{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,5]],"date-time":"2026-09-05T01:42:08Z","timestamp":1788572528692,"version":"build-2803163510"},"reference-count":46,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T00:00:00Z","timestamp":1742342400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>The rumen microbiome serves as a reservoir of antibiotic-resistance genes (ARGs) with significant implications for public health. This study aimed to investigate the effects of different feeding systems on the rumen resistome in yaks. Yaks that grazed naturally on pasture were used as controls, while the experimental yaks were housed in a high-density pen environment and fed a specially designed diet to optimally meet their nutritional requirements, with increased interactions with farm workers. Metagenomic analysis was performed to assess changes in the rumen microbiome and resistome. Dietary factors influencing changes in the rumen microbiome and resistome were identified. A greater variety of microbiomes associated with carbohydrate digestion was found in yaks under a house-feeding system, such as <jats:italic>Stomatobaculum longum<\/jats:italic> and <jats:italic>Succiniclasticum ruminis.<\/jats:italic> Although grazing yaks exhibited various dominant antibiotic resistance genes (ARGs) at the class level, house-fed yaks were mainly enriched with tetracycline-resistant genes. A random forest model identified specific ARG signatures for each group, such as Sent_cmlA and Sliv_cmlR (Phenicol) and vanHD (Glycopeptide) prevalent in grazing yaks, while tet44, tetW, tetW\/N\/W, and tet40 were abundant in house-fed yaks. ARG interactions varied by feeding system, with signature ARGs in each group showing distinct correlations. Nevertheless, strong correlations among ARGs existed regardless of the treatments, such as the positive correlation between tetW and tetW\/N\/W in both groups. The rumen microbiome was strongly associated with the resistome, especially regarding abundant microbiomes and ARGs. Proteobacteria carrying ARGs were observed in grazing yaks, while Firmicutes served as hosts for ARGs in yaks under a housed feeding system. The specific bacteria contributing to the distinct ARGs in each group were identified. For instance, members of Firmicutes (<jats:italic>Clostridium tepidiprofundi<\/jats:italic>) carried their ARG signatures, such as tet44. These findings emphasized that diet, along with environmental factors and farmworker interactions, contributed to changes in the rumen resistome of yaks. This study is the first to discuss how multiple factors within a feeding regime influence the gut resistome, highlighting the drawbacks of intensive feedings with respect to the gut resistome.<\/jats:p>","DOI":"10.3389\/fmicb.2025.1505938","type":"journal-article","created":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T07:13:11Z","timestamp":1742368391000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Feeding systems influence the rumen resistome in yaks by changing the microbiome"],"prefix":"10.3389","volume":"16","author":[{"given":"Shuli","family":"Yang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jialuo","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jieyi","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huaming","family":"Mao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feilong","family":"Deng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongwang","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianmin","family":"Chai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,3,19]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1186\/s42523-021-00095-3","article-title":"Evolution of rumen and oral microbiota in calves is influenced by age and time of weaning","volume":"3","author":"Amin","year":"2021","journal-title":"Animal Microbiome"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1186\/s40168-017-0378-z","article-title":"The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle","volume":"5","author":"Auffret","year":"2017","journal-title":"Microbiome"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"122","DOI":"10.3389\/fmicb.2019.00122","article-title":"A multi-kingdom study reveals the plasticity of the rumen microbiota in response to a shift from non-grazing to grazing diets in sheep","volume":"10","author":"Belanche","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"5775","DOI":"10.1016\/j.cell.2024.07.039","article-title":"Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome","volume":"187","author":"Carlino","year":"2024","journal-title":"Cell"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"6557","DOI":"10.1111\/1462-2920.15757","article-title":"Solid diet manipulates rumen epithelial microbiota and its interactions with host transcriptomic in young ruminants","volume":"23","author":"Chai","year":"2021","journal-title":"Environ. Microbiol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/s40104-023-00967-5","article-title":"Diet and monensin influence the temporal dynamics of the rumen microbiome in stocker and finishing cattle","volume":"15","author":"Chai","year":"","journal-title":"J Anim Sci Biotechnol"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/s40168-023-01733-5","article-title":"Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids","volume":"12","author":"Chai","year":"","journal-title":"Microbiome"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1007\/s10311-013-0404-8","article-title":"Tetracycline antibiotics in the environment: a review","volume":"11","author":"Daghrir","year":"2013","journal-title":"Environ. Chem. Lett."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"14","DOI":"10.3389\/fmicb.2023.1124917","article-title":"Effects of dietary crude protein levels in the concentrate supplement after grazing on rumen microbiota and metabolites by using metagenomics and metabolomics in Jersey-yak","volume":"14","author":"Dai","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"1398","DOI":"10.3390\/ani12111398","article-title":"Effects of concentrate supplementation on growth performance, rumen fermentation, and bacterial community composition in grazing yaks during the warm season","volume":"12","author":"Dai","year":"2022","journal-title":"Animals"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"215","DOI":"10.3390\/fermentation9030215","article-title":"High-grain diet feeding altered blood metabolites, rumen microbiome, and metabolomics of yaks","volume":"9","author":"Dai","year":"2023","journal-title":"Fermentation"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"280","DOI":"10.1038\/s41579-022-00820-y","article-title":"Molecular mechanisms of antibiotic resistance revisited","volume":"21","author":"Darby","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"150685","DOI":"10.1016\/j.scitotenv.2021.150685","article-title":"Effect of cattle farm exposure on oropharyngeal and gut microbial communities and antibiotic resistance genes in workers","volume":"806","author":"Ding","year":"2022","journal-title":"Sci. Total Environ."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"1858","DOI":"10.1038\/ncomms2860","article-title":"Draft genome sequence of the Tibetan antelope","volume":"4","author":"Ge","year":"2013","journal-title":"Nat. Commun."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1093\/tas\/txab065","article-title":"Effects of supplementation of nonforage fiber source in diets with different starch levels on growth performance, rumen fermentation, nutrient digestion, and microbial flora of Hu lambs","volume":"5","author":"Guo","year":"2021","journal-title":"Transl Anim Sci"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"755255","DOI":"10.3389\/fnut.2021.755255","article-title":"Effects of management, dietary intake, and genotype on rumen morphology, fermentation, and microbiota, and on meat quality in yaks and cattle","volume":"8","author":"Hu","year":"2021","journal-title":"Front. Nutr."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"708512","DOI":"10.3389\/fvets.2021.708512","article-title":"Metagenomic analysis of fecal archaea, bacteria, eukaryota, and virus in przewalski's horses following anthelmintic treatment","volume":"8","author":"Hu","year":"2021","journal-title":"Front Vet Sci"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"682989","DOI":"10.3389\/fmicb.2021.682989","article-title":"Microbiome and metabolomics reveal the effects of different feeding systems on the growth and ruminal development of yaks","volume":"12","author":"Huang","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"1481","DOI":"10.1007\/s10068-022-01157-1","article-title":"Emergence and spread of antibiotic-resistant foodborne pathogens from farm to table","volume":"31","author":"Kim","year":"2022","journal-title":"Food Sci. Biotechnol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"975","DOI":"10.1016\/j.chom.2021.03.017","article-title":"The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition","volume":"29","author":"Li","year":"2021","journal-title":"Cell Host Microbe"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"115591","DOI":"10.1016\/j.anifeedsci.2023.115591","article-title":"Effects of supplementary concentrate and\/or rumen-protected lysine plus methionine on productive performance, milk composition, rumen fermentation, and bacterial population in grazing, lactating yaks","volume":"297","author":"Liu","year":"2023","journal-title":"Anim. Feed Sci. Technol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1186\/2047-217X-1-18","article-title":"SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler","volume":"1","author":"Luo","year":"2012","journal-title":"Gigascience"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1038\/s41564-024-01639-4","article-title":"Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes","volume":"9","author":"Mahmud","year":"2024","journal-title":"Nat. Microbiol."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"176","DOI":"10.3389\/fmicb.2019.00176","article-title":"High prevalence of cefotaxime resistant Bacteria in grazing beef cattle: a cross sectional study","volume":"10","author":"Markland","year":"2019","journal-title":"Front Microbiol"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"3348","DOI":"10.1128\/AAC.00419-13","article-title":"The comprehensive antibiotic resistance database","volume":"57","author":"McArthur","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"926824","DOI":"10.3389\/fsufs.2022.926824","article-title":"One or many? Multi-species livestock grazing influences soil microbiome community structure and antibiotic resistance potential","volume":"6","author":"Mhuireach","year":"2022","journal-title":"Front. Sustain. Food Syst"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"100297","DOI":"10.1016\/j.animal.2021.100297","article-title":"New feeds and new feeding systems in intensive and semi-intensive forage-fed ruminant livestock systems","volume":"15","author":"Moorby","year":"2021","journal-title":"Animal"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"2087","DOI":"10.3168\/jds.2020-19118","article-title":"Gene function adjustment for carbohydrate metabolism and enrichment of rumen microbiota with antibiotic resistance genes during subacute rumen acidosis induced by a high-grain diet in lactating dairy cows","volume":"104","author":"Mu","year":"2021","journal-title":"J. Dairy Sci."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"5623","DOI":"10.1093\/nar\/gkl723","article-title":"MetaGene: prokaryotic gene finding from environmental genome shotgun sequences","volume":"34","author":"Noguchi","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"119","DOI":"10.3389\/fmicb.2020.00119","article-title":"Feed additives differentially impact the epimural microbiota and host epithelial gene expression of the bovine rumen fed diets rich in concentrates","volume":"11","author":"Petri","year":"2020","journal-title":"Front Microbiol"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"10283","DOI":"10.1038\/ncomms10283","article-title":"Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions","volume":"6","author":"Qiu","year":"2015","journal-title":"Nat Commun"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"5252","DOI":"10.1038\/s41467-019-13118-0","article-title":"Characterization of antibiotic resistance genes in the species of the rumen microbiota","volume":"10","author":"Sabino","year":"2019","journal-title":"Nat. Commun."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biol."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1186\/s40643-019-0264-6","article-title":"Systematic review of publicly available non-Dikarya fungal proteomes for understanding their plant biomass-degrading and bioremediation potentials","volume":"6","author":"Sista Kameshwar","year":"2019","journal-title":"Bioresour. Bioprocess."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"aaw1944","DOI":"10.1126\/science.aaw1944","article-title":"Global trends in antimicrobial resistance in animals in low-and middle-income countries","volume":"365","author":"Van Boeckel","year":"2019","journal-title":"Science"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"508","DOI":"10.1038\/s41429-021-00425-2","article-title":"The occurrence of antibiotic resistance genes in the microbiota of yak, beef and dairy cattle characterized by a metagenomic approach","volume":"74","author":"Wang","year":"2021","journal-title":"J. Antibiot."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"e1000352","DOI":"10.1371\/journal.pcbi.1000352","article-title":"Statistical methods for detecting differentially abundant features in clinical metagenomic samples","volume":"5","author":"White","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"642959","DOI":"10.3389\/fmicb.2021.642959","article-title":"Multi-omics analysis reveals a dependent relationship between rumen bacteria and diet of grass-and grain-fed yaks","volume":"12","author":"Xu","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/s40168-021-01211-w","article-title":"Investigation of fiber utilization in the rumen of dairy cows based on metagenome-assembled genomes and single-cell RNA sequencing","volume":"10","author":"Xue","year":"2022","journal-title":"Microbiome"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1038\/s41522-024-00609-2","article-title":"Multiomics of yaks reveals significant contribution of microbiome into host metabolism","volume":"10","author":"Yang","year":"2024","journal-title":"npj Biofilms Microbiomes"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"2991","DOI":"10.3390\/ani12212991","article-title":"Rumen microbiome reveals the differential response of co2 and ch4 emissions of yaks to feeding regimes on the Qinghai-Tibet plateau","volume":"12","author":"Zhang","year":"2022","journal-title":"Animals"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1186\/s44280-023-00029-5","article-title":"Current status and trends in antimicrobial use in food animals in China, 2018\u20132020","volume":"1","author":"Zhao","year":"2023","journal-title":"One Health Adv."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"e0131423","DOI":"10.1128\/spectrum.01314-23","article-title":"Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer","volume":"12","author":"Zhuang","year":"2024","journal-title":"Microbiol Spectr"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1505938\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T07:13:13Z","timestamp":1742368393000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1505938\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,19]]},"references-count":46,"alternative-id":["10.3389\/fmicb.2025.1505938"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1505938","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,19]]},"article-number":"1505938"}}