{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T00:11:00Z","timestamp":1778199060087,"version":"3.51.4"},"posted":{"date-parts":[[2026,5,7]]},"group-title":"Epidemiology","reference-count":0,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T00:00:00Z","timestamp":1778112000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.medrxiv.org\/about\/FAQ#license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,5,7]]},"abstract":"<jats:p>Understanding the acquisition and dissemination of microbiomes and antimicrobial resistance genes (ARGs) that circulate across human-animal-environment interfaces remains a central One Health challenge, largely because of complex ecological interactions and multiple confounding factors. Although occupational exposure is known to influence the microbiomes and resistomes of farmers, how environmental compartments involve in this system is unclear. Here, we conducted a one-year longitudinal study combining strain-resolved metagenomics (500 metagenomes) with isolate-based whole-genome sequencing (28 isolates) in an ecologically managed, antibiotic-free farming ecosystem spanning animals, farmers, environmental compartments and non-exposed individuals. Assembling 6,075 species-level genomes, we show that animal-associated occupancy reshapes the microbiome and resistome of occupationally exposed farmers and their surrounding environments. Animals and their associated habitats formed the dominant interface for both strain sharing and ARG dissemination across connected ecological compartments, whereas village residents and surrounding river samples - used as ecological controls - showed limited integration into this sharing network. Tracking a frequently shared lineage further revealed within-lineage genetic turnover together with selection-consistent changes following cross-species spread, suggestive of ecological selection across hosts and habitats. Finally, we identify Klebsiella pneumoniae as the most widespread ESKAPE pathogen in this ecosystem, with repeated occurrence across animal, human and environmental compartments, consistent with a neglected but clinically critical broad profile of ecological generalist. Together, these findings identify animals as central interfaces for microbiome and resistome sharing and show how agricultural ecosystems can sustain circulation of opportunistic pathogens and resistance determinants across human-animal-environment interfaces even in the absence of routine antibiotic use.<\/jats:p>","DOI":"10.64898\/2026.05.06.26352545","type":"posted-content","created":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T23:35:12Z","timestamp":1778196912000},"source":"Crossref","is-referenced-by-count":0,"title":["Longitudinal cross-species transmission of microbiomes and resistomes across farmers, animals and environment"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1212-265X","authenticated-orcid":false,"given":"Jiabao","family":"Xing","sequence":"first","affiliation":[{"name":"Fudan University School of Public Health;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiying","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yichao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leyin","family":"Zheng","sequence":"additional","affiliation":[{"name":"Faculty of Pharmacy and Pharmaceutical Sciences, Monash University;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People Hospital, Fudan University;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Guo","sequence":"additional","affiliation":[{"name":"Kyungpook National University;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianhua","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yushan","family":"Pan","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junkai","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhijun","family":"Jie","sequence":"additional","affiliation":[{"name":"Department of Pulmonary and Critical Care Medicine, Shanghai Fifth Peoples Hospital, Fudan University;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1915-7732","authenticated-orcid":false,"given":"Guy","family":"Baele","sequence":"additional","affiliation":[{"name":"KU Leuven;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Changchao","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alaric","family":"D'Souza","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinxin","family":"Zhao","sequence":"additional","affiliation":[{"name":"Monash University"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jian","family":"Li","sequence":"additional","affiliation":[{"name":"Monash University"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tianmu","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hua","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University;"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.05.06.26352545","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T23:35:12Z","timestamp":1778196912000},"score":1,"resource":{"primary":{"URL":"http:\/\/medrxiv.org\/lookup\/doi\/10.64898\/2026.05.06.26352545"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,7]]},"references-count":0,"URL":"https:\/\/doi.org\/10.64898\/2026.05.06.26352545","relation":{},"subject":[],"published":{"date-parts":[[2026,5,7]]},"subtype":"preprint"}}