{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T11:41:36Z","timestamp":1777981296409,"version":"3.51.4"},"reference-count":40,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2022,1,10]],"date-time":"2022-01-10T00:00:00Z","timestamp":1641772800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Saskatchewan Agricultural Development Fund","award":["#20060116, #20130170, #20160253"],"award-info":[{"award-number":["#20060116, #20130170, #20160253"]}]},{"DOI":"10.13039\/501100005019","name":"Beef Cattle Research Council","doi-asserted-by":"publisher","award":["ANH.30.17"],"award-info":[{"award-number":["ANH.30.17"]}],"id":[{"id":"10.13039\/501100005019","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>A comparative study of microbiota of the respiratory tract and joints of bovine respiratory disease (BRD) cattle mortalities was undertaken. Nasopharynx, trachea, lung and joint samples were collected from 32 cattle that died of BRD, \u201ccases\u201d, and 8 that died of other causes, \u201ccontrols\u201d. Bacterial diversity was lower (p &lt; 0.05) in the nasopharynx, trachea and lungs of cases as compared to controls. In cases, alpha-diversity (p &lt; 0.05) was lower in the lungs and joints than the nasopharynx. Proteobacteria, Tenericutes, Bacteroidetes, Firmicutes and Actinobacteria were the most abundant phyla in all samples. Relative abundances of Mycoplasma spp. in the lung, Pasteurella spp. in the trachea and lung, and Histophilus spp. in the lung, trachea and nasopharynx of cases were higher (p &lt; 0.001) than controls. Mycoplasma spp. comprised 20.5% of bacterial flora in the joint, 36.0% in the lung, 22.4% in the trachea and 8.8% in the nasopharynx. Mannheimia spp. (21.8%) and Histophilus spp. (10.4%) were more abundant in lungs. Cattle that died of BRD possessed less diverse respiratory microbiomes with a higher abundance of respiratory pathogens. Mycoplasma spp. were prominent members of pneumonic lungs and joints displaying septic arthritis.<\/jats:p>","DOI":"10.3390\/microorganisms10010134","type":"journal-article","created":{"date-parts":[[2022,1,10]],"date-time":"2022-01-10T22:03:13Z","timestamp":1641852193000},"page":"134","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Comparative Microbiomes of the Respiratory Tract and Joints of Feedlot Cattle Mortalities"],"prefix":"10.3390","volume":"10","author":[{"given":"Chunli","family":"Li","sequence":"first","affiliation":[{"name":"Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3307-4666","authenticated-orcid":false,"given":"Rahat","family":"Zaheer","sequence":"additional","affiliation":[{"name":"Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0009-0432","authenticated-orcid":false,"given":"Andrea","family":"Kinnear","sequence":"additional","affiliation":[{"name":"Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6239-4496","authenticated-orcid":false,"given":"Murray","family":"Jelinski","sequence":"additional","affiliation":[{"name":"Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8266-6513","authenticated-orcid":false,"given":"Tim A.","family":"McAllister","sequence":"additional","affiliation":[{"name":"Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,1,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1016\/S0749-0720(15)30302-9","article-title":"Economic Impact Associated with Respiratory Disease in Beef Cattle","volume":"13","author":"Griffin","year":"1997","journal-title":"Vet. Clin. N. Am. Food Anim. Pract."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"300","DOI":"10.2460\/ajvr.74.2.300","article-title":"Evaluation of Economic and Performance Outcomes Associated with the Number of Treatments after an Initial Diagnosis of Bovine Respiratory Disease in Commercial Feeder Cattle","volume":"74","author":"Cernicchiaro","year":"2013","journal-title":"Am. J. Vet. Res."},{"key":"ref_3","first-page":"189","article-title":"Market Impacts of Reducing the Prevalence of Bovine Respiratory Disease in United States Beef Cattle Feedlots. Front","volume":"4","author":"Johnson","year":"2017","journal-title":"Vet. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/s13028-015-0099-x","article-title":"Mycoplasma Bovis Infections in Swiss Dairy Cattle: A Clinical Investigation","volume":"57","author":"Aebi","year":"2015","journal-title":"Acta Vet. Scand."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1016\/j.vetmic.2015.07.031","article-title":"The Nasopharyngeal Microbiota of Feedlot Cattle That Develop Bovine Respiratory Disease","volume":"180","author":"Holman","year":"2015","journal-title":"Vet. Microbiol."},{"key":"ref_6","first-page":"145","article-title":"Update on Bacterial Pathogenesis in BRD. Anim","volume":"10","author":"Confer","year":"2009","journal-title":"Health Res. Rev."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"15557","DOI":"10.1038\/srep15557","article-title":"The Nasopharyngeal Microbiota of Feedlot Cattle","volume":"5","author":"Holman","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Holman, D.B., Timsit, E., Amat, S., Abbott, D.W., Buret, A.G., and Alexander, T.W. (2017). The Nasopharyngeal Microbiota of Beef Cattle before and after Transport to a Feedlot. BMC Microbiol., 17.","DOI":"10.1186\/s12866-017-0978-6"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1002\/cfg.474","article-title":"Effect of Stress on Viral\u2013Bacterial Synergy in Bovine Respiratory Disease: Novel Mechanisms to Regulate Inflammation","volume":"6","author":"Hodgson","year":"2005","journal-title":"Comp. Funct. Genom."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1017\/S1466252307001375","article-title":"Mannheimia Haemolytica and Bovine Respiratory Disease","volume":"8","author":"Rice","year":"2007","journal-title":"Anim. Health Res. Rev."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1177\/0300985813502821","article-title":"Failure of Respiratory Defenses in the Pathogenesis of Bacterial Pneumonia of Cattle","volume":"51","author":"Caswell","year":"2014","journal-title":"Vet. Pathol."},{"key":"ref_12","first-page":"473","article-title":"Microbiological and Histopathological Findings in Cases of Fatal Bovine Respiratory Disease of Feedlot Cattle in Western Canada","volume":"49","author":"Booker","year":"2008","journal-title":"Can. Vet. J."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Dungworth, D., Tyler, W., and Plopper, C. (1985). Morphological Methods for Gross and Microscopic Pathology. Toxicology of Inhaled Materials, Springer.","DOI":"10.1007\/978-3-642-69521-6_9"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1177\/104063870601800104","article-title":"Diseases and Pathogens Associated with Mortality in Ontario Beef Feedlots","volume":"18","author":"Gagea","year":"2006","journal-title":"J. Vet. Diagn. Investig."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/j.cvfa.2008.10.011","article-title":"Mycoplasma Bovis Infections in Young Calves","volume":"25","author":"Maunsell","year":"2009","journal-title":"Vet. Clin. N. Am. Food Anim. Pract."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.vetmic.2018.06.007","article-title":"Distinct Bacterial Metacommunities Inhabit the Upper and Lower Respiratory Tracts of Healthy Feedlot Cattle and Those Diagnosed with Bronchopneumonia","volume":"221","author":"Timsit","year":"2018","journal-title":"Vet. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1186\/s40168-017-0372-5","article-title":"Characterization of the Upper and Lower Respiratory Tract Microbiota in Piedmontese Calves","volume":"5","author":"Nicola","year":"2017","journal-title":"Microbiome"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.vetmic.2016.03.020","article-title":"Evolution of the Nasopharyngeal Microbiota of Beef Cattle from Weaning to 40 Days after Arrival at a Feedlot","volume":"187","author":"Timsit","year":"2016","journal-title":"Vet. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.3168\/jds.2016-11522","article-title":"Deciphering Upper Respiratory Tract Microbiota Complexity in Healthy Calves and Calves That Develop Respiratory Disease Using Shotgun Metagenomics","volume":"100","author":"Gaeta","year":"2017","journal-title":"J. Dairy Sci."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.vetmic.2017.07.006","article-title":"Disparity in the Nasopharyngeal Microbiota between Healthy Cattle on Feed, at Entry Processing and with Respiratory Disease","volume":"208","author":"Zeineldin","year":"2017","journal-title":"Vet. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"5890","DOI":"10.1038\/s41598-018-24280-8","article-title":"Impact of Sequencing Depth on the Characterization of the Microbiome and Resistome","volume":"8","author":"Zaheer","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e00009-15","DOI":"10.1128\/mSystems.00009-15","article-title":"Improved Bacterial 16S RRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys","volume":"1","author":"Walters","year":"2016","journal-title":"mSystems"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Na\u00efve Bayesian Classifier for Rapid Assignment of RRNA Sequences into the New Bacterial Taxonomy","volume":"73","author":"Wang","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1038\/ismej.2011.139","article-title":"An Improved Greengenes Taxonomy with Explicit Ranks for Ecological and Evolutionary Analyses of Bacteria and Archaea","volume":"6","author":"McDonald","year":"2012","journal-title":"ISME J."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"McMurdie, P.J., and Holmes, S. (2013). Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0061217"},{"key":"ref_27","unstructured":"Oksanen, J., Blanchet, F.G., Kindt, R., Legendre, P., Minchin, P.R., O\u2019hara, R., Simpson, G.L., Solymos, P., Stevens, M.H.H., and Wagner, H. (2021, December 14). Vegan: Community Ecology Package. R Package Version 2.2\u20131. Available online: http:\/\/cran.rproject.org\/package=vegan."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v067.i01","article-title":"Fitting Linear Mixed-Effects Models Using Lme4","volume":"67","author":"Bates","year":"2015","journal-title":"J. Stat. Softw."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"29050","DOI":"10.1038\/srep29050","article-title":"The Upper Respiratory Tract Microbiome and Its Potential Role in Bovine Respiratory Disease and Otitis Media","volume":"6","author":"Lima","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1007\/s00248-019-01361-3","article-title":"Lower Respiratory Tract Microbiome and Resistome of Bovine Respiratory Disease Mortalities","volume":"78","author":"Klima","year":"2019","journal-title":"Microb. Ecol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1016\/j.vetmic.2018.08.007","article-title":"Effects of Transportation to and Co-Mingling at an Auction Market on Nasopharyngeal and Tracheal Bacterial Communities of Recently Weaned Beef Cattle","volume":"223","author":"Stroebel","year":"2018","journal-title":"Vet. Microbiol."},{"key":"ref_33","first-page":"1019","article-title":"Chronic Pneumonia and Polyarthritis Syndrome in a Feedlot Calf","volume":"47","author":"Krysak","year":"2006","journal-title":"Can. Vet. J."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1663","DOI":"10.14202\/vetworld.2018.1663-1668","article-title":"Mycoplasma Bovis Arthritis and Pneumonia in Calves in Jordan: An Emerging Disease","volume":"11","author":"Hananeh","year":"2018","journal-title":"Vet. World"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"995","DOI":"10.2460\/javma.252.8.995","article-title":"Clinical Findings and Diagnostic Test Results for Calves with Septic Arthritis: 64 Cases (2009\u20132014)","volume":"252","author":"Constant","year":"2018","journal-title":"J. Am. Vet. Med. Assoc."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1907","DOI":"10.1128\/jcm.25.10.1907-1910.1987","article-title":"Relationship of CDC group EO-2 and Psychrobacter immobilis","volume":"25","author":"Hudson","year":"1987","journal-title":"J. Clin. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.vetmic.2008.12.024","article-title":"Respiratory Disease in Calves: Microbiological Investigations on Trans-Tracheally Aspirated Bronchoalveolar Fluid and Acute Phase Protein Response","volume":"137","author":"Angen","year":"2009","journal-title":"Vet. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/j.cvfa.2010.04.004","article-title":"Bacterial Pathogens of the Bovine Respiratory Disease Complex","volume":"26","author":"Griffin","year":"2010","journal-title":"Vet. Clin. N. Am. Food Anim. Pract."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1111\/jvim.12531","article-title":"Respiratory Pathogens in Qu\u00e9bec Dairy Calves and Their Relationship with Clinical Status, Lung Consolidation, and Average Daily Gain","volume":"29","author":"Francoz","year":"2015","journal-title":"J. Vet. Intern. Med."},{"key":"ref_40","first-page":"38","article-title":"Characterization of Mannheimia haemolytica Isolated from Feedlot Cattle That Were Healthy or Treated for Bovine Respiratory Disease","volume":"78","author":"Klima","year":"2014","journal-title":"Can. J. Vet. Res."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/1\/134\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T14:01:51Z","timestamp":1760364111000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/1\/134"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,10]]},"references-count":40,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,1]]}},"alternative-id":["microorganisms10010134"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms10010134","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,1,10]]}}}