{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T18:27:06Z","timestamp":1793039226310,"version":"4.5.0"},"reference-count":39,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005270","name":"Fujian Provincial Department of Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005270","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiomes"],"abstract":"<jats:p>\n                    Contamination of duck litter is a major contributor to frequent disease outbreaks in the scaled dry-litter rearing system, posing serious threats to duck health. Although compound microbial intelligent membrane fermentation has multiple advantages, its impacts on the litter virome and resistome remain poorly characterized. This study employed metaviromics to examine the effects of compound microbial intelligent membrane high-temperature fermentation on duck litter from four treatment groups: deep-layer fermentation (DL-D), shallow-layer fermentation (DL-S-NAF), shallow-layer without fermentation (DL-S), and shallow-layer from an antibiotic-using farm without fermentation (DL-S-ANF). We observed that fermentation treatments (DL-D and DL-S-NAF) significantly reduced RNA viral abundance, with a corresponding decreasing trend for DNA viruses. Fermentation treatments also markedly decreased the loads of antibiotic resistance genes (ARGs) including\n                    <jats:italic>sul1<\/jats:italic>\n                    ,\n                    <jats:italic>sul2<\/jats:italic>\n                    ,\n                    <jats:italic>tetB(P)<\/jats:italic>\n                    , and\n                    <jats:italic>qacEdelta1<\/jats:italic>\n                    ; metal resistance genes (\n                    <jats:italic>MRGs<\/jats:italic>\n                    ) including\n                    <jats:italic>arsC<\/jats:italic>\n                    ,\n                    <jats:italic>arsM<\/jats:italic>\n                    ,\n                    <jats:italic>merA<\/jats:italic>\n                    ,\n                    <jats:italic>copR<\/jats:italic>\n                    , and\n                    <jats:italic>corR<\/jats:italic>\n                    ; biocide resistance genes including\n                    <jats:italic>mdeA<\/jats:italic>\n                    ,\n                    <jats:italic>actP<\/jats:italic>\n                    ,\n                    <jats:italic>smdB<\/jats:italic>\n                    ,\n                    <jats:italic>cpxA<\/jats:italic>\n                    , and\n                    <jats:italic>galE<\/jats:italic>\n                    ; and bacterial virulence factors including g\n                    <jats:italic>groEL2<\/jats:italic>\n                    and\n                    <jats:italic>lirB<\/jats:italic>\n                    . In duck litter, viral communities were dominated by\n                    <jats:italic>Uroviricota<\/jats:italic>\n                    and\n                    <jats:italic>Nucleocytoviricota<\/jats:italic>\n                    (DNA viruses) and\n                    <jats:italic>Pisuviricota<\/jats:italic>\n                    and\n                    <jats:italic>Lenarviricota<\/jats:italic>\n                    (RNA viruses), with\n                    <jats:italic>Caudoviricetes<\/jats:italic>\n                    and\n                    <jats:italic>Megaviricetes<\/jats:italic>\n                    as the predominant DNA virus classes. Single-sample metavirome analysis identified 34 viral operational taxonomic units (vOTUs) and 343 viral genes.\n                    <jats:italic>ARG<\/jats:italic>\n                    abundance followed a hierarchical trend of DL-D &amp;lt; DL-S-NAF &amp;lt; DL-S &amp;lt; DL-S-ANF, while MRG abundance showed DL-D &amp;lt; DL-S-NAF &amp;lt; DL-S-ANF &amp;lt; DL-S. Compound microbial intelligent membrane fermentation effectively reduced both DNA and RNA viral abundance, diminished resistance gene loads, and attenuated virulence factors in duck litter. These data indicate that RNA viruses, particularly\n                    <jats:italic>Pisuviricota<\/jats:italic>\n                    , are sensitive bioindicators for ecological health assessment. Additionally, this antibiotic-free fermentation system may provide an important strategy for curbing dissemination of antimicrobial resistance at its source.\n                  <\/jats:p>","DOI":"10.3389\/frmbi.2026.1897965","type":"journal-article","created":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T05:34:52Z","timestamp":1788759292000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Compound microbial intelligent membrane fermentation reshapes the virome and reduces various resistance genes in duck litter"],"prefix":"10.3389","volume":"5","author":[{"given":"Tiecheng","family":"Sun","sequence":"first","affiliation":[{"name":"Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University","place":["Fuzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guiheng","family":"Mei","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University","place":["Fuzhou, China"]},{"name":"Gut Microbiome Research Center, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences","place":["Fuzhou, Fujian, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junru","family":"Mo","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University","place":["Fuzhou, China"]},{"name":"Gut Microbiome Research Center, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences","place":["Fuzhou, Fujian, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meiqin","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University","place":["Fuzhou, China"]},{"name":"Gut Microbiome Research Center, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences","place":["Fuzhou, Fujian, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanmei","family":"Ma","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University","place":["Fuzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengshi","family":"Zhao","sequence":"additional","affiliation":[{"name":"Gut Microbiome Research Center, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences","place":["Fuzhou, Fujian, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Song","family":"Peng","sequence":"additional","affiliation":[{"name":"Gut Microbiome Research Center, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences","place":["Fuzhou, Fujian, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fengqiang","family":"Lin","sequence":"additional","affiliation":[{"name":"Gut Microbiome Research Center, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences","place":["Fuzhou, Fujian, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jilong","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University","place":["Fuzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaxiong","family":"Ma","sequence":"additional","affiliation":[{"name":"Gut Microbiome Research Center, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences","place":["Fuzhou, Fujian, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaolong","family":"Li","sequence":"additional","affiliation":[{"name":"Gut Microbiome Research Center, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences","place":["Fuzhou, Fujian, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,7]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"5444","DOI":"10.1016\/j.biortech.2008.11.027","article-title":"Composting of animal manures and chemical criteria for compost maturity assessment: a review","volume":"100","author":"Bernal","year":"2009","journal-title":"Bioresour. 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