{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T12:33:30Z","timestamp":1793450010615,"version":"4.5.0"},"reference-count":32,"publisher":"American Association of Avian Pathologists (AAAP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Avian Diseases"],"published-print":{"date-parts":[[2020,3,16]]},"abstract":"<jats:p>Although poultry microbiome discoveries are increasing due to the potential impact on poultry performance, studies examining the poultry respiratory microbiome are challenging because of the low microbial biomass and uniqueness of the avian respiratory tract, making it difficult to sample enough material for microbial analysis. Invasive sampling techniques requiring euthanasia are currently used to increase microbial mass for the analysis, thus making it impossible to sample individual birds longitudinally. In this study, we compared invasive (nasal wash, upper tracheal wash, lower tracheal wash, and lower respiratory lavage) and noninvasive (tracheal and choanal swabs) respiratory sampling techniques in two independent experiments by using 4-wk-old chickens. We first established the experimental baseline of respiratory microbiota by using invasive techniques to enable reasonable comparisons between sampling methods and between experiments. Although noninvasive sampling (live-bird swabs) resulted in lower 16S ribosomal RNA gene copy numbers compared with invasive sampling, live swabs were able to detect the dominant microbes captured by invasive techniques. Nevertheless, swabs from euthanatized birds were more reflective of the microbiota captured through invasive methods than live swab. Furthermore, from two separate experiments, we also demonstrated that respiratory microbiota sampling is highly reproducible, especially in the trachea and lower respiratory tract. Our study provides new insights and perspectives on decision making when sampling and studying poultry respiratory microbiota.<\/jats:p>","DOI":"10.1637\/aviandiseases-d-19-00200","type":"journal-article","created":{"date-parts":[[2020,11,5]],"date-time":"2020-11-05T07:27:21Z","timestamp":1604561241000},"page":"277-285","source":"Crossref","is-referenced-by-count":9,"title":["Evaluation of Sampling Methods for the Study of Avian Respiratory Microbiota"],"prefix":"10.1637","volume":"64","author":[{"given":"Michael Edward","family":"C. Abundo","sequence":"first","affiliation":[{"name":"Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John M.","family":"Ngunjiri","sequence":"additional","affiliation":[{"name":"Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kara J. M.","family":"Taylor","sequence":"additional","affiliation":[{"name":"Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hana","family":"Ji","sequence":"additional","affiliation":[{"name":"Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amir","family":"Ghorbani","sequence":"additional","affiliation":[{"name":"Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahesh","family":"KC","sequence":"additional","affiliation":[{"name":"Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed","family":"Elaish","sequence":"additional","affiliation":[{"name":"Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyesun","family":"Jang","sequence":"additional","affiliation":[{"name":"Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bonnie","family":"Weber","sequence":"additional","affiliation":[{"name":"Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy J.","family":"Johnson","sequence":"additional","affiliation":[{"name":"Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chang-Won","family":"Lee","sequence":"additional","affiliation":[{"name":"Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1212","reference":[{"key":"2","doi-asserted-by":"crossref","unstructured":"D Pan  and Z Yu  \"Gut Microbes.\"  5, \"Intestinal microbiome of poultry and its interaction with host and diet.\" 108 (2014)","DOI":"10.4161\/gmic.26945"},{"key":"1","doi-asserted-by":"crossref","unstructured":"MD Dumas, SW Polson, D Ritter, et al.  \"PLOS ONE.\"  6, \"Impacts of poultry house environment on poultry litter bacterial community composition.\" e24785 (2011)","DOI":"10.1371\/journal.pone.0024785"},{"key":"3","doi-asserted-by":"crossref","unstructured":"BB Oakley, HS Lillehoj, MH Kogut, et al.  \"FEMS Microbiol Lett.\"  360, \"The 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Martin,  \"EMBnet.journal.\"  17, \"Cutadapt removes adapter sequences from high-throughput sequencing reads.\" 10 (2011)","DOI":"10.14806\/ej.17.1.200"},{"key":"10","doi-asserted-by":"crossref","unstructured":"SJ Salter, MJ Cox, EM Turek, et al.  \"BMC Biol.\"  12, \"Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.\" 87 (2014)","DOI":"10.1186\/s12915-014-0087-z"},{"key":"17","doi-asserted-by":"publisher","unstructured":"BJ Callahan, PJ McMurdie, MJ Rosen, et al.  \"Nat Methods.\"  13, \"DADA2: High-resolution sample inference from Illumina amplicon data.\" 581 (2016)","DOI":"10.1038\/nmeth.3869"},{"key":"22","doi-asserted-by":"crossref","unstructured":"NA Bokulich, BD Kaehler, JR Rideout, et al.  \"Microbiome.\"  6, \"Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.\" 90 (2018)","DOI":"10.1186\/s40168-018-0470-z"},{"key":"20","doi-asserted-by":"publisher","unstructured":"K Katoh  and DM Standley  \"Mol Biol Evol.\"  30, \"MAFFT multiple sequence alignment software version 7: Improvements in performance and usability.\" 772 (2013)","DOI":"10.1093\/molbev\/mst010"},{"key":"26","doi-asserted-by":"crossref","unstructured":"FS. Nahm,  \"Korean J Anesthesiol.\"  69, \"Nonparametric statistical tests for the continuous data: the basic concept and the practical use.\" 8 (2016)","DOI":"10.4097\/kjae.2016.69.1.8"}],"container-title":["Avian Diseases"],"original-title":[],"link":[{"URL":"https:\/\/bioone.org\/journals\/avian-diseases\/volume-64\/issue-3\/aviandiseases-D-19-00200\/Evaluation-of-Sampling-Methods-for-the-Study-of-Avian-Respiratory\/10.1637\/aviandiseases-D-19-00200.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T12:06:41Z","timestamp":1793448401000},"score":1,"resource":{"primary":{"URL":"https:\/\/bioone.org\/journals\/avian-diseases\/volume-64\/issue-3\/aviandiseases-D-19-00200\/Evaluation-of-Sampling-Methods-for-the-Study-of-Avian-Respiratory\/10.1637\/aviandiseases-D-19-00200.full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,3,16]]},"references-count":32,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2020,9,1]]}},"URL":"https:\/\/doi.org\/10.1637\/aviandiseases-d-19-00200","relation":{},"ISSN":["0005-2086","1938-4351"],"issn-type":[{"value":"0005-2086","type":"print"},{"value":"1938-4351","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,3,16]]}}}