{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T03:20:22Z","timestamp":1792812022314,"version":"4.5.0"},"reference-count":52,"publisher":"American Society for Microbiology","issue":"12","license":[{"start":{"date-parts":[[2018,6,15]],"date-time":"2018-06-15T00:00:00Z","timestamp":1529020800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"USDA-AFRI","award":["2016-67015-24911"],"award-info":[{"award-number":["2016-67015-24911"]}]},{"name":"USDA-AFRI","award":["2015-68004-23131"],"award-info":[{"award-number":["2015-68004-23131"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2018,6,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:p>Defining the baseline bacterial microbiome is critical to understanding its relationship with health and disease. In broiler chickens, the core microbiome and its possible relationships with health and disease have been difficult to define, due to high variability between birds and flocks. Presented here are data from a large, comprehensive microbiota-based study in commercial broilers. The primary goals of this study included understanding what constitutes the core bacterial microbiota in the broiler gastrointestinal, respiratory, and barn environments; how these core players change across age, geography, and time; and which bacterial taxa correlate with enhanced bird performance in antibiotic-free flocks. Using 2,309 samples from 37 different commercial flocks within a vertically integrated broiler system and metadata from these and an additional 512 flocks within that system, the baseline bacterial microbiota was defined using 16S rRNA gene sequencing. The effects of age, sample type, flock, and successive flock cycles were compared, and results indicate a consistent, predictable, age-dependent bacterial microbiota, irrespective of flock. The tracheal bacterial microbiota of broilers was comprehensively defined, and<jats:named-content content-type=\"genus-species\">Lactobacillus<\/jats:named-content>was the dominant bacterial taxon in the trachea. Numerous bacterial taxa were identified, which were strongly correlated with broiler chicken performance across multiple tissues. While many positively correlated taxa were identified, negatively associated potential pathogens were also identified in the absence of clinical disease, indicating that subclinical dynamics occur that impact performance. Overall, this work provides necessary baseline data for the development of effective antibiotic alternatives, such as probiotics, for sustainable poultry production.<\/jats:p><jats:p><jats:bold>IMPORTANCE<\/jats:bold>Multidrug-resistant bacterial pathogens are perhaps the greatest medical challenge we will face in the 21st century and beyond. Antibiotics are necessary in animal production to treat disease. As such, animal production is a contributor to the problem of antibiotic resistance. Efforts are underway to reduce antibiotic use in animal production. However, we are also challenged to feed the world's increasing population, and sustainable meat production is paramount to providing a safe and quality protein source for human consumption. In the absence of antibiotics, alternative approaches are needed to maintain health and prevent disease, and probiotics have great promise as one such approach. This work paves the way for the development of alternative approaches to raising poultry by increasing our understandings of what defines the poultry microbiome and of how it can potentially be modulated to improve animal health and performance.<\/jats:p>","DOI":"10.1128\/aem.00362-18","type":"journal-article","created":{"date-parts":[[2018,4,5]],"date-time":"2018-04-05T10:48:47Z","timestamp":1522925327000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":133,"title":["A Consistent and Predictable Commercial Broiler Chicken Bacterial Microbiota in Antibiotic-Free Production Displays Strong Correlations with Performance"],"prefix":"10.1128","volume":"84","author":[{"given":"Timothy J.","family":"Johnson","sequence":"first","affiliation":[{"name":"Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA"},{"name":"Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bonnie P.","family":"Youmans","sequence":"additional","affiliation":[{"name":"Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sally","family":"Noll","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, University of Minnesota, Saint Paul, Minnesota, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carol","family":"Cardona","sequence":"additional","affiliation":[{"name":"Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA"},{"name":"Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas P.","family":"Evans","sequence":"additional","affiliation":[{"name":"PMI Nutritional Additives, Shoreview, Minnesota, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T. Peter","family":"Karnezos","sequence":"additional","affiliation":[{"name":"PMI Nutritional Additives, Shoreview, Minnesota, USA"}],"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, Ohio, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael C.","family":"Abundo","sequence":"additional","affiliation":[{"name":"Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA"},{"name":"Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA"}],"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, Ohio, USA"},{"name":"Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0182426"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0184890"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2016.00154"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.vaccine.2017.04.073"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00253-017-8448-5"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-017-0315-1"},{"key":"e_1_3_3_8_2","doi-asserted-by":"crossref","unstructured":"Crisol-Mart\u00ednez E Stanley D Geier MS Hughes RJ Moore RJ. 2017. Sorghum and wheat differentially affect caecal microbiota and associated performance characteristics of meat chickens. PeerJ PrePrints 5:e3071. doi:10.7717\/peerj.3071. e3071","DOI":"10.7717\/peerj.3071"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.02033"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01616-15"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.3382\/ps\/pex014"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0171642"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0027949"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2015.00056"},{"key":"e_1_3_3_15_2","doi-asserted-by":"crossref","unstructured":"Donaldson EE Stanley D Hughes RJ Moore RJ. 2017. The time-course of broiler intestinal microbiota development after administration of cecal contents to incubating eggs. PeerJ PrePrints 5:e3587. doi:10.7717\/peerj.3587. e3587","DOI":"10.7717\/peerj.3587"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2016.00011"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02549-15"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40064-016-2604-8"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.3382\/ps\/pev010"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1080\/03079457.2015.1004622"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0188455"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1111\/1574-6968.12608"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.00593"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00180-10"},{"key":"e_1_3_3_25_2","doi-asserted-by":"crossref","unstructured":"Danzeisen JL Calvert AJ Noll SL McComb B Sherwood JS Logue CM Johnson TJ. 2013. Succession of the turkey gastrointestinal bacterial microbiome related to weight gain. PeerJ PrePrints 1:e237. doi:10.7717\/peerj.237. e237","DOI":"10.7717\/peerj.237"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12744"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-015-0388-6"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0057190"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00165-11"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0723-2020(84)80042-9"},{"key":"e_1_3_3_31_2","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1002\/9781118728291.ch21","volume-title":"Clostridial diseases in animals","author":"Shivaprasad HL","year":"2016","unstructured":"Shivaprasad HL. 2016. Gangrenous dermatitis in poultry, p 255\u2013264. In Uzal FA, Songer JG, Prescott JF, Popoff MR, Clostridial diseases in animals. John Wiley and Sons, Inc, Hoboken, NJ."},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1177\/0300985816658098"},{"key":"e_1_3_3_33_2","first-page":"299","article-title":"Avian pathogenic Escherichia coli (APEC)","volume":"30","author":"Dho-Moulin M","year":"1999","unstructured":"Dho-Moulin M, Fairbrother JM. 1999. Avian pathogenic Escherichia coli (APEC). Vet Res 30:299\u2013316.","journal-title":"Vet Res"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.12.4.627"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2009.08.012"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13567-015-0206-z"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1080\/03079459994704"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.00187"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01927-05"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/ahr\/119.2.519"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.3382\/ps.2012-02822"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1155\/2016\/4320412"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2012.8"},{"key":"e_1_3_3_44_2","first-page":"64","article-title":"Modeling the earth microbiome","volume":"7","author":"Gilbert JA","year":"2012","unstructured":"Gilbert JA, Meyer F. 2012. Modeling the earth microbiome. Microbe 7:64\u201369.","journal-title":"Microbe"},{"key":"e_1_3_3_45_2","doi-asserted-by":"crossref","unstructured":"Gohl DM Vangay P Garbe J MacLean A Hauge A Becker A Gould RJ Clayton JB Johnson TJ Hunter R Knights D Beckman KB. 25 July 2016. Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nat Biotechnol https:\/\/www.nature.com\/articles\/nbt.3601.","DOI":"10.1038\/nbt.3601"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.f.303"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq461"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.112730.110"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.12.8228-8235.2005"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2011.139"},{"key":"e_1_3_3_51_2","doi-asserted-by":"crossref","first-page":"782","DOI":"10.1093\/bioinformatics\/btw725","article-title":"Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions","volume":"33","author":"Zakrzewski M","year":"2017","unstructured":"Zakrzewski M, Proietti C, Ellis JJ, Hasan S, Brion MJ, Berger B, Krause L. 2017. Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions. Bioinformatics 33:782\u2013783.","journal-title":"Bioinformatics"},{"key":"e_1_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2010-11-10-r106"},{"key":"e_1_3_3_53_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-98141-3"}],"container-title":["Applied and Environmental Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AEM.00362-18","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AEM.00362-18","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T23:01:58Z","timestamp":1693609318000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/AEM.00362-18"}},"subtitle":[],"editor":[{"given":"Christopher A.","family":"Elkins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,6,15]]},"references-count":52,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2018,6,15]]}},"alternative-id":["10.1128\/AEM.00362-18"],"URL":"https:\/\/doi.org\/10.1128\/aem.00362-18","relation":{},"ISSN":["0099-2240","1098-5336"],"issn-type":[{"value":"0099-2240","type":"print"},{"value":"1098-5336","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,6,15]]},"assertion":[{"value":"2018-02-13","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2018-04-02","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2018-05-31","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00362-18"}}