identification of primary metabolic gene clusters from the gut microbiota.","volume":"50","author":"Palladino","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"B56","first-page":"1245","article-title":"Comparative genomics reveals a natural evolutionary adaptation of bacteria to their environment.","volume":"8","author":"Qin","year":"2014","journal-title":"ISME J."},{"key":"B57","first-page":"334","article-title":"Lactobacillus reuteri modulates tight junction proteins, ameliorates intestinal barrier dysfunction and attenuates endotoxemia in weaned piglets challenged with enterotoxigenic Escherichia coli K88.","volume":"26","author":"Qi-Xiang","year":"2020","journal-title":"Innate Immun."},{"key":"B58","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1016\/j.copbio.2017.09.007","article-title":"Shared mechanisms among probiotic taxa: Implications for general probiotic claims.","volume":"49","author":"Sanders","year":"2018","journal-title":"Curr. Opin. Biotechnol."},{"key":"B59","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1038\/s41575-019-0173-3","article-title":"Probiotics and prebiotics in intestinal health and disease: From biology to the clinic.","volume":"16","author":"Sanders","year":"2019","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"B60","first-page":"803","article-title":"Probiotics for human use: Systematic review of safety and efficacy.","volume":"74","author":"Sanders","year":"2016","journal-title":"Nutr. Rev."},{"key":"B61","doi-asserted-by":"publisher","first-page":"7419","DOI":"10.1186\/1475-2859-10-55","article-title":"Functional identification in Lactobacillus reuteri of the genes involved in the production of reuterin and cobalamin.","volume":"190","author":"Santos","year":"2008","journal-title":"J. Bacteriol."},{"key":"B62","doi-asserted-by":"publisher","first-page":"e526","DOI":"10.1542\/peds.2010-0433","article-title":"Lactobacillus reuteri DSM 17938 in infantile colic: A randomized, double-blind, placebo-controlled trial.","volume":"126","author":"Savino","year":"2010","journal-title":"Pediatrics"},{"key":"B63","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid prokaryotic genome annotation.","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B64","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1016\/j.neuron.2018.11.018","article-title":"Mechanisms underlying microbial-mediated changes in social behavior in mouse models of autism spectrum disorder.","volume":"101","author":"Sgritta","year":"2019","journal-title":"Neuron"},{"key":"B65","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1093\/femsre\/fuw045","article-title":"Intestinal microbiome landscaping: Insight in community assemblage and implications for microbial modulation strategies.","volume":"41","author":"Shetty","year":"2017","journal-title":"FEMS Microbiol. Rev."},{"key":"B66","doi-asserted-by":"publisher","first-page":"1772","DOI":"10.1093\/gbe\/evu137","article-title":"Human-specific ecotypes of Lactobacillus reuteri have diverged in carbohydrate metabolism functions.","volume":"6","author":"Spinler","year":"2014","journal-title":"Genome Biol. Evol."},{"key":"B67","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1016\/j.anaerobe.2008.02.001","article-title":"Human-derived probiotic Lactobacillus reuteri demonstrate antimicrobial activities targeting diverse enteric bacterial pathogens.","volume":"14","author":"Spinler","year":"2008","journal-title":"Anaerobe"},{"key":"B68","doi-asserted-by":"publisher","first-page":"18979","DOI":"10.1128\/JB.01535-07","article-title":"Lactobacillus reuteri DSM 20016 produces cobalamin-dependent diol dehydratase in metabolosomes and metabolizes 1,2-propanediol by disproportionation.","volume":"190","author":"Sriramulu","year":"2008","journal-title":"J. Bacteriol."},{"key":"B69","doi-asserted-by":"publisher","first-page":"1069","DOI":"10.1038\/s41586-018-0617-x","article-title":"Temporal development of the gut microbiome in early childhood from the TEDDY study.","volume":"562","author":"Stewart","year":"2018","journal-title":"Nature"},{"key":"B70","doi-asserted-by":"publisher","first-page":"1854","DOI":"10.1128\/AAC.32.12.1854","article-title":"Production and isolation of reuterin, a growth inhibitor produced by Lactobacillus reuteri.","volume":"32","author":"Talarico","year":"1988","journal-title":"Antimicrob. Agents Chemother."},{"key":"B71","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1016\/j.mib.2008.09.006","article-title":"Comparative genomics: The bacterial pan-genome.","volume":"11","author":"Tettelin","year":"2008","journal-title":"Curr. Opin. Microbiol."},{"key":"B72","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":"B73","doi-asserted-by":"publisher","first-page":"4645","DOI":"10.1073\/pnas.1000099107","article-title":"Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm.","volume":"108","author":"Walter","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U S A."},{"key":"B74","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.copbio.2017.08.008","article-title":"To engraft or not to engraft: An ecological framework for gut microbiome modulation with live microbes.","volume":"49","author":"Walter","year":"2018","journal-title":"Curr. Opin. Biotechnol."},{"key":"B75","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1038\/s41587-018-0004-z","article-title":"Errors in long-read assemblies can critically affect protein prediction.","volume":"37","author":"Watson","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"B76","first-page":"1918","article-title":"Complete genome sequence of Lactobacillus reuteri DSM 17938 and comparison with related probiotic and nonprobiotic strains.","volume":"161","author":"Wegmann","year":"2015","journal-title":"Microbiology"},{"key":"B77","first-page":"e00826","article-title":"Benchmarking hybrid assemblers for bacterial genomes.","volume":"8","author":"Wick","year":"2022","journal-title":"Microb. Genom."},{"key":"B78","doi-asserted-by":"publisher","first-page":"e1005595","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.","volume":"13","author":"Wick","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"B79","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/nature11053","article-title":"Human gut microbiome viewed across age and geography.","volume":"486","author":"Yatsunenko","year":"2012","journal-title":"Nature"},{"key":"B80","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/j.chom.2018.11.009","article-title":"A diet-sensitive commensal Lactobacillus strain mediates TLR7-dependent systemic autoimmunity.","volume":"25","author":"Zegarra-Ruiz","year":"2019","journal-title":"Cell Host Microbe"},{"key":"B81","doi-asserted-by":"publisher","first-page":"1089200","DOI":"10.3389\/fimmu.2022.1089200","article-title":"DSS-induced colitis activates the kynurenine pathway in serum and brain by affecting IDO-1 and gut microbiota","volume":"13","author":"Zhao","year":"2023","journal-title":"Front. Immunol."},{"key":"B82","first-page":"806","article-title":"A genomic view of lactobacilli and pediococci and their metabolic roles in food and health.","volume":"9","author":"Zheng","year":"2015","journal-title":"ISME J."},{"key":"B83","doi-asserted-by":"publisher","first-page":"2782","DOI":"10.1099\/ijsem.0.004107","article-title":"A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae.","volume":"70","author":"Zheng","year":"2020","journal-title":"Int J Syst Evol Microbiol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1780782\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T05:19:51Z","timestamp":1776403191000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1780782\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,17]]},"references-count":83,"alternative-id":["10.3389\/fmicb.2026.1780782"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1780782","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,17]]},"article-number":"1780782"}}