{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T16:41:17Z","timestamp":1790181677385,"version":"4.1.0"},"reference-count":77,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T00:00:00Z","timestamp":1773619200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002383","name":"King Saud University, Riyadh, Saudi Arabia","doi-asserted-by":"publisher","award":["ORF-RC-2026-2600"],"award-info":[{"award-number":["ORF-RC-2026-2600"]}],"id":[{"id":"10.13039\/501100002383","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Veterinary Sciences"],"abstract":"<jats:p>Fecal microbiota are shaped by upstream digestive processes and reflect the outcome of host\u2013microbe interactions, including the resistant microbial fraction that survives to be excreted. This is particularly crucial for assessing zoonotic risks and environmental contamination, as feces are the primary source of dissemination, which is considered an emerging One Health threat. Therefore, we conducted a pilot study to obtain the exploratory findings regarding the cattle GIT microbial composition, potential resistome, and their transmission drivers, such as plasmids, using metagenomic analysis from different districts in Khyber Pakhtunkhwa (KP) province, Pakistan. For this purpose, a total of 150 fecal samples (50 from each district) of healthy cattle were collected from various farms in Mardan (FC1), Peshawar (FC2), and Dera Ismail Khan (FC3) districts. Total DNA from each sample was extracted, pooled (FC1, FC2, and FC3), and sequenced via the Illumina platform. Bacteria were the highly abundant kingdom, while Pseudomonadota and Bacillota were dominant phyla in all samples. Caryophanon latum and Escherichia coli were highly abundant at the species level. A large resistome (40\u201349 genes), including critical genes, such as tet(X), blaOXA-427, and plasmidomes (16\u201322), such as IncF, was detected in the samples. The prominence of certain commensal or opportunistic pathogens in the fecal microbiota may indicate the presence of sub-clinical gastrointestinal disruptions or disease that may affect cattle herds. The fecal resistome is extensive, identifying dairy cattle in these regions as important reservoirs for AMR genes capable of spreading via HGT. This pilot study establishes that the fecal microbiota of dairy cattle in this region are not merely a waste product but a complex ecosystem, rich in microbiota of One Health significance.<\/jats:p>","DOI":"10.3390\/vetsci13030275","type":"journal-article","created":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T13:32:07Z","timestamp":1773667927000},"page":"275","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Shotgun Metagenomics Reveals Microbial Diversity, Resistome, and Plasmidome in Dairy Cattle Feces"],"prefix":"10.3390","volume":"13","author":[{"given":"Shehla","family":"Shehla","sequence":"first","affiliation":[{"name":"Department of Zoology, Abdul Wali Khan University, Garden Campus Mardan, Mardan 23200, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Kashif","family":"Obaid","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, College of Veterinary Medicine, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China"},{"name":"Key Laboratory of Veterinary Parasitology of Gansu Province, Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sadaf","family":"Niaz","sequence":"additional","affiliation":[{"name":"Department of Zoology, Abdul Wali Khan University, Garden Campus Mardan, Mardan 23200, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0485-0390","authenticated-orcid":false,"given":"Munir Ahmad","family":"Khan","sequence":"additional","affiliation":[{"name":"Department of Medicine, Gomal Medical College, Dera Ismail Khan 29050, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6876-4961","authenticated-orcid":false,"given":"Anum Ali","family":"Ahmad","sequence":"additional","affiliation":[{"name":"The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mostafa A.","family":"Abdel-Maksoud","sequence":"additional","affiliation":[{"name":"Research Chair of Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-3942-5455","authenticated-orcid":false,"given":"Abdulaziz","family":"Alamri","sequence":"additional","affiliation":[{"name":"Biochemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salman","family":"Alrokayan","sequence":"additional","affiliation":[{"name":"Research Chair of Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8695-1840","authenticated-orcid":false,"given":"Muhammad","family":"Shoaib","sequence":"additional","affiliation":[{"name":"Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sumaira","family":"Shams","sequence":"additional","affiliation":[{"name":"Department of Zoology, Abdul Wali Khan University, Garden Campus Mardan, Mardan 23200, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiaoyun","family":"Ren","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, College of Veterinary Medicine, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China"},{"name":"Key Laboratory of Veterinary Parasitology of Gansu Province, Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China"},{"name":"Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education, Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"343","DOI":"10.3168\/jds.S0022-0302(79)83246-4","article-title":"Role of the Dairy Cow in World Food Production","volume":"62","author":"Hodgson","year":"1979","journal-title":"J. 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