{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T15:17:15Z","timestamp":1791818235813,"version":"4.3.4"},"reference-count":52,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,10,4]],"date-time":"2022-10-04T00:00:00Z","timestamp":1664841600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006033","name":"U.S. Poultry and Egg Association","doi-asserted-by":"publisher","award":["714"],"award-info":[{"award-number":["714"]}],"id":[{"id":"10.13039\/100006033","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Physiol."],"abstract":"\n Despite the negative impacts of\n Salmonella<\/jats:italic>\n intestinal colonization on human health,\n Salmonella<\/jats:italic>\n is a natural colonizer of the gastrointestinal tract and is not overtly pathogenic to the avian host. It is of interest to understand the impacts and colonization rates of\n Salmonella<\/jats:italic>\n across selected genetic lines such as slow-growing (SG) and conventional (CONV) broilers. The objective of this study was to characterize the relationship between\n Salmonella enterica<\/jats:italic>\n serovar Typhimurium challenge and selected broiler genetic lines on the ileal and cecal microbiome. Male chicks of two broiler breeds (\n n<\/jats:italic>\n = 156\/breed) were cohoused in an open floor pen until day 7. On day 13, the chicks were then separated into 12 isolators per breed (4 rooms, 6 isolators\/room, 11 chicks\/isolator). On day 14, chicks in the 12 treatment isolators (6 isolators\/breed, 108 total) were challenged with\n Salmonella<\/jats:italic>\n Typhimurium (ST) (1 \u00d7\n \n \n \n \n \n 10<\/mml:mn>\n <\/mml:mrow>\n 8<\/mml:mn>\n <\/mml:msup>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:inline-formula>\n CFU\/ml) via oral gavage while the remaining chicks (\n n<\/jats:italic>\n = 108) were given an oral gavage of sterile tryptic soy broth control (C). Ileal and cecal contents were collected on day 7 from 24 chicks of each breed, and on days 13, 17, 21, and 24 from two chicks per isolator. Samples underwent DNA extraction and PCR amplification to obtain 16S rRNA amplicons that were sequenced with Illumina MiSeq.\n Salmonella<\/jats:italic>\n Typhimurium colonization in the cecum was not different in the two broiler breeds. The main effect of breed had the greatest impact on the ileum microbiota of broilers 7\u00a0days of age where SG broilers had significantly lower diversity and richness compared to CONV broilers (\n p<\/jats:italic>\n &lt; 0.05).\n Salmonella<\/jats:italic>\n Typhimurium challenge consistently caused a change in beta diversity. Regardless of day or intestinal location, challenged broilers had many amplicon sequence variants (ASVs) with decreased abundance of likely beneficial bacteria such as\n Mollicutes<\/jats:italic>\n RF39,\n Shuttleworthia<\/jats:italic>\n ,\n Flavonifractor<\/jats:italic>\n , and\n Oscillibacter<\/jats:italic>\n compared to broilers that were unchallenged with\n Salmonella<\/jats:italic>\n Typhimurium (\n p<\/jats:italic>\n &lt; 0.05). Additionally, there was a difference in the timing of when the microbiota alpha and beta diversity of each breed responded to\n Salmonella<\/jats:italic>\n Typhimurium challenge. Thus, both broiler breed and\n Salmonella<\/jats:italic>\n Typhimurium can impact the intestinal microbiota.\n <\/jats:p>","DOI":"10.3389\/fphys.2022.971255","type":"journal-article","created":{"date-parts":[[2022,10,4]],"date-time":"2022-10-04T01:19:21Z","timestamp":1664846361000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":7,"title":["Ileal and cecal microbiota response to Salmonella Typhimurium challenge in conventional and slow-growing broilers"],"prefix":"10.3389","volume":"13","author":[{"given":"Tessa R.","family":"Sheets","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carmen L.","family":"Wickware","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashlyn M.","family":"Snyder","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shawna L.","family":"Weimer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy A.","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,10,4]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/s0168-1605(02)00251-9","article-title":"Incidence of Salmonella from poultry products and their susceptibility to antimicrobial agents","volume":"82","author":"Antunes","year":"2003","journal-title":"Int. J. Food Microbiol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1016\/S0168-1591(02)00251-4","article-title":"Behaviour of fast- and slow growing broilers to 12 weeks of age and the physical consequences","volume":"81","author":"Bokkers","year":"2003","journal-title":"Appl. Animal Behav. Sci."},{"key":"B3","doi-asserted-by":"publisher","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":"B4","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-Resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"B5","doi-asserted-by":"publisher","first-page":"335","DOI":"10.5194\/aab-62-335-2019","article-title":"Effects of different floor materials on the welfare and behaviour of slow- and fast-growing broilers","volume":"62","author":"\u00c7avu\u015fo\u011flu","year":"2019","journal-title":"Arch. Anim. Breed."},{"key":"B6","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1186\/s13071-020-3897-6","article-title":"Dissection of the cecal microbial community in chickens after Eimeria tenella infection","volume":"13","author":"Chen","year":"2020","journal-title":"Parasites Vectors"},{"key":"B7","doi-asserted-by":"publisher","first-page":"1006","DOI":"10.3382\/ps\/pex359","article-title":"The gastrointestinal microbiome and its association with the control of pathogens in broiler chicken production: A review","volume":"97","author":"Clavijo","year":"2018","journal-title":"Poult. Sci."},{"key":"B8","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1186\/1471-2164-13-213","article-title":"Identification of differentially expressed genes and pathways for intramuscular fat deposition in pectoralis major tissues of fast-and slow-growing chickens","volume":"13","author":"Cui","year":"2012","journal-title":"BMC Genomics"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2015.00056","article-title":"Temporal relationships exist between cecum, ileum, and litter bacterial microbiomes in a commercial Turkey flock, and subtherapeutic penicillin treatment impacts ileum bacterial community establishment","volume":"2","author":"Danzeisen","year":"2015","journal-title":"Front. Veterinary Sci."},{"key":"B10","doi-asserted-by":"publisher","first-page":"e0216080","DOI":"10.1371\/journal.pone.0216080","article-title":"Using fecal microbiota as biomarkers for predictions of performance in the selective breeding process of pedigree broiler breeders","volume":"14","author":"D\u00edaz-S\u00e1nchez","year":"2019","journal-title":"PLoS One"},{"key":"B11","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/j.foodres.2011.03.057","article-title":"Salmonella and broiler processing in the United States: Relationship to foodborne Salmonellosis","volume":"45","author":"Finstad","year":"2012","journal-title":"Food Res. Int."},{"key":"B12","doi-asserted-by":"publisher","first-page":"4273","DOI":"10.1128\/AEM.00598-11","article-title":"Population dynamics of Salmonella enterica serotypes in commercial egg and poultry production","volume":"77","author":"Foley","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1186\/s40168-017-0315-1","article-title":"Feed-additive probiotics accelerate yet antibiotics delay intestinal microbiota maturation in broiler chicken","volume":"5","author":"Gao","year":"2017","journal-title":"Microbiome"},{"key":"B14","doi-asserted-by":"publisher","first-page":"e12660","DOI":"10.1111\/pim.12660","article-title":"Differential immune response to Eimeria maxima infection in fast- and slow-growing broiler genotypes","volume":"41","author":"Giles","year":"2019","journal-title":"Parasite Immunol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1372","DOI":"10.1111\/j.1365-2672.2007.03699.x","article-title":"Effects of zinc bacitracin, bird age and access to range on bacterial microbiota in the ileum and caeca of broiler chickens","volume":"104","author":"Gong","year":"2008","journal-title":"J. Appl. Microbiol."},{"key":"B16","first-page":"81","article-title":"Comparison of resistance of various poultry lines to infection by Salmonella enteritidis","volume":"26","author":"Guillot","year":"1995","journal-title":"Veterinary Res."},{"key":"B17","doi-asserted-by":"publisher","first-page":"101912","DOI":"10.1016\/j.psj.2022.101912","article-title":"Effect of novel Lactobacillus paracaesi microcapsule on growth performance, gut health and microbiome community of broiler chickens","volume":"101","author":"Gyawali","year":"2022","journal-title":"Poult. Sci."},{"key":"B18","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1046\/j.1472-765X.2001.00994.x","article-title":"Prevalence and antimicrobial susceptibility of thermophilic Campylobacter in organic and conventional broiler flocks","volume":"334","author":"Heuer","year":"2001","journal-title":"Lett. Appl. Microbiol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"e56411","DOI":"10.1371\/journal.pone.0056411","article-title":"Comparison of the genome-wide DNA methylation profiles between fast-growing and slow-growing broilers","volume":"8","author":"Hu","year":"2013","journal-title":"PLOS ONE"},{"key":"B20","doi-asserted-by":"publisher","first-page":"1100","DOI":"10.1093\/ps\/82.7.1100","article-title":"Poultry digestive microflora biodiversity as indicated by denaturing gradient gel electrophoresis","volume":"82","author":"Hume","year":"2003","journal-title":"Poult. Sci."},{"key":"B21","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1186\/s40104-021-00597-9","article-title":"Understanding the effects of intramuscular injection and feed withdrawal on Salmonella typhimurium shedding and gut microbiota in pullets","volume":"12","author":"Joat","year":"2021","journal-title":"J. Animal Sci. Biotechnol."},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.00235","article-title":"Host and environmental factors affecting the intestinal microbiota in chickens","volume":"9","author":"Kers","year":"2018","journal-title":"Front. Microbiol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1016\/j.rvsc.2015.07.022","article-title":"Dietary capsicum and curcuma longa oleoresins increase intestinal microbiome and necrotic enteritis in three commercial broiler breeds","volume":"102","author":"Kim","year":"2015","journal-title":"Res. Veterinary Sci."},{"key":"B24","doi-asserted-by":"publisher","first-page":"5112","DOI":"10.1128\/AEM.01043-13","article-title":"Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the miseq Illumina sequencing platform","volume":"79","author":"Kozich","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1080\/00071660310001616174","article-title":"Comparison of natural resistance in seven genetic groups of meat-type chicken","volume":"44","author":"Kramer","year":"2003","journal-title":"Br. Poult. Sci."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2018.00199","article-title":"Evaluation of the epithelial barrier function and ileal microbiome in an established necrotic enteritis challenge model in broiler chickens","volume":"5","author":"Latorre","year":"2018","journal-title":"Front. Veterinary Sci."},{"key":"B27","doi-asserted-by":"publisher","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":"B28","doi-asserted-by":"publisher","first-page":"4159","DOI":"10.3382\/ps\/pey301","article-title":"Consumer preferences for and beliefs about slow growth chicken","volume":"97","author":"Lusk","year":"2018","journal-title":"Poult. Sci."},{"key":"B29","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/ani11010001","article-title":"Multienzyme super-dosing in broiler chicken diets: The implications for gut morphology, microbial profile, nutrient digestibility, and bone mineralization","volume":"11","author":"Madigan-Stretton","year":"2020","journal-title":"Animals"},{"key":"B30","doi-asserted-by":"publisher","first-page":"103823","DOI":"10.1016\/j.fm.2021.103823","article-title":"The changing microbiome of poultry meat; from farm to fridge","volume":"99","author":"Marmion","year":"2021","journal-title":"Food Microbiol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"e0135488","DOI":"10.1371\/journal.pone.0135488","article-title":"Impact of selection for digestive efficiency on microbiota composition in the chicken","volume":"10","author":"Mignon-Grasteau","year":"2015","journal-title":"PloS One"},{"key":"B32","doi-asserted-by":"publisher","first-page":"1407","DOI":"10.5713\/ajas.2011.11038","article-title":"Growth performance, carcass traits and meat quality of slower-growing and fast-growing chickens raised with and without outdoor access","volume":"24","author":"Mikulski","year":"2011","journal-title":"Asian-Australas J. Anim. Sci."},{"key":"B33","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1111\/1574-6968.12608","article-title":"The chicken gastrointestinal microbiome","volume":"360","author":"Oakley","year":"2014","journal-title":"FEMS Microbiol. Lett."},{"key":"B34","doi-asserted-by":"publisher","first-page":"e57190","DOI":"10.1371\/journal.pone.0057190","article-title":"The poultry-associated microbiome: Network analysis and farm-to-fork characterizations","volume":"8","author":"Oakley","year":"2013","journal-title":"PloS One"},{"key":"B35","doi-asserted-by":"publisher","first-page":"3204","DOI":"10.1016\/j.vaccine.2017.04.073","article-title":"Microbial compositional changes in broiler chicken cecal contents from birds challenged with different Salmonella vaccine candidate strains","volume":"35","author":"Park","year":"2017","journal-title":"Vaccine"},{"key":"B36","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1111\/j.1439-0442.2006.00789.x","article-title":"The distribution of Salmonella serovars in chicken and humans in Lithuania","volume":"53","author":"Pieskus","year":"2006","journal-title":"J. Veterinary Med. Ser. A"},{"key":"B37","doi-asserted-by":"publisher","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"Fasttree 2--approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"B38","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1007\/s00284-019-01647-2","article-title":"A preliminary study on probiotic characteristics of Sporosarcina spp. for poultry applications","volume":"76","author":"Priyodip","year":"2019","journal-title":"Curr. Microbiol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"e0225921","DOI":"10.1371\/journal.pone.0225921","article-title":"Cecal microbiome composition and metabolic function in probiotic treated broilers","volume":"15","author":"Rodrigues","year":"2020","journal-title":"PLOS ONE"},{"key":"B42","doi-asserted-by":"publisher","first-page":"104486","DOI":"10.1016\/j.livsci.2021.104486","article-title":"Factors influencing the succession of the fecal microbiome in broilers","volume":"247","author":"Schokker","year":"2021","journal-title":"Livest. Sci."},{"key":"B44","doi-asserted-by":"publisher","first-page":"e91941","DOI":"10.1371\/journal.pone.0091941","article-title":"Extensive microbial and functional diversity within the chicken cecal microbiome","volume":"9","author":"Sergeant","year":"2014","journal-title":"PloS One"},{"key":"B46","doi-asserted-by":"publisher","first-page":"100966","DOI":"10.1016\/j.psj.2020.12.063","article-title":"Comparison of performance and carcass composition of a novel slow-growing crossbred broiler with fast-growing broiler for chicken meat in Australia","volume":"100","author":"Singh","year":"2021","journal-title":"Poult. Sci."},{"key":"B47","doi-asserted-by":"publisher","DOI":"10.3389\/fphys.2022.890848","article-title":"Behavior and immune response of conventional and slow-growing broilers to Salmonella typhimurium","volume":"13","author":"Snyder","year":"2022","journal-title":"Front. Physiology"},{"key":"B48","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1016\/j.vetmic.2013.01.030","article-title":"Identification of chicken intestinal microbiota correlated with the efficiency of energy extraction from feed","volume":"164","author":"Stanley","year":"2013","journal-title":"Veterinary Microbiol."},{"key":"B49","doi-asserted-by":"publisher","first-page":"100955","DOI":"10.1016\/j.psj.2020.12.052","article-title":"In pursuit of a better broiler: Growth, efficiency, and mortality of 16 strains of broiler chickens","volume":"100","author":"Torrey","year":"2021","journal-title":"Poult. Sci."},{"key":"B50","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1016\/j.chom.2008.02.015","article-title":"Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome","volume":"3","author":"Turnbaugh","year":"2008","journal-title":"Cell Host Microbe"},{"key":"B51","doi-asserted-by":"publisher","first-page":"2536","DOI":"10.1128\/aem.66.6.2536-2540.2000","article-title":"Role of volatile fatty acids in development of the cecal microflora in broiler chickens during growth","volume":"66","author":"van der Wielen","year":"2000","journal-title":"Appl. Environ. Microbiol."},{"key":"B52","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1007\/s00248-002-2015-y","article-title":"Spatial and temporal variation of the intestinal bacterial community in commercially raised broiler chickens during growth","volume":"44","author":"van der Wielen","year":"2002","journal-title":"Microb. Ecol."},{"key":"B53","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/j.vetimm.2006.08.007","article-title":"Gene expression responses to a Salmonella infection in the chicken intestine differ between lines","volume":"114","author":"van Hemert","year":"2006","journal-title":"Veterinary Immunol. Immunopathol."},{"key":"B54","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1637\/10442-110212-Reg.1","article-title":"Campylobacter infection has different outcomes in fast- and slow-growing broiler chickens","volume":"57","author":"Williams","year":"2013","journal-title":"Avian Dis."},{"key":"B55","doi-asserted-by":"publisher","first-page":"100935","DOI":"10.1016\/j.psj.2020.12.032","article-title":"Dietary supplementation with Bacillus subtilis promotes growth performance of broilers by altering the dominant microbial community","volume":"100","author":"Zhang","year":"2021","journal-title":"Poult. Sci."},{"key":"B56","doi-asserted-by":"publisher","first-page":"1163","DOI":"10.1038\/srep01163","article-title":"Quantitative genetic background of the host influences gut microbiomes in chickens","volume":"3","author":"Zhao","year":"2013","journal-title":"Sci. Rep."}],"container-title":["Frontiers in Physiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fphys.2022.971255\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,10,4]],"date-time":"2022-10-04T01:19:25Z","timestamp":1664846365000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fphys.2022.971255\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,4]]},"references-count":52,"alternative-id":["10.3389\/fphys.2022.971255"],"URL":"https:\/\/doi.org\/10.3389\/fphys.2022.971255","relation":{},"ISSN":["1664-042X"],"issn-type":[{"value":"1664-042X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,10,4]]},"article-number":"971255"}}