{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T14:20:05Z","timestamp":1789741205946,"version":"4.0.1"},"reference-count":101,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T00:00:00Z","timestamp":1765497600000},"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":["U22A20540"],"award-info":[{"award-number":["U22A20540"]}],"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>Limosilactobacillus reuteri<\/jats:italic>\n                    is a widely utilized probiotic, however, the genomic diversity and evolutionary mechanisms underlying its adaptation to various hosts and environments remain incompletely understood. This study employed comparative genomics to analyze 176\n                    <jats:italic>L. reuteri<\/jats:italic>\n                    genomes from animal (rodents, mammals, ruminants, and birds), human intestinal, and food sources (dairy products, fermented foods; 89 newly sequenced and 92 retrieved, 5 excluded by ANI\u202f&amp;lt;\u202f95%). We assessed genomic features, average nucleotide identity, pan\/core genomes, carbohydrate-active enzymes, bacteriocin production, CRISPR-Cas systems, and antibiotic resistance genes. The pan-genome consisted of 16,814 genes, while the core genome contained 553 genes. Core-gene phylogeny revealed seven clades, rodents isolates were positioned closer to the root. The clustering trend of fermented foods isolates in the phylogenetic tree may indicate that these strains have undergone convergent evolution or adaptive evolution in a specific environment. CAZymes varied across sources, and the predicted bacteriocin clusters were enriched in animal-derived, particularly in rodent isolates. CAZy functional composition in\n                    <jats:italic>L. reuteri<\/jats:italic>\n                    is shaped by the ecological niche and host environment, reflecting a pattern of host-driven evolutionary adaptation. CRISPR\u2013Cas systems were present in 23.3% of genomes, predominantly in rodents isolates, indicating strong anti-phage capabilities. The heterogeneity of CRISPR-Cas systems among sources suggests that subpopulations of\n                    <jats:italic>L. reuteri<\/jats:italic>\n                    have been subjected to different evolutionary pressures. The predominance of Type II systems agrees with their widespread occurrence in\n                    <jats:italic>lactobacilli<\/jats:italic>\n                    . The presence of multiple probiotic function-related genes across all separation sources confirms the robust probiotic potential of\n                    <jats:italic>L. reuteri.<\/jats:italic>\n                    Antibiotic resistance genes, including\n                    <jats:italic>tet<\/jats:italic>\n                    ,\n                    <jats:italic>erm<\/jats:italic>\n                    B, and\n                    <jats:italic>vat<\/jats:italic>\n                    E, were most prevalent among animal-derived isolates, with the highest numbers occurring in mammals and the lowest in rodents. Therefore, strain-specific safety assessments are necessary prior to clinical or food applications. The findings underscore the significance of host-specific adaptations in shaping the genetic and functional profiles of\n                    <jats:italic>L. reuteri<\/jats:italic>\n                    , offering valuable implications for its application in food-derived, human-derived, animal-derived and therapeutics.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2025.1732127","type":"journal-article","created":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T06:33:40Z","timestamp":1765521220000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":10,"title":["Genomic diversity and functional adaptation of Limosilactobacillus reuteri isolated from diverse ecological niches"],"prefix":"10.3389","volume":"16","author":[{"given":"Yuexin","family":"Sun","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weicheng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lai-Yu","family":"Kwok","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heping","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,12,12]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"522","DOI":"10.3390\/microorganisms10030522","article-title":"Limosilactobacillus reuteri in health and disease","volume":"10","author":"Abuqwider","year":"2022","journal-title":"Microorganisms"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"3171","DOI":"10.1038\/s41598-023-29404-3","article-title":"Subspecies-level genome comparison of Lactobacillus delbrueckii","volume":"13","author":"Baek","year":"2023","journal-title":"Sci. Rep."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1186\/s13068-020-01683-2","article-title":"Isopod holobionts as promising models for lignocellulose degradation","volume":"13","author":"Bredon","year":"2020","journal-title":"Biotechnol. Biofuels"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"2361","DOI":"10.1126\/science.286.5448.2361","article-title":"Use of the cell wall precursor lipid II by a pore-forming peptide antibiotic","volume":"286","author":"Breukink","year":"1999","journal-title":"Science"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"3135","DOI":"10.1007\/s00253-019-09701-6","article-title":"Uncovering carbohydrate metabolism through a genotype-phenotype association study of 56 lactic acid bacteria genomes","volume":"103","author":"Buron-Moles","year":"2019","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"136","DOI":"10.3389\/fmicb.2021.793136","article-title":"Positive interactions between lactic acid Bacteria could be mediated by peptides containing branched-chain amino acids","volume":"12","author":"Canon","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/s13062-019-0234-0","article-title":"Genome and pan-genome analysis to classify emerging bacteria","volume":"14","author":"Caputo","year":"2019","journal-title":"Biol. Direct"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"595991","DOI":"10.3389\/fchem.2021.595991","article-title":"Current advancements in Sactipeptide natural products","volume":"9","author":"Chen","year":"2021","journal-title":"Front. Chem."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1089\/crispr.2017.0022","article-title":"CRISPRdisco: an automated pipeline for the discovery and analysis of CRISPR-Cas systems","volume":"1","author":"Crawley","year":"2018","journal-title":"CRISPR J"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"CD007239","DOI":"10.1002\/14651858.CD007239.pub4","article-title":"Interventions for preventing mastitis after childbirth","volume":"9","author":"Crepinsek","year":"2020","journal-title":"Cochrane Database Syst. Rev."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"5391","DOI":"10.1021\/acs.jafc.4c00104","article-title":"Insights into the structure-function relationship of GH70 GtfB \u03b1-glucanotransferases from the crystal structure and molecular dynamic simulation of a newly characterized Limosilactobacillus reuteri N1 GtfB enzyme","volume":"72","author":"Dong","year":"2024","journal-title":"J. Agric. Food Chem."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"AEM.00132-17","DOI":"10.1128\/AEM.00132-17","article-title":"Experimental evaluation of host adaptation of Lactobacillus reuteri to different vertebrate species","volume":"83","author":"Duar","year":"","journal-title":"Appl. Environ. Microbiol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"S27","DOI":"10.1093\/femsre\/fux030","article-title":"Lifestyles in transition: evolution and natural history of the genus Lactobacillus","volume":"41","author":"Duar","year":"","journal-title":"FEMS Microbiol. Rev."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"340207","DOI":"10.17957\/JAB\/15.2355","article-title":"In vitro safety evaluation of novel phyto lactic acid bacteria isolated from fruits as potential probiotics","volume":"34","author":"Fasiha Fayyaz Khan","year":"2025","journal-title":"Int. J. Agric. Biol."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"483","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":"ref17","doi-asserted-by":"publisher","first-page":"586667","DOI":"10.3389\/fcimb.2020.586667","article-title":"The microbiota of the human mammary ecosystem","volume":"10","author":"Fern\u00e1ndez","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"570","DOI":"10.1016\/j.sbi.2012.07.009","article-title":"Insights into the recognition of the human glycome by microbial carbohydrate-binding modules","volume":"22","author":"Ficko-Blean","year":"2012","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref19","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":"ref1102","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":"2024","journal-title":"PLoS Genet."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"19584","DOI":"10.1038\/s41598-024-70549-6","article-title":"Effects of Limosilactobacillus reuteri strains PTA-126787 and PTA-126788 on intestinal barrier integrity and immune homeostasis in an alcohol-induced leaky gut model","volume":"14","author":"Gangaiah","year":"2024","journal-title":"Sci. Rep."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.3389\/fmicb.2020.01166","article-title":"Isolation and comparative genomic analysis of reuterin-producing Lactobacillus reuteri from the chicken gastrointestinal tract","volume":"11","author":"Greppi","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1186\/1471-2105-8-172","article-title":"The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats","volume":"8","author":"Grissa","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1016\/j.fgb.2018.04.003","article-title":"On the origin of vanillyl alcohol oxidases","volume":"116","author":"Gygli","year":"2018","journal-title":"Fungal Genet. Biol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"979","DOI":"10.3390\/ani11040979","article-title":"Bacteriocins from lactic acid bacteria. A powerful alternative as antimicrobials, probiotics, and immunomodulators in veterinary medicine","volume":"11","author":"Hernandez-Gonzalez","year":"2021","journal-title":"Animals (Basel)"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"2115","DOI":"10.1093\/molbev\/msx148","article-title":"Fast genome-wide functional annotation through Orthology assignment by eggNOG-mapper","volume":"34","author":"Huerta-Cepas","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"1893","DOI":"10.1136\/gutjnl-2024-333378","article-title":"What defines a healthy gut microbiome?","volume":"73","author":"Hul","year":"2024","journal-title":"Gut"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"ref28","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1016\/S0172-5564(80)80007-8","article-title":"Lactobacillus reuteri sp. nov., a new species of heterofermentative lactobacilli","volume":"1","author":"Kandler","year":"1980","journal-title":"Zentralblatt f\u00fcr Bakteriologie: I. Abt. Originale C: Allgemeine, angewandte und \u00f6kologische Mikrobiologie"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"2009","DOI":"10.1007\/s10068-024-01621-0","article-title":"Important roles of Ruminococcaceae in the human intestine for resistant starch utilization","volume":"33","author":"Kim","year":"2024","journal-title":"Food Sci. Biotechnol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"390","DOI":"10.1128\/JB.00390-20","article-title":"Virulence genetics of an Erwinia amylovora putative polysaccharide transporter family member","volume":"202","author":"Klee","year":"2020","journal-title":"J. Bacteriol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1007\/s11692-010-9093-4","article-title":"Genome size and species diversification","volume":"37","author":"Kraaijeveld","year":"2010","journal-title":"Evol. Biol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"768","DOI":"10.1039\/c3np70127a","article-title":"Secondary metabolomics: the impact of mass spectrometry-based approaches on the discovery and characterization of microbial natural products","volume":"31","author":"Krug","year":"2014","journal-title":"Nat. Prod. Rep."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1099\/mgen.0.000847","article-title":"Genomic diversity of genus Limosilactobacillus","volume":"8","author":"Ksiezarek","year":"2022","journal-title":"Microb Genom"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"102143","DOI":"10.1016\/j.mib.2022.102143","article-title":"Glycan processing in gut microbiomes","volume":"67","author":"La Rosa","year":"2022","journal-title":"Curr. Opin. Microbiol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1186\/s12915-023-01541-1","article-title":"A phylogenomic analysis of Limosilactobacillus reuteri reveals ancient and stable evolutionary relationships with rodents and birds and zoonotic transmission to humans","volume":"21","author":"Li","year":"2023","journal-title":"BMC Biol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1186\/s40168-024-01863-4","article-title":"Trait-based study predicts glycerol\/diol dehydratases as a key function of the gut microbiota of hindgut-fermenting carnivores","volume":"12","author":"Li","year":"2024","journal-title":"Microbiome"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"0017","DOI":"10.34133\/bdr.0017","article-title":"CRISPR-Cas-based engineering of probiotics","volume":"5","author":"Liu","year":"2023","journal-title":"Biodes Res"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"010","DOI":"10.1093\/gpbjnl\/qzaf010","article-title":"The updated genome warehouse: enhancing data value, security, and usability to address data expansion","volume":"23","author":"Ma","year":"2025","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1093\/bioinformatics\/bti012","article-title":"Tracker: continuous HMMER and BLAST searching","volume":"21","author":"Marchin","year":"2005","journal-title":"Bioinformatics"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"1863","DOI":"10.1007\/s10787-025-01676-3","article-title":"Bacillus subtilis (NMCC-path-14) ameliorates acute phase of arthritis via modulating NF-kappaB and Nrf-2 signaling in mice model","volume":"33","author":"Mazhar","year":"2025","journal-title":"Inflammopharmacology"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"909","DOI":"10.3168\/jds.2018-15385","article-title":"Symposium review: genomic investigations of flavor formation by dairy microbiota","volume":"102","author":"McAuliffe","year":"2019","journal-title":"J. Dairy Sci."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"1457","DOI":"10.1099\/mic.0.045997-0","article-title":"The dlt operon confers resistance to cationic antimicrobial peptides in Clostridium difficile","volume":"157","author":"McBride","year":"2011","journal-title":"Microbiology (Reading)"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1038\/s41467-020-15053-x","article-title":"Multiplexed CRISPR technologies for gene editing and transcriptional regulation","volume":"11","author":"McCarty","year":"2020","journal-title":"Nat. Commun."},{"key":"ref44","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-025-01205-7","article-title":"Lactobacilli biology, applications and host interactions","author":"Mejia-Caballero","year":"2025","journal-title":"Nat. Rev. Microbiol."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"D30","DOI":"10.1093\/nar\/gkae978","article-title":"Database resources of the National Genomics Data Center, China National Center for bioinformation in 2025","volume":"53","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref46","doi-asserted-by":"crossref","first-page":"738","DOI":"10.3168\/jds.S0022-0302(87)80068-1","article-title":"Purification and characterization of X-prolyl-dipeptidyl-aminopeptidase from Lactobacillus lactis and from Streptococcus thermophilus","volume":"70","author":"Meyer","year":"1987","journal-title":"J. Dairy Sci."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"D457","DOI":"10.1093\/nar\/gkv1070","article-title":"KEGG as a reference resource for gene and protein annotation","volume":"44","author":"Minoru","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"11786302221109720","DOI":"10.1177\/11786302221109720","article-title":"Determination of tetracycline residues in kidney and muscle of beef cattle slaughtered in Dire Dawa and Harar municipal abattoirs, eastern Ethiopia","volume":"16","author":"Mohammed","year":"2022","journal-title":"Environ. Health Insights"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1038\/s41587-021-00898-4","article-title":"Author correction: a genomic catalog of earth's microbiomes","volume":"39","author":"Nayfach","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"1384","DOI":"10.1038\/s41467-023-36988-x","article-title":"Abiotic selection of microbial genome size in the global ocean","volume":"14","author":"Ngugi","year":"2023","journal-title":"Nat. Commun."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"110735","DOI":"10.1016\/j.ijfoodmicro.2024.110735","article-title":"A novel antifungal nanoemulsion based on reuterin-assisted synergistic essential oils: preparation and in vitro\/in vivo characterization","volume":"418","author":"Nikkhah","year":"2024","journal-title":"Int. J. Food Microbiol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"2975","DOI":"10.1128\/AEM.69.5.2975-2984.2003","article-title":"Enterolysin a, a cell wall-degrading bacteriocin from Enterococcus faecalis LMG 2333","volume":"69","author":"Nilsen","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"key":"ref53","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":"ref54","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1128\/mSystems.00731-19","article-title":"Consistent metagenome-derived metrics verify and delineate bacterial species boundaries","volume":"5","author":"Olm","year":"2020","journal-title":"mSystems"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"292","DOI":"10.3390\/foods14132292","article-title":"Fermented foods as functional systems: microbial communities and metabolites influencing gut health and systemic outcomes","volume":"14","author":"Park","year":"2025","journal-title":"Foods"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"1466437","DOI":"10.3389\/fvets.2025.1466437","article-title":"Current understanding of the Streptococcus bovis\/equinus complex and its bacteriophages in ruminants: a review","volume":"12","author":"Park","year":"2025","journal-title":"Front Vet Sci"},{"key":"ref58","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1016\/j.cell.2019.01.001","article-title":"Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle","volume":"176","author":"Pasolli","year":"2019","journal-title":"Cell"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1093\/femsre\/fuv019","article-title":"DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes","volume":"39","author":"Plagens","year":"2015","journal-title":"FEMS Microbiol. Rev."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"297","DOI":"10.3390\/microorganisms8020297","article-title":"Safety aspects of genetically modified lactic acid Bacteria","volume":"8","author":"Plavec","year":"2020","journal-title":"Microorganisms"},{"key":"ref61","doi-asserted-by":"publisher","first-page":"104334","DOI":"10.1016\/j.fm.2023.104334","article-title":"Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family","volume":"115","author":"Rajput","year":"2023","journal-title":"Food Microbiol."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"19126","DOI":"10.1073\/pnas.0906412106","article-title":"Shifting the genomic gold standard for the prokaryotic species definition","volume":"106","author":"Richter","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref63","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1089\/sur.2018.184","article-title":"Bacteriophages: a therapy concept against multi-drug-resistant Bacteria","volume":"19","author":"Rohde","year":"2018","journal-title":"Surg. Infect."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1186\/s12864-022-08459-y","article-title":"The genomic basis of the Streptococcus thermophilus health-promoting properties","volume":"23","author":"Roux","year":"2022","journal-title":"BMC Genomics"},{"key":"ref65","doi-asserted-by":"publisher","first-page":"2901","DOI":"10.1099\/mic.0.26435-0","article-title":"Characterization of Enterococcus faecium mutants resistant to mundticin KS, a class IIa bacteriocin","volume":"149","author":"Sakayori","year":"2003","journal-title":"Microbiology (Reading)"},{"key":"ref66","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1099\/mic.0.035642-0","article-title":"The antimicrobial compound reuterin (3-hydroxypropionaldehyde) induces oxidative stress via interaction with thiol groups","volume":"156","author":"Schaefer","year":"2010","journal-title":"Microbiology (Reading)"},{"key":"ref67","doi-asserted-by":"publisher","first-page":"102675","DOI":"10.1016\/j.mib.2025.102675","article-title":"The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem","volume":"88","author":"Schubert","year":"2025","journal-title":"Curr. Opin. Microbiol."},{"key":"ref68","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":"ref69","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1038\/s41576-018-0032-z","article-title":"Population genomics of bacterial host adaptation","volume":"19","author":"Sheppard","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"039","DOI":"10.1093\/femsre\/fuaa039","article-title":"Bacteriocins as a new generation of antimicrobials: toxicity aspects and regulations","volume":"45","author":"Soltani","year":"2021","journal-title":"FEMS Microbiol. 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Parasitol."},{"key":"ref90","doi-asserted-by":"publisher","first-page":"2284","DOI":"10.3390\/foods10102284","article-title":"Colonized niche, evolution and function signatures of Bifidobacterium pseudolongum within Bifidobacterial genus","volume":"10","author":"Xiao","year":"2021","journal-title":"Foods"},{"key":"ref91","doi-asserted-by":"publisher","first-page":"1660","DOI":"10.1093\/bioinformatics\/btu077","article-title":"SOAPdenovo-trans: de novo transcriptome assembly with short RNA-Seq reads","volume":"30","author":"Xie","year":"2014","journal-title":"Bioinformatics"},{"key":"ref92","doi-asserted-by":"publisher","first-page":"2401","DOI":"10.1016\/j.csbj.2020.08.031","article-title":"CRISPR-Cas systems: overview, innovations and applications in human disease research and gene therapy","volume":"18","author":"Xu","year":"2020","journal-title":"Comput. Struct. Biotechnol. 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