{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T18:13:33Z","timestamp":1790792013544,"version":"4.1.0"},"reference-count":72,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T00:00:00Z","timestamp":1771632000000},"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":"crossref","award":["32560040"],"award-info":[{"award-number":["32560040"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Science and Technology Plan Project of the Xinjiang Production and Construction Corps","award":["2024ZD105"],"award-info":[{"award-number":["2024ZD105"]}]},{"name":"Graduate Innovation Project of Tarim University","award":["TDGRI202306"],"award-info":[{"award-number":["TDGRI202306"]}]},{"name":"Modern Agricultural Industry Technology System of Xinjiang Uygur Autonomous Region","award":["XJARS-12-06"],"award-info":[{"award-number":["XJARS-12-06"]}]},{"name":"Science and Technology Achievement Transformation Demonstration Project of Xinjiang Uygur Autonomous Region","award":["2022NC118"],"award-info":[{"award-number":["2022NC118"]}]},{"name":"Undergraduate Innovation and Entrepreneurship Training Program of Tarim University","award":["202510757003"],"award-info":[{"award-number":["202510757003"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Drawing on two indigenous chicken breeds that have adapted for centuries to the hyper-arid Tarim Basin, namely the Baicheng You Chicken and Hotan Black Chicken, this study provides a high-resolution map of their gut microbiota across the duodenum, jejunum, ileum and cecum and subsequently isolates putative probiotic strains from cecal contents using conventional culture techniques. In the duodenum, Lactobacillus dominated Hotan Black Chicken (43.16%), whereas Ligilactobacillus prevailed in Baicheng You Chicken (37.03%). This segregation persisted in the jejunum, with Lactobacillus accounting for 62.55% of Hotan Black Chicken reads and Ligilactobacillus accounting for 60.76% reads in Baicheng You Chicken. The ileal core of Hotan Black Chicken remained Lactobacillus (50.63%), while Baicheng You Chicken shifted to Enterococcus (32.37%). In the cecum, both breeds converged on the Rikenellaceae RC9 gut group as the single dominant lineage (Hotan Black Chicken, 46.87%; Baicheng You Chicken, 46.23%). At the genus level, Hotan Black Chicken was enriched in Lactobacillus and Ligilactobacillus, whereas Baicheng You Chicken harbored a greater proportion of Enterococcus. Concurrently, eight strains with in vitro probiotic attributes were isolated, four from each breed, identified as Ligilactobacillus salivarius, Limosilactobacillus reuteri, Lactobacillus gallinarum, Enterococcus lactis, Enterococcus faecium, Enterococcus faecalis, and Bacillus velezensis. This study deciphers the intestinal microbiome of two native Tarim Basin chicken breeds, Hotan Black Chicken and Baicheng You Chicken, and mines them for autochthonous probiotic strains. The obtained dataset has established a foundational resource for poultry-related probiotics adapted to extremely arid environments, providing theoretical insights and practical value for poultry nutritionists in water-scarce regions in the future.<\/jats:p>","DOI":"10.3390\/ani16040672","type":"journal-article","created":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T11:39:10Z","timestamp":1771846750000},"page":"672","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Intestinal Microbiota and Probiotic Characteristics of Two Indigenous Chicken Breeds (Hotan Black Chicken and Baicheng You Chicken) from the Tarim Basin"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-2821-1431","authenticated-orcid":false,"given":"Xufeng","family":"Dou","sequence":"first","affiliation":[{"name":"College of Life Science and Technology, Tarim University, Alar 843300, China"},{"name":"Key Laboratory of Conservation and Utilization of Biological Resources in the Tarim Basin, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-4230-0255","authenticated-orcid":false,"given":"Guodong","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-8819-6155","authenticated-orcid":false,"given":"Xiaomei","family":"Dong","sequence":"additional","affiliation":[{"name":"College of Life Science and Technology, Tarim University, Alar 843300, China"},{"name":"Key Laboratory of Conservation and Utilization of Biological Resources in the Tarim Basin, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengqian","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Dong","sequence":"additional","affiliation":[{"name":"Xinjiang Nuoqi Baicheng You Chickens Development Co., Ltd., Aksu 843000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xu\u2019na","family":"Ding","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui\u2019e","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2663-6085","authenticated-orcid":false,"given":"Yuxia","family":"Mei","sequence":"additional","affiliation":[{"name":"College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haihong","family":"Jiao","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1480-9962","authenticated-orcid":false,"given":"Min","family":"Ren","sequence":"additional","affiliation":[{"name":"College of Life Science and Technology, Tarim University, Alar 843300, China"},{"name":"Key Laboratory of Conservation and Utilization of Biological Resources in the Tarim Basin, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,2,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1241214","DOI":"10.1126\/science.1241214","article-title":"Gut microbiota from twins discordant for obesity modulate metabolism in mice","volume":"341","author":"Ridaura","year":"2013","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/j.anifeedsci.2018.10.008","article-title":"The effect of microbiome modulation on the intestinal health of poultry","volume":"250","author":"Kogut","year":"2019","journal-title":"Anim. 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