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Lacking systematic methods, understanding probiotic community traits becomes challenging, leading to various conclusions about their probiotic effects among different publications. We developed language model\u2013based metaProbiotics to rapidly detect probiotic bins from metagenomes, demonstrating superior performance in simulated benchmark datasets. Testing on gut metagenomes from probiotic-treated individuals, it revealed the probioticity of intervention strains\u2013derived bins and other probiotic-associated bins beyond the training data, such as a plasmid-like bin. Analyses of these bins revealed various probiotic mechanisms and bai operon as probiotic Ruminococcaceae\u2019s potential marker. In different health\u2013disease cohorts, these bins were more common in healthy individuals, signifying their probiotic role, but relevant health predictions based on the abundance profiles of these bins faced cross-disease challenges. To better understand the heterogeneous nature of probiotics, we used metaProbiotics to construct a comprehensive probiotic genome set from global gut metagenomic data. Module analysis of this set shows that diseased individuals often lack certain probiotic gene modules, with significant variation of the missing modules across different diseases. Additionally, different gene modules on the same probiotic have heterogeneous effects on various diseases. We thus believe that gene function integrity of the probiotic community is more crucial in maintaining gut homeostasis than merely increasing specific gene abundance, and adding probiotics indiscriminately might not boost health. We expect that the innovative language model\u2013based metaProbiotics tool will promote novel probiotic discovery using large-scale metagenomic data and facilitate systematic research on bacterial probiotic effects. The metaProbiotics program can be freely downloaded at https:\/\/github.com\/zhenchengfang\/metaProbiotics.<\/jats:p>","DOI":"10.1093\/bib\/bbae085","type":"journal-article","created":{"date-parts":[[2024,3,15]],"date-time":"2024-03-15T06:30:57Z","timestamp":1710484257000},"source":"Crossref","is-referenced-by-count":33,"title":["metaProbiotics: a tool for mining probiotic from metagenomic binning data based on a language model"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7793-2509","authenticated-orcid":false,"given":"Shufang","family":"Wu","sequence":"first","affiliation":[{"name":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"},{"name":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"}]},{"given":"Tao","family":"Feng","sequence":"additional","affiliation":[{"name":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"},{"name":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"}]},{"given":"Waijiao","family":"Tang","sequence":"additional","affiliation":[{"name":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"},{"name":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"}]},{"given":"Cancan","family":"Qi","sequence":"additional","affiliation":[{"name":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"},{"name":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"}]},{"given":"Jie","family":"Gao","sequence":"additional","affiliation":[{"name":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"},{"name":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"},{"name":"Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou Medical University , Guangzhou , China"}]},{"given":"Xiaolong","family":"He","sequence":"additional","affiliation":[{"name":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"},{"name":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"}]},{"given":"Jiaxuan","family":"Wang","sequence":"additional","affiliation":[{"name":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"},{"name":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2472-8541","authenticated-orcid":false,"given":"Hongwei","family":"Zhou","sequence":"additional","affiliation":[{"name":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"},{"name":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0137-4683","authenticated-orcid":false,"given":"Zhencheng","family":"Fang","sequence":"additional","affiliation":[{"name":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"},{"name":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China"}]}],"member":"286","published-online":{"date-parts":[[2024,3,14]]},"reference":[{"issue":"8","key":"2024031506262166000_ref1","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1038\/nrgastro.2014.66","article-title":"Expert consensus document. 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