{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T16:00:29Z","timestamp":1792166429276,"version":"4.4.0"},"reference-count":56,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2021,6,9]],"date-time":"2021-06-09T00:00:00Z","timestamp":1623196800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>When conducting metagenomic analysis on gut microbiomes, there is no general consensus concerning the mode of sampling: non-contact (feces), noninvasive (rectal swabs), or cecal. This study aimed to determine the feasibility and comparative merits and disadvantages of using fecal samples or rectal swabs as a proxy for the cecal microbiome. Using broiler as a model, gut microbiomes were obtained from cecal, cloacal, and fecal samples and were characterized according to an analysis of the microbial community, function, and resistome. Cecal samples had higher microbial diversity than feces, while the cecum and cloaca exhibited higher levels of microbial community structure similarity compared with fecal samples. Cecal microbiota possessed higher levels of DNA replicative viability than feces, while fecal microbiota were correlated with increased metabolic activity. When feces were excreted, the abundance of antibiotic resistance genes like tet and ErmG decreased, but some antibiotic genes became more prevalent, such as fexA, tetL, and vatE. Interestingly, Lactobacillus was a dominant bacterial genus in feces that led to differences in microbial community structure, metabolism, and resistome. In conclusion, fecal microbiota have limited potential as a proxy in chicken gut microbial community studies. Thus, feces should be used with caution for characterizing gut microbiomes by metagenomic analysis.<\/jats:p>","DOI":"10.3390\/ani11061718","type":"journal-article","created":{"date-parts":[[2021,6,9]],"date-time":"2021-06-09T04:22:22Z","timestamp":1623212542000},"page":"1718","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":28,"title":["Comparative Metagenomic Analysis of Chicken Gut Microbial Community, Function, and Resistome to Evaluate Noninvasive and Cecal Sampling Resources"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8720-1395","authenticated-orcid":false,"given":"Kelang","family":"Kang","sequence":"first","affiliation":[{"name":"Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Hu","sequence":"additional","affiliation":[{"name":"Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China"},{"name":"Center of Effective Evaluation of Feed and Feed Additive (Poultry Institute) Ministry of Agriculture, Yangzhou 225000, China"},{"name":"Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shu","family":"Wu","sequence":"additional","affiliation":[{"name":"Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8011-2883","authenticated-orcid":false,"given":"Shourong","family":"Shi","sequence":"additional","affiliation":[{"name":"Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou 225000, China"},{"name":"Center of Effective Evaluation of Feed and Feed Additive (Poultry Institute) Ministry of Agriculture, Yangzhou 225000, China"},{"name":"Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,6,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e00786","DOI":"10.1002\/mbo3.786","article-title":"Comparative analysis of the gut microbiota of hornbill and toucan in captivity","volume":"8","author":"Sun","year":"2018","journal-title":"Microbiologyopen"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1016\/j.mehy.2009.10.025","article-title":"The microbial organ in the gut as a driver of homeostasis and disease","volume":"74","author":"Lyte","year":"2010","journal-title":"Med. 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