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Given the favorable safety profile and beneficial effects on gut health, probiotics have emerged as a promising means for improving constipation. This study investigated the probiotic potential of\n                    <jats:italic>Lacticaseibacillus paracasei<\/jats:italic>\n                    BGI-N2 (BGI-N2) using integrated genomic and phenotypic analyses. The complete genome of BGI-N2 comprised 3,102,337\u00a0bp with a 46.4% GC content and 2,937 coding sequences, including multiple genes related to carbon source fermentation, gastrointestinal tolerance, and antioxidant activities. Furthermore, genomic analysis confirmed the favorable safety profile of BGI-N2. In vitro, this strain showed robust tolerance to extreme gastrointestinal conditions and significant inhibition against common enteropathogens. In constipated zebrafish, it enhanced motility by increasing motilin (MTL) and 5-hydroxytryptamine (5-HT) while decreasing nitric oxide levels. Mechanistically, BGI-N2 upregulated\n                    <jats:italic>kitla<\/jats:italic>\n                    ,\n                    <jats:italic>kitlb<\/jats:italic>\n                    , and\n                    <jats:italic>kitb<\/jats:italic>\n                    genes to promote Cajal interstitial cell development, while enhancing 5-HT accumulation through coordinated regulation of biosynthetic genes (\n                    <jats:italic>tph1a<\/jats:italic>\n                    ,\n                    <jats:italic>tph1b<\/jats:italic>\n                    ,\n                    <jats:italic>tph2<\/jats:italic>\n                    ) and the transporter gene (\n                    <jats:italic>sert<\/jats:italic>\n                    ). This study provides comprehensive genomic insights for BGI-N2 while establishing a theoretical foundation for understanding host-microbe interactions in intestinal motility disorders.\n                  <\/jats:p>","DOI":"10.1186\/s12866-026-04831-0","type":"journal-article","created":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T08:33:03Z","timestamp":1771576383000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Mechanisms of constipation alleviation by Lacticaseibacillus paracasei BGI-N2: insights from genes to phenotypes"],"prefix":"10.1186","volume":"26","author":[{"given":"Xing","family":"Rao","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiang","family":"Luo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wanting","family":"Wei","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benliang","family":"Wei","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinyu","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanhong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yangfeng","family":"Wen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhihui","family":"Ma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhinan","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haifeng","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liang","family":"Xiao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yiyi","family":"Zhong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuanqiang","family":"Zou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,2,20]]},"reference":[{"issue":"1","key":"4831_CR1","doi-asserted-by":"publisher","first-page":"7","DOI":"10.2169\/internalmedicine.2867-23","volume":"64","author":"M Hojo","year":"2025","unstructured":"Hojo M, Shibuya T, Nagahara A. 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