{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T14:40:41Z","timestamp":1793198441248,"version":"4.5.0"},"reference-count":39,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T00:00:00Z","timestamp":1760918400000},"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>Pneumonia frequently causes mass mortality in raccoon dogs, resulting in significant economic loss. Additionally, raccoon dogs carry various zoonotic pathogens. This study systematically assessed pulmonary pathogens in raccoon dogs and their potential public health implications utilizing 2bRAD microbiome sequencing (2bRAD-M) and viral metagenomics. We analyzed 30 lung tissue samples for microbial composition. Sequencing revealed Pseudomonadota, Ascomycota, and Actinobacteria as dominant phyla and <jats:italic>Acinetobacter<\/jats:italic>, <jats:italic>Escherichia<\/jats:italic>, and <jats:italic>Klebsiella<\/jats:italic> as predominant genera. The most abundant species were <jats:italic>Acinetobacter baumannii<\/jats:italic>, <jats:italic>Escherichia coli<\/jats:italic>, and <jats:italic>Klebsiella pneumoniae<\/jats:italic>. In total, 158 species across 84 genera were identified, including 49 potentially zoonotic species. Viral metagenomics revealed <jats:italic>Peduoviridae<\/jats:italic>, <jats:italic>Rountreeviridae<\/jats:italic>, and <jats:italic>Parvoviridae<\/jats:italic> as dominant families, with <jats:italic>Valbvirus ValB1MD2<\/jats:italic>, <jats:italic>Andhravirus andhra<\/jats:italic>, and <jats:italic>Amdoparvovirus carnivoran3<\/jats:italic> comprising over 80% of the viral composition. These findings highlight the pathogenic complexity of raccoon dog pneumonia and its zoonotic risks, providing crucial insights for disease control and public health management.<\/jats:p>","DOI":"10.3389\/fmicb.2025.1677761","type":"journal-article","created":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T05:24:00Z","timestamp":1760937840000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Lung microbiota of raccoon dogs (Nyctereutes procyonoides) using high-throughput sequencing"],"prefix":"10.3389","volume":"16","author":[{"given":"Wei","family":"Li","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingran","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinjun","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanzhe","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erjun","family":"Ren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,10,20]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"165","DOI":"10.17236\/sat00387","article-title":"Update on the zoonotic potential of Chlamydia","volume":"165","author":"Albini","year":"2023","journal-title":"Schweiz. Arch. Tierheilkd."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"100040","DOI":"10.1016\/j.infpip.2020.100040","article-title":"Molecular characterisation of an Acinetobacter baumannii outbreak","volume":"2","author":"Al-Hassan","year":"2020","journal-title":"Infect. Prev. Pract."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref4","author":"Biagini","year":"2011"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"2450","DOI":"10.1128\/jcm.29.11.2450-2460.1991","article-title":"Proposal of Afipia gen. Nov., with Afipia felis sp. nov. (formerly the cat scratch disease bacillus), Afipia clevelandensis sp. nov. (formerly the Cleveland Clinic Foundation strain), Afipia broomeae sp. nov., and three unnamed genospecies","volume":"29","author":"Brenner","year":"1991","journal-title":"J. Clin. Microbiol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1128\/CMR.17.2.311-322.2004","article-title":"Salmonella enterica serotype Choleraesuis: epidemiology, pathogenesis, clinical disease, and treatment","volume":"17","author":"Chiu","year":"2004","journal-title":"Clin. Microbiol. Rev."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"e1012400","DOI":"10.1371\/journal.ppat.1012400","article-title":"Genomic and functional determinants of host spectrum in group B Streptococcus","volume":"20","author":"Crestani","year":"2024","journal-title":"PLoS Pathog."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"e0154646","DOI":"10.1371\/journal.pone.0154646","article-title":"Composition and predicted metabolic capacity of upper and lower airway microbiota of healthy dogs in relation to the fecal microbiota","volume":"11","author":"Ericsson","year":"2016","journal-title":"PLoS One"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"e02802","DOI":"10.1016\/j.heliyon.2019.e02802","article-title":"Effect of an antimicrobial drug on lung microbiota in healthy dogs","volume":"5","author":"Fastr\u00e8s","year":"2019","journal-title":"Heliyon."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1126\/science.1087139","article-title":"Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China","volume":"302","author":"Guan","year":"2003","journal-title":"Science (New York, N.Y.)"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"1117","DOI":"10.1016\/j.cell.2022.02.014","article-title":"Virome characterization of game animals in China reveals a spectrum of emerging pathogens","volume":"185","author":"He","year":"2022","journal-title":"Cell"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/1751-7915.13353","article-title":"Microbial communities in swine lungs and their association with lung lesions","volume":"12","author":"Huang","year":"2019","journal-title":"Microb. Biotechnol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1007\/s00284-018-1613-y","article-title":"Illumina MiSeq sequencing investigation of microbiota in bronchoalveolar lavage fluid and cecum of the swine infected with PRRSV","volume":"76","author":"Jiang","year":"2019","journal-title":"Curr. Microbiol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"1611","DOI":"10.2147\/IDR.S502175","article-title":"A comprehensive overview of Klebsiella pneumoniae: resistance dynamics, clinical manifestations, and therapeutic options","volume":"18","author":"Jin","year":"2025","journal-title":"Infect. Drug Resist."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"198546","DOI":"10.1016\/j.virusres.2021.198546","article-title":"First report of norovirus sequences isolated from raccoon dogs in mainland China","volume":"305","author":"Li","year":"2021","journal-title":"Virus Res."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1007\/s00438-020-01722-5","article-title":"Comparative analysis of the pulmonary microbiome in healthy and diseased pigs","volume":"296","author":"Li","year":"2021","journal-title":"Mol. Gen. Genomics."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"11","DOI":"10.3390\/vetsci8010011","article-title":"The complex diseases of Staphylococcus pseudintermedius in canines: where to next?","volume":"8","author":"Lynch","year":"2021","journal-title":"Vet. Sci."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"280","DOI":"10.21037\/jtd.2018.12.88","article-title":"The microbiome and lung cancer","volume":"11","author":"Maddi","year":"2019","journal-title":"J. Thorac. Dis."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"562","DOI":"10.3855\/jidc.6912","article-title":"Global impact of torque Teno virus infection in wild and domesticated animals","volume":"9","author":"Manzin","year":"2015","journal-title":"J. Infect. Dev. Ctries."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"e1003531","DOI":"10.1371\/journal.pcbi.1003531","article-title":"Waste not, want not: why rarefying microbiome data is inadmissible","volume":"10","author":"McMurdie","year":"2014","journal-title":"PLoS Comput. Biol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"2763","DOI":"10.3390\/ani13172763","article-title":"Characterization of lung microbiomes in pneumonic Hu sheep using culture technique and 16S rRNA gene sequencing","volume":"13","author":"Miao","year":"2023","journal-title":"Animals"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1006\/bbrc.1997.7765","article-title":"A novel DNA virus (TTV) associated with elevated transaminase levels in posttransfusion hepatitis of unknown etiology","volume":"241","author":"Nishizawa","year":"1997","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"e4682","DOI":"10.1371\/journal.pone.0004682","article-title":"Molecular characterization of highly pathogenic H5N1 avian influenza a viruses isolated from raccoon dogs in China","volume":"4","author":"Qi","year":"2009","journal-title":"PLoS One"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1016\/j.rvsc.2020.11.006","article-title":"Molecular characteristics of H9N2 influenza viruses isolated from farmed raccoon dogs and arctic foxes in China","volume":"135","author":"Qian","year":"2021","journal-title":"Res. Vet. Sci."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"100786","DOI":"10.1016\/j.ijmmb.2024.100786","article-title":"Ralstonia pickettii bacteremia: a retrospective review of records","volume":"53","author":"Sebastian","year":"2025","journal-title":"Indian J. Med. Microbiol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"2085","DOI":"10.3201\/eid2012.140289","article-title":"Novel amdoparvovirus infecting farmed raccoon dogs and arctic foxes","volume":"20","author":"Shao","year":"2014","journal-title":"Emerg. Infect. Dis."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1007\/s00203-022-02832-x","article-title":"Seasonal taxonomic composition of microbial communal shaping the bioaerosols milieu of the urban city of Lanzhou","volume":"204","author":"Sharma Ghimire","year":"2022","journal-title":"Arch. Microbiol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1186\/s12917-019-1856-2","article-title":"First detection and phylogenetic analysis of porcine circovirus type 2 in raccoon dogs","volume":"15","author":"Song","year":"2019","journal-title":"BMC Vet. Res."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1186\/s13059-021-02576-9","article-title":"Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M","volume":"23","author":"Sun","year":"2022","journal-title":"Genome Biol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"354","DOI":"10.3389\/fvets.2019.00354","article-title":"Respiratory dysbiosis in canine bacterial pneumonia: standard culture vs. microbiome sequencing","volume":"6","author":"Vient\u00f3s-Plotts","year":"2019","journal-title":"Front. Vet. Sci."},{"key":"ref31","first-page":"74","article-title":"Statistics and market analysis of mink, fox, and raccoon dog skins produced in China in 2024","volume":"50","author":"Wang","year":"2025","journal-title":"Beijing Leather"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1186\/s12879-025-10484-7","article-title":"Morphological variability of Escherichia coli colonizing human wounds: a case report","volume":"25","author":"Wang","year":"2025","journal-title":"BMC Infect. Dis."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"3325","DOI":"10.3390\/ani12233325","article-title":"First identification and phylogenetic analysis of porcine circovirus type 4 in fur animals in Hebei, China","volume":"12","author":"Wang","year":"2022","journal-title":"Animals"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"1231354","DOI":"10.3389\/fmicb.2023.1231354","article-title":"2bRAD-M reveals the difference in microbial distribution between cancerous and benign ovarian tissues","volume":"14","author":"Wang","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"560","DOI":"10.7883\/yoken.JJID.2022.153","article-title":"Diversity of fungi and bacteria in bronchoalveolar lavage fluid during development of chronic obstructive pulmonary disease","volume":"75","author":"Wu","year":"2022","journal-title":"Jpn. J. Infect. Dis."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"693564","DOI":"10.3389\/fvets.2021.693564","article-title":"Viral metagenomics reveals diverse viruses in the feces samples of raccoon dogs","volume":"8","author":"Yang","year":"2021","journal-title":"Front Vet Sci."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"671","DOI":"10.2217\/fmb-2020-0189","article-title":"Pathogenic mechanism, detection methods and clinical significance of group B Streptococcus","volume":"16","author":"Yuan","year":"2021","journal-title":"Future Microbiol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"1370736","DOI":"10.3389\/fcvm.2024.1370736","article-title":"Rothia dentocariosa endocarditis with brain abscess and splenic abscess: case report and brief review","volume":"11","author":"Zheng","year":"2024","journal-title":"Front. Cardiovasc Med."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"1995","DOI":"10.1111\/tbed.13847","article-title":"Outbreak of a novel disease caused by Staphylococcus pseudintermedius in raccoon dogs (Nyctereutes procyonoides)","volume":"68","author":"Zhu","year":"2021","journal-title":"Transbound. Emerg. Dis."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1677761\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T05:24:00Z","timestamp":1760937840000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1677761\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,20]]},"references-count":39,"alternative-id":["10.3389\/fmicb.2025.1677761"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1677761","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,20]]},"article-number":"1677761"}}