{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T22:14:15Z","timestamp":1794003255857,"version":"4.8.0"},"reference-count":44,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T00:00:00Z","timestamp":1775433600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Southwest Minzu University Research Startup Funds","award":["Grant No. RQD2025005"],"award-info":[{"award-number":["Grant No. RQD2025005"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32472888"],"award-info":[{"award-number":["32472888"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["32472888"],"award-info":[{"award-number":["32472888"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Science and Technology Projects of Xizang Autonomous Region","award":["XZ202501ZY0147"],"award-info":[{"award-number":["XZ202501ZY0147"]}]},{"name":"Sichuan Science and Technology Program","award":["2024YFHZ0373"],"award-info":[{"award-number":["2024YFHZ0373"]}]},{"name":"Program for Pig Industry Technology System Innovation Team of Sichuan Province","award":["sccxtd-2026-08"],"award-info":[{"award-number":["sccxtd-2026-08"]}]},{"name":"he Sichuan Provincial Administration of Traditional Chinese Medicine Science and Technology Research Special Project","award":["2024MS150"],"award-info":[{"award-number":["2024MS150"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Environmental stressors and host genetics influence gut microbiota and antimicrobial resistance, but their combined effects across intestinal niches remain poorly unexplored. We conducted a metagenomic analysis of 60 jejunal and cecal samples from 30 native Chinese pigs across three altitudes (500 m, 1400 m, and 3850 m). The aim was to disentangle the interactive impacts of altitude, breed, and intestinal site on microbiome structure and antibiotic resistome dynamics. The cecal microbiota was taxonomically conserved and strongly associated with breed. Conversely, while jejunal communities exhibited structural variations among the sampled cohorts, differences in alpha diversity (Shannon index, p &lt; 0.01) appeared to be primarily associated with breed differences rather than an independent altitudinal effect. High-altitude Tibetan pigs showed an enrichment of Bifidobacterium and Pseudomonas, which may be linked to hypoxia adaptation. Despite a shared core resistome (88 ARG types), the cecum harbored significantly higher ARG abundance than the jejunum within-breed comparisons of Tibetan pigs across altitudes; this revealed stable ARG profiles (p &gt; 0.05) suggesting that, although some descriptive differences were observed, the independent effect of altitude weakens when the genetic effect is taken into account. Furthermore, carbohydrate-active enzymes (e.g., CBM13, GH33) correlated positively with ARG abundance. In conclusion, the jejunum appears to act as an environmentally responsive niche, while the cecum exhibits a higher ARG abundance that is closely associated with the host breed.<\/jats:p>","DOI":"10.3390\/microorganisms14040832","type":"journal-article","created":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T09:40:31Z","timestamp":1775554831000},"page":"832","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Environmental Altitude and Host Genetics Shape Divergent Microbiota and a Conserved Resistome in Porcine Intestinal Niches"],"prefix":"10.3390","volume":"14","author":[{"given":"Renhao","family":"Lai","sequence":"first","affiliation":[{"name":"College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China"},{"name":"Colleges of Animal Science & Technology, Huazhong Agricultural University, Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuomacairang","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengliang","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China"},{"name":"Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayin","family":"Tong","sequence":"additional","affiliation":[{"name":"College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5082-1227","authenticated-orcid":false,"given":"Zulfiqar","family":"Ahmed","sequence":"additional","affiliation":[{"name":"NCLBG&G, Faculty of Veterinary and Animal Sciences, University of Poonch, Rawalakot 12350, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richeng","family":"Cui","sequence":"additional","affiliation":[{"name":"College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiren","family":"Gu","sequence":"additional","affiliation":[{"name":"College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China"},{"name":"Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8180-0760","authenticated-orcid":false,"given":"Gan","family":"Luo","sequence":"additional","affiliation":[{"name":"College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China"},{"name":"Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,4,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/s44324-025-00066-1","article-title":"Mechanisms and implications of the gut microbial modulation of intestinal metabolic processes","volume":"3","author":"Jyoti","year":"2025","journal-title":"npj Metab. 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