{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T08:59:45Z","timestamp":1776502785746,"version":"3.51.2"},"reference-count":54,"publisher":"Elsevier BV","issue":"11","license":[{"start":{"date-parts":[[2019,11,1]],"date-time":"2019-11-01T00:00:00Z","timestamp":1572566400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2019,11,1]],"date-time":"2019-11-01T00:00:00Z","timestamp":1572566400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2019,10,21]],"date-time":"2019-10-21T00:00:00Z","timestamp":1571616000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Poultry Science"],"published-print":{"date-parts":[[2019,11]]},"DOI":"10.3382\/ps\/pez380","type":"journal-article","created":{"date-parts":[[2019,7,26]],"date-time":"2019-07-26T05:20:46Z","timestamp":1564118446000},"page":"5809-5819","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":21,"title":["Changes in cecum microbial community in response to total sulfur amino acid (TSAA: DL-methionine) in antibiotic-free and supplemented poultry birds"],"prefix":"10.1016","volume":"98","author":[{"given":"S","family":"Kumar","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"P","family":"Adhikari","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"B","family":"Oakley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"W K","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.3382\/ps\/pez380_bib1","first-page":"2066","article-title":"A new method for non-parametric multivariate analysis of variance","volume":"26","author":"Anderson","year":"2001","journal-title":"Mol. Nutr. Food Res."},{"key":"10.3382\/ps\/pez380_bib2","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/j.anifeedsci.2016.05.004","article-title":"Interaction between chicken intestinal microbiota and protein digestion","volume":"221","author":"Apajalahti","year":"2016","journal-title":"Anim. Feed. Sci. Technol."},{"key":"10.3382\/ps\/pez380_bib3","doi-asserted-by":"crossref","first-page":"e02517","DOI":"10.1128\/AEM.02526-17","article-title":"An attenuated Salmonella enterica serovar Typhimurium strain and galacto-oligosaccharide accelerate clearance of Salmonella infects in poultry through modification of gut microbiome","volume":"84","author":"Azcarate-Peril","year":"2018","journal-title":"Appl. Environ. Microbiol"},{"key":"10.3382\/ps\/pez380_bib4","doi-asserted-by":"crossref","first-page":"737","DOI":"10.3382\/ps.0750737","article-title":"Sulfur amino acid requirement and cystine replacement value of broiler chicks during the period three to six weeks posthatching","volume":"75","author":"Baker","year":"1996","journal-title":"Poult. Sci."},{"key":"10.3382\/ps\/pez380_bib5","doi-asserted-by":"crossref","first-page":"2","DOI":"10.3389\/fvets.2016.00002","article-title":"Development of the chick microbiome: how early exposure influences future microbial diversity","volume":"3","author":"Ballou","year":"2016","journal-title":"Front. Vet. Sci."},{"key":"10.3382\/ps\/pez380_bib6","series-title":"lme4: Linear mixed-effects models using S4 classes","author":"Bates","year":"2013"},{"key":"10.3382\/ps\/pez380_bib7","doi-asserted-by":"crossref","first-page":"169","DOI":"10.2141\/jpsa.46.169","article-title":"Role of dietary methionine in poultry production","volume":"46","author":"Bunchasak","year":"2009","journal-title":"Poult. Sci."},{"key":"10.3382\/ps\/pez380_bib8","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. Meth."},{"key":"10.3382\/ps\/pez380_bib9","series-title":"Analysis of diversity and function of the human small intestinal microbiota","author":"Carien","year":"2009"},{"key":"10.3382\/ps\/pez380_bib10","doi-asserted-by":"crossref","first-page":"285","DOI":"10.2217\/17460913.2.3.285","article-title":"Microbial communities in the human small intestine: coupling diversity to metagenomics","volume":"2","author":"Carien","year":"2007","journal-title":"Future Microbiol."},{"key":"10.3382\/ps\/pez380_bib11","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1099\/ijs.0.63686-0","article-title":"Sporacetigenium mesophilum gen. nov., sp. nov., isolated from an anaerobic digester treating municipal solid waste and sewage","volume":"56","author":"Chen","year":"2006","journal-title":"Int. J. Syst. Evol. Microbiol"},{"key":"10.3382\/ps\/pez380_bib12","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1111\/j.1442-9993.1993.tb00438.x","article-title":"Non-parametric multivariate analyses of changes in community structure","volume":"18","author":"Clarke","year":"1993","journal-title":"Austr. J. Ecol."},{"key":"10.3382\/ps\/pez380_bib13","doi-asserted-by":"crossref","first-page":"D141","DOI":"10.1093\/nar\/gkn879","article-title":"The ribosomal database project: improved alignments and new tools for rRNA analysis","volume":"37","author":"Cole","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"10.3382\/ps\/pez380_bib14","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1099\/00207713-44-4-812","article-title":"The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations","volume":"44","author":"Collins","year":"1994","journal-title":"Int. J. Syst. Bacteriol."},{"key":"10.3382\/ps\/pez380_bib15","doi-asserted-by":"crossref","first-page":"1768","DOI":"10.2741\/3820","article-title":"Amino-acid metabolism in intestinal bacteria: links between gut ecology and host health","volume":"16","author":"Dai","year":"2011","journal-title":"Front. Biosci."},{"key":"10.3382\/ps\/pez380_bib16","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1007\/s00726-010-0556-9","article-title":"Utilization of amino-acids by bacteria from the pig small intestine","volume":"39","author":"Dai","year":"2010","journal-title":"Amino Acids"},{"key":"10.3382\/ps\/pez380_bib17","doi-asserted-by":"crossref","first-page":"e237","DOI":"10.7717\/peerj.237","article-title":"Succession of the turkey gastrointestinal bacterial microbiome related to weight gain","volume":"1","author":"Danzeisen","year":"2013","journal-title":"Peer J"},{"key":"10.3382\/ps\/pez380_bib18","first-page":"2","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":"2015","author":"Danzeisen","year":"2015","journal-title":"Front. Vet. Sci."},{"key":"10.3382\/ps\/pez380_bib19","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0027949","article-title":"Modulations of the chicken cecal microbiome and metagenome in response to anticoccidial and growth promoter treatment","volume":"6","author":"Danzeisen","year":"2011","journal-title":"PLoS One."},{"key":"10.3382\/ps\/pez380_bib20","doi-asserted-by":"crossref","first-page":"2815","DOI":"10.1128\/AEM.72.4.2815-2823.2006","article-title":"Characterization of intestinal microbiota and response to dietary virginiamycin supplementation in the broiler chicken","volume":"72","author":"Dumonceaux","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"10.3382\/ps\/pez380_bib21","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0042543","article-title":"Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels","volume":"7","author":"Faircloth","year":"2012","journal-title":"PLoS One."},{"key":"10.3382\/ps\/pez380_bib22","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1016\/j.syapm.2010.04.003","article-title":"A small variation in diet influences the Lactobacillus strain composition in the crop of broiler chickens","volume":"33","author":"Hammons","year":"2010","journal-title":"Syst. Appl. Microbiol"},{"key":"10.3382\/ps\/pez380_bib23","author":"Jari Oksanen"},{"key":"10.3382\/ps\/pez380_bib24","doi-asserted-by":"crossref","first-page":"2703","DOI":"10.1093\/jn\/135.11.2703","article-title":"Nutritional epigenetics: Impact of folate deficiency on DNA methylation and colon cancer susceptibility","volume":"135","author":"Kim","year":"2005","journal-title":"J. Nutr."},{"key":"10.3382\/ps\/pez380_bib25","doi-asserted-by":"crossref","first-page":"15485","DOI":"10.1073\/pnas.1205147109","article-title":"Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin","volume":"109","author":"Kim","year":"2012","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"10.3382\/ps\/pez380_bib26","first-page":"11","article-title":"Spatial and temporal changes in the broiler chicken cecal and fecal microbiomes and correlations of bacterial taxa with cytokine gene expression","volume":"3","author":"Kogut","year":"2016","journal-title":"Front. Vet. Sci."},{"key":"10.3382\/ps\/pez380_bib27","article-title":"Effect of antibiotic withdrawal in feed on chicken gut microbial dynamics, immunity, growth performance and prevalence of foodborne pathogens","volume":"13","author":"Kumar","year":"2018","journal-title":"PLoS ONE."},{"key":"10.3382\/ps\/pez380_bib28","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1038\/nbt.2676","article-title":"PICRUST","volume":"31","author":"Langille","year":"2013","journal-title":"Nat. Biotechnol"},{"key":"10.3382\/ps\/pez380_bib29","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1111\/1462-2920.13589","article-title":"Formation of propionate and butyrate by the human colonic microbiota","volume":"19","author":"Louis","year":"2017","journal-title":"Environ. Microbiol."},{"key":"10.3382\/ps\/pez380_bib30","doi-asserted-by":"crossref","first-page":"8228","DOI":"10.1128\/AEM.71.12.8228-8235.2005","article-title":"UniFrac: a new phylogenetic method for comparing microbial communities","volume":"71","author":"Lozupone","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"10.3382\/ps\/pez380_bib31","doi-asserted-by":"crossref","first-page":"6816","DOI":"10.1128\/AEM.69.11.6816-6824.2003","article-title":"Diversity and succession of the intestinal bacterial community of the maturing broiler chicken","volume":"69","author":"Lu","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"key":"10.3382\/ps\/pez380_bib32","doi-asserted-by":"crossref","first-page":"2358","DOI":"10.3382\/ps.2012-02935","article-title":"Broilers fed dietary vitamins harbor higher diversity of cecal bacteria and higher ratio of Clostridium, Faecalibacterium, and Lactobacillus than broilers with no dietary vitamins revealed by 16S rRNA gene clone libraries","volume":"92","author":"Luo","year":"2013","journal-title":"Poult. Sci."},{"key":"10.3382\/ps\/pez380_bib33","doi-asserted-by":"crossref","first-page":"2930","DOI":"10.3390\/nu7042930","article-title":"The role of microbial amino acids metabolism in host metabolism","volume":"7","author":"Neis","year":"2015","journal-title":"Nutrients"},{"key":"10.3382\/ps\/pez380_bib34","series-title":"Nutrient Requirements of Poultry","author":"NRC","year":"1994"},{"key":"10.3382\/ps\/pez380_bib35","doi-asserted-by":"crossref","first-page":"e282","DOI":"10.1186\/s12917-014-0282-8","article-title":"Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives","volume":"10","author":"Oakley","year":"2014","journal-title":"BMC Vet. Res."},{"key":"10.3382\/ps\/pez380_bib36","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.diagmicrobio.2011.11.001","article-title":"Pyrosequencing-based validation of a simple cell-suspension polymerase chain reaction assay for Campylobacter with application of high-processivity polymerase and novel internal amplification controls for rapid and specific detection","volume":"72","author":"Oakley","year":"2012","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"10.3382\/ps\/pez380_bib37","doi-asserted-by":"crossref","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":"10.3382\/ps\/pez380_bib38","author":"Oksanen"},{"key":"10.3382\/ps\/pez380_bib39","doi-asserted-by":"crossref","first-page":"108","DOI":"10.4161\/gmic.26945","article-title":"Intestinal microbiome of poultry and its interaction with host and diet","volume":"5","author":"Pan","year":"2014","journal-title":"Gut Microbes"},{"key":"10.3382\/ps\/pez380_bib40","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0002945","article-title":"Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome","volume":"3","author":"Qu","year":"2008","journal-title":"PLoS One"},{"key":"10.3382\/ps\/pez380_bib41","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1080\/17450390701556817","article-title":"Indigenous bacteria and bacterial metabolic products in the gastrointestinal tract of broiler chickens","volume":"61","author":"Rehman","year":"2007","journal-title":"Arch. Anim. Nutr."},{"key":"10.3382\/ps\/pez380_bib42","doi-asserted-by":"crossref","first-page":"1112","DOI":"10.1111\/j.1462-2920.2006.01234.x","article-title":"Microbial community structure of ethanol type fermentation in bio-hydrogen production","volume":"9","author":"Ren","year":"2007","journal-title":"Environ. Microbiol."},{"key":"10.3382\/ps\/pez380_bib43","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1007\/BF00689291","article-title":"Caecal water and electrolyte absorption and the effects of acetate and glucose, in dehydrated, low-NaCl diet hens","volume":"147","author":"Rice","year":"1982","journal-title":"J. Comp. Physiol B: Biochem. Syst. Environ. Physiol."},{"key":"10.3382\/ps\/pez380_bib44","series-title":"Biotechnology in Animal Feeds and Animal Feeding","first-page":"172","article-title":"Antibacterial in poultry and pig nutrition","author":"Rosen","year":"1995"},{"key":"10.3382\/ps\/pez380_bib45","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00394-017-1445-8","article-title":"Gut microbiota functions: metabolism of nutrients and other food components","volume":"57","author":"Rowland","year":"2017","journal-title":"Eur. J. Nutr"},{"key":"10.3382\/ps\/pez380_bib46","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing Mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"Schloss","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"10.3382\/ps\/pez380_bib47","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/s13099-015-0051-7","article-title":"Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses","volume":"7","author":"Shaufi","year":"2015","journal-title":"Gut Pathog"},{"key":"10.3382\/ps\/pez380_bib48","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1093\/japr\/13.4.579","article-title":"Effects of excess methionine from meeting needs for total sulfur amino acids on utilization of diets low in crude protein by broiler chicks","volume":"13","author":"Si","year":"2004","journal-title":"J. Appl. Poult. Res."},{"key":"10.3382\/ps\/pez380_bib49","doi-asserted-by":"crossref","first-page":"4301","DOI":"10.1007\/s00253-014-5646-2","article-title":"Microbiota of the chicken gastrointestinal tract: Influence on health, productivity and disease","volume":"98","author":"Stanley","year":"2014","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"10.3382\/ps\/pez380_bib50","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/j.femsec.2005.03.012","article-title":"Comparison of bacterial diversity along human intestinal tract by direct cloning and sequencing of 16S rRNA genes","volume":"54","author":"Wang","year":"2005","journal-title":"FEMS Microbiol. Ecol."},{"key":"10.3382\/ps\/pez380_bib51","doi-asserted-by":"crossref","first-page":"1387","DOI":"10.3382\/ps\/pew372","article-title":"Microbial community mapping in intestinal tract of broiler chicken","volume":"96","author":"Xiao","year":"2017","journal-title":"Poult. Sci"},{"key":"10.3382\/ps\/pez380_bib52","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1017\/S1466252312000138","article-title":"The microbiome of the chicken gastrointestinal tract","volume":"13","author":"Yeoman","year":"2012","journal-title":"Anim. Health Res. Rev."},{"key":"10.3382\/ps\/pez380_bib53","doi-asserted-by":"crossref","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"},{"key":"10.3382\/ps\/pez380_bib54","doi-asserted-by":"crossref","first-page":"2066","DOI":"10.1002\/mnfr.201500187","article-title":"Modulation of gut microbiota in rats fed high fat diets by processing whole-grain barley to barley malt","volume":"59","author":"Zhong","year":"2015","journal-title":"Mol. Nutr. Food. Res."}],"container-title":["Poultry Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0032579119457842?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0032579119457842?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/academic.oup.com\/ps\/advance-article-pdf\/doi\/10.3382\/ps\/pez380\/29004004\/pez380.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/ps\/article-pdf\/98\/11\/5809\/30093333\/pez380.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,21]],"date-time":"2025-09-21T21:55:48Z","timestamp":1758491748000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0032579119457842"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,11]]},"references-count":54,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2019,11]]}},"alternative-id":["S0032579119457842"],"URL":"https:\/\/doi.org\/10.3382\/ps\/pez380","relation":{},"ISSN":["0032-5791"],"issn-type":[{"value":"0032-5791","type":"print"}],"subject":[],"published":{"date-parts":[[2019,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Changes in cecum microbial community in response to total sulfur amino acid (TSAA: DL-methionine) in antibiotic-free and supplemented poultry birds","name":"articletitle","label":"Article Title"},{"value":"Poultry Science","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.3382\/ps\/pez380","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Copyright \u00a9 2019 Poultry Science Association Inc. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}