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The caecotrophic and dynamic nature of rabbit gut make them a promising site for probiotic prospecting. This study therefore, investigated the probiotic properties and whole genome sequence profile of Lactic Acid Bacteria (LAB) isolated from the gut microflora of domestic rabbit. Gastrointestinal contents of rabbits were cultured anaerobically on de Mann Rogosa Sharpe (MRS) agar using the pour-plate method. Isolates obtained were initially identified using 16S rRNA sequencing and later using Whole genome sequencing. Probiotic properties of the LAB were determined using conventional in vitro tests such as acid and phenol tolerance, adhesion ability, susceptibility to commonly-used antibiotics and the antimicrobial activity of their cell-free supernatants against selected test microorganisms. Whole genome analysis was carried out on selected isolates to further confirm their probiotic and safety properties.<\/jats:p>\n                  <jats:p>\n                    Three LAB showing probiotic properties were obtained and identified:\n                    <jats:italic>Enterococcus lactis<\/jats:italic>\n                    UIADO22,\n                    <jats:italic>E. lactis<\/jats:italic>\n                    UIADO37, and\n                    <jats:italic>Enterococcus hirae<\/jats:italic>\n                    UIADO30. All isolates were non-haemolytic, DNAse-negative, tolerant to pH 2, and maintaining viability in simulated duodenal juice. They were all sensitive to the tested antibiotics and their cell-free supernatants demonstrated antibacterial activity against selected test bacteria. Whole genome sequencing revealed the absence of vancomycin resistance and virulence genes (\n                    <jats:italic>IS16<\/jats:italic>\n                    ,\n                    <jats:italic>esp<\/jats:italic>\n                    ,\n                    <jats:italic>hyl<\/jats:italic>\n                    ) in the LAB, confirming their safety. Probiotic potential was further supported by the detection of genes encoding bacteriocins such as\n                    <jats:italic>Enterolysin_A<\/jats:italic>\n                    ,\n                    <jats:italic>Subtilosin_A<\/jats:italic>\n                    ,\n                    <jats:italic>Enterocin_L50a\/L50b<\/jats:italic>\n                    ,\n                    <jats:italic>Lanthionine synthetase<\/jats:italic>\n                    , and\n                    <jats:italic>Enterocin_P<\/jats:italic>\n                    . Biosynthetic gene clusters for antimicrobial metabolites, including cyclic-lactone autoinducers, Type III polyketide synthase, terpene precursors, sactipeptides, RIPP-like peptides, and Lanthipeptide Class II, were also detected. Genes associated with stress resistance especially bile, acid and phenol (such as\n                    <jats:italic>dltA<\/jats:italic>\n                    ,\n                    <jats:italic>dltB<\/jats:italic>\n                    ,\n                    <jats:italic>ssb<\/jats:italic>\n                    and\n                    <jats:italic>dltC<\/jats:italic>\n                    ), DNA\/protein repair (such as\n                    <jats:italic>recA<\/jats:italic>\n                    ,\n                    <jats:italic>uvrA<\/jats:italic>\n                    ,\n                    <jats:italic>uvrB<\/jats:italic>\n                    ,and\n                    <jats:italic>recN<\/jats:italic>\n                    ), adhesion and anti-pathogenic activity (such\n                    <jats:italic>agrB<\/jats:italic>\n                    ,\n                    <jats:italic>agrD<\/jats:italic>\n                    ,\n                    <jats:italic>fsrA<\/jats:italic>\n                    ,and\n                    <jats:italic>fbp3)<\/jats:italic>\n                    were detected in the genomes of the three LAB. Overall, the rabbit-derived\n                    <jats:italic>Enterococcus<\/jats:italic>\n                    spp. from this study exhibited both in vitro and genomic characteristics of safe, functional probiotics with strong antimicrobial potential.\n                    <jats:italic>Enterococcus hirae<\/jats:italic>\n                    UIADO30 is the most promising isolate because it lacks plasmids and virulence markers thereby reducing the risk of gene transfer\u2014while carrying markers for bile and acid resistance.\n                  <\/jats:p>","DOI":"10.1186\/s12866-026-04871-6","type":"journal-article","created":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T11:44:17Z","timestamp":1775735057000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Functional and Genomic insights into probiotic Lactic Acid Bacteria isolated from the Gastrointestinal microbiota of domestic rabbits (Oryctolagus cuniculus)"],"prefix":"10.1186","volume":"26","author":[{"given":"Oluwatosin Olubunmi","family":"Oladipo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abimbola Olumide","family":"Adekanmbi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Opeyemi U.","family":"Lawal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valeria R.","family":"Parreira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bolaji Fatai","family":"Oyeyemi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olatunji Abubakar","family":"Jimoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aderemi","family":"Akinyemi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles Ayorinde","family":"Ologunde","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayonposi Bukola","family":"Olaoye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olugbenga David","family":"Oloruntola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mitra","family":"Soni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harmanpreet","family":"Kaur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lawrence","family":"Goodridge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,4,9]]},"reference":[{"issue":"1","key":"4871_CR1","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1007\/s12602-024-10328-x","volume":"17","author":"K Chakravarty","year":"2025","unstructured":"Chakravarty K, Gaur S, Kumar R, Jha NK, Gupta PK. 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