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First, we applied multiple machine learning models to determine if we can distinguish strains of the same species isolated from two different habitats based on their gene content. Surprisingly, we show that no species is differentially adapted to the oral cavity versus the human gut, or food versus the human gut, while only Lactobacillus crispatus showed specialization to the human urogenital system versus human gut. We then asked which species of Lactobacillaceae are habitat-specialized and how they could be identified. Using multiple lifestyle predictors incorporated in logistic regression models, we found that Limosilactobacillus reuteri, Ligilactobacillus ruminis, L. salivarius, L. crispatus, and L. mucosae displayed the highest degrees of host specialization. Applying our microbial genome-wide association study tool, aurora, to these species identified genes encoding adhesins and bacteriocins as the strongest and most common adaptation factors. This work establishes a generalizable framework for identifying novel species\u2013habitat pairs with strong evidence of specialization and for uncovering the genomic features underlying within-species host and habitat adaptation.<\/jats:p>","DOI":"10.1093\/ismejo\/wrag198","type":"journal-article","created":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T11:58:04Z","timestamp":1785412684000},"source":"Crossref","is-referenced-by-count":1,"title":["Genome-wide association analysis reveals specialization to hosts and niches in multiple species of the\n                    <i>Lactobacillaceae<\/i>"],"prefix":"10.1093","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1709-8289","authenticated-orcid":false,"given":"Dalimil","family":"Bujdo\u0161","sequence":"first","affiliation":[{"name":"APC Microbiome Ireland, University College Cork, National University of Ireland , Cork, T12 K8AF ,","place":["Ireland"]},{"name":"School of Microbiology, University College Cork, National University of Ireland , Cork, T12 K8AF ,","place":["Ireland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jens","family":"Walter","sequence":"additional","affiliation":[{"name":"APC Microbiome Ireland, University College Cork, National University of Ireland , Cork, T12 K8AF ,","place":["Ireland"]},{"name":"School of Microbiology, University College Cork, National University of Ireland , Cork, T12 K8AF ,","place":["Ireland"]},{"name":"Department of Medicine, University College Cork, National University of Ireland , Cork, T12 K8AF ,","place":["Ireland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5377-0824","authenticated-orcid":false,"given":"Paul W","family":"O\u2019Toole","sequence":"additional","affiliation":[{"name":"APC Microbiome Ireland, University College Cork, National University of Ireland , Cork, T12 K8AF ,","place":["Ireland"]},{"name":"School of Microbiology, University College Cork, National 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