A reference gene catalogue of chicken gut antibiotic resistomes

A reference gene catalogue of chicken gut antibiotic resistomes | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research A reference gene catalogue of chicken gut antibiotic resistomes Jintao Yang, Cuihong Tong, Danyu Xiao, Longfei Xie, Ruonan Zhao, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-665224/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background: The chicken gut microbiota, as a reservoir of antibiotic resistance genes (ARGs), poses a high risk to humans and animals worldwide. Yet a comprehensive exploration of the chicken gut antibiotic resistomes remains incomplete. Results: In this study, we established the largest chicken gut resistance gene catalogue to date through metagenomic analysis of 629 chicken gut samples. We found significantly higher abundance of ARGs in the Chinese chicken gut than that in the Europe. tetX, mcr, and blaNDM, the genes resistant to antibiotics of last resort for human and animal health, were frequently detected in the Chinese chicken gut. The abundance of ARGs was linearly correlated with that of mobile genetic elements (MGEs). The host-tracking analysis identified Escherichia, Enterococcus, Staphylococcus, Klebsiella, and Lactobacillus as the major ARG hosts. Especially, Lactobacillus, an intestinal probiotic, carried multiple drug resistance genes, and was proportional to ISLhe63, highlighting its potential risk in agricultural production processes. Conclusions: We first established a reference gene catalogue of chicken gut antibiotic resistomes. Our study help to improve the knowledge and understanding of chicken antibiotic resistomes for knowledge-based sustainable chicken meat production. General Microbiology Antibiotic resistance genes Metagenome Chicken gut Host-tracking Mobile genetic elements Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Full Text Supplementary Files SupplementaryfileTableS.xlsx SupplementaryFig1.pdf SupplementaryFig2.pdf SupplementaryFig3.pdf Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-665224","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research","associatedPublications":[],"authors":[{"id":37181813,"identity":"7ab55eaa-5d3f-47bc-bbad-add1ba574988","order_by":0,"name":"Jintao Yang","email":"","orcid":"","institution":"South China Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Jintao","middleName":"","lastName":"Yang","suffix":""},{"id":37181814,"identity":"86ddbff1-cfb7-4729-a04a-42f46cfd4770","order_by":1,"name":"Cuihong Tong","email":"","orcid":"","institution":"South China Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Cuihong","middleName":"","lastName":"Tong","suffix":""},{"id":37181815,"identity":"58110c0b-bd0c-4e4f-b0e0-cd8ed3e24f84","order_by":2,"name":"Danyu Xiao","email":"","orcid":"","institution":"South China Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Danyu","middleName":"","lastName":"Xiao","suffix":""},{"id":37181816,"identity":"d3a58806-c6d3-4428-8a3b-94eed7e944bf","order_by":3,"name":"Longfei Xie","email":"","orcid":"","institution":"South China Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Longfei","middleName":"","lastName":"Xie","suffix":""},{"id":37181817,"identity":"760153cd-2e10-4a6d-8706-de303a3f392d","order_by":4,"name":"Ruonan Zhao","email":"","orcid":"","institution":"South China Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Ruonan","middleName":"","lastName":"Zhao","suffix":""},{"id":37181818,"identity":"b5472a91-f802-4b74-942e-753ed6948e27","order_by":5,"name":"Zhipeng Huo","email":"","orcid":"","institution":"South China Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Zhipeng","middleName":"","lastName":"Huo","suffix":""},{"id":37181819,"identity":"698c1689-f8a3-44f6-9183-1f7f89a33b9d","order_by":6,"name":"Ziyun Tang","email":"","orcid":"","institution":"South China Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Ziyun","middleName":"","lastName":"Tang","suffix":""},{"id":37181820,"identity":"cf6bb5e8-b308-496a-b17f-e400d8997394","order_by":7,"name":"Jie Hao","email":"","orcid":"","institution":"South China Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Jie","middleName":"","lastName":"Hao","suffix":""},{"id":37181821,"identity":"216fd773-fdce-498d-b75c-5148b618af77","order_by":8,"name":"Zhenling Zeng","email":"","orcid":"","institution":"South China Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Zhenling","middleName":"","lastName":"Zeng","suffix":""},{"id":37181822,"identity":"6f687f90-296a-42b3-99bd-34ad4c2ac217","order_by":9,"name":"Wenguang Xiong","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA1klEQVRIiWNgGAWjYDACZgglh8olRosxCVqgILGBaC0Gx5mPPfzaVps+v/3wMwmGCuvEBvazB/BqkWxmSzeWbTueu+FMmpkEw5n0xAaevAS8WviZecykJbcdy90gwWAmwdh2OLFBgscArxY2qJZ0+Rns3yQY/xGhBWSL5MdtNQkMN3iAtjQQoQXolzRpxn8HDDecySm2SDiWbtzGk4Nfi8H5w8ckf5ypk5dvP77xxocaa9l+9jP4tYAAMw/DYQgrAeQ7guqBgPEHQx0x6kbBKBgFo2CkAgBxyz7ZBSDCXAAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0002-8965-2915","institution":"South China Agricultural University","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Wenguang","middleName":"","lastName":"Xiong","suffix":""}],"badges":[],"createdAt":"2021-06-28 01:46:47","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-665224/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-665224/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":11212481,"identity":"e9312b04-fb55-402f-9d47-7b409b536f87","added_by":"auto","created_at":"2021-07-07 14:52:08","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":1166689,"visible":true,"origin":"","legend":"Distribution map of chicken gutl samples and diversity of ARGs, pie chart\nshowing the profile of ARG abundance (top 3 ARG types). Europe(n=178) includes\nNetherlands(n=20), Germany(n=19), France(n=20), Spain(n=20), Belgium(n=20),\nItaly(n=20), Poland(n=20), Denmark(n= 20) and Bulgaria (n=19).","description":"","filename":"Figure1.png","url":"https://assets-eu.researchsquare.com/files/rs-665224/v1/e084e9f162e62277549a8607.png"},{"id":11212574,"identity":"ec9dcc1c-259a-44af-b116-ad7fafaa1c67","added_by":"auto","created_at":"2021-07-07 14:55:02","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":546511,"visible":true,"origin":"","legend":"ARG composition structure distribution. (a) PCA plots showing the ARG\nsubtypes composition differences among the 618 chicken gut samples. (b)\nComparison of ARG types in China and Europe. (c) ARGs abundance comparison. (d)\nDiversity of ARGs subtypes. (e) ARGs subtype of Shannon's Diversity Index","description":"","filename":"Figure2.png","url":"https://assets-eu.researchsquare.com/files/rs-665224/v1/7f14173899924981736c95c6.png"},{"id":11212472,"identity":"da8b72cc-cb7f-4130-b042-4920b377304a","added_by":"auto","created_at":"2021-07-07 14:52:04","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":3131683,"visible":true,"origin":"","legend":"ARGs heatmap and phylogenetic tree of tetX, mcr, and blaNDM detected in the\nchicken gut.","description":"","filename":"Figure3.png","url":"https://assets-eu.researchsquare.com/files/rs-665224/v1/c4a6cc60046871f643392947.png"},{"id":11212475,"identity":"8885d6e2-44ad-49fc-855b-4b72538561ab","added_by":"auto","created_at":"2021-07-07 14:52:05","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":676923,"visible":true,"origin":"","legend":"Bacterial population structure distribution. (a) PCA plots showing the Bacterial \nflora (genus level) composition differences among the 618 chicken gut samples. (b) Comparison of Bacterial flora in China and Europe. (c) Differentially abundant bacteria. Differences in genus abundance between China and Europe. The y-axis represents the log2-fold change and the x-axis represents the genus name.","description":"","filename":"Figure4.png","url":"https://assets-eu.researchsquare.com/files/rs-665224/v1/a68ed79bd3416d138d1eb674.png"},{"id":11212479,"identity":"fb2213be-2c86-4fd4-9f76-114de383636c","added_by":"auto","created_at":"2021-07-07 14:52:08","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":885068,"visible":true,"origin":"","legend":"The taxonomy of ACCs (in genus level) and the percentages of ARG types\nthese contigs carried. For example, Escherichia (6.3%) represents that 6.3% of ACCs were annotated as Escherichia. b Bar chart shows the percentages of ARG types that were carried by the annotated ACCs.For example, 44.1% of the ARG-carrying contigs originating from Escherichia carried aminoglycoside resistance genes.","description":"","filename":"Figure5.png","url":"https://assets-eu.researchsquare.com/files/rs-665224/v1/99da52676c859e9be1714dc7.png"},{"id":11212440,"identity":"a867bb09-0070-49d4-8faf-55d426cec5d4","added_by":"auto","created_at":"2021-07-07 14:52:01","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":613697,"visible":true,"origin":"","legend":"Correlation between ARGs and MGEs.(a)Overall correlation of ARGs\nabundance and MGEs abundance in 629 chicken gut samples(b)Correlation of ARGs abundance and MGEs abundance by Chinese and European groups. (c)Heatmap of correlation between MGEs, IS, plasmid and integron.","description":"","filename":"Figure6.png","url":"https://assets-eu.researchsquare.com/files/rs-665224/v1/35e682ec970a7707056ba58c.png"},{"id":11212579,"identity":"e622a434-0683-47f5-9e8d-a3a999202b6e","added_by":"auto","created_at":"2021-07-07 14:55:04","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":2351598,"visible":true,"origin":"","legend":"The network analysis revealing the co-occurrence patterns between major\nMAGs(in genus level) and ARG subtypes. The nodes were colored according to the modularity class. Modularity index 0.68. The size of each node was proportional to the number of connections, that is, the average weighted.","description":"","filename":"Figure7.png","url":"https://assets-eu.researchsquare.com/files/rs-665224/v1/a83f03082a2b58d0049f41e5.png"},{"id":13656001,"identity":"56c2bdab-7f6f-4c00-af8a-c01321f2e513","added_by":"auto","created_at":"2021-09-17 10:04:31","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1044756,"visible":true,"origin":"","legend":"","description":"","filename":"article.pdf","url":"https://assets-eu.researchsquare.com/files/rs-665224/v1_covered.pdf"},{"id":11212584,"identity":"9cc53515-bd79-4b08-889e-86711557731c","added_by":"auto","created_at":"2021-07-07 14:55:21","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1041032,"visible":true,"origin":"","legend":"","description":"","filename":"article.pdf","url":"https://assets-eu.researchsquare.com/files/rs-665224/v1_covered.pdf"},{"id":11212470,"identity":"b60ddfea-f69c-4d3a-aa30-d7038d7c9846","added_by":"auto","created_at":"2021-07-07 14:52:03","extension":"xlsx","order_by":11,"title":"","display":"","copyAsset":false,"role":"supplement","size":773169,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryfileTableS.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-665224/v1/8abbbeb25cf21c1ab9256f1b.xlsx"},{"id":11212469,"identity":"69beb41d-62d1-49a0-87bd-0184c274dd5d","added_by":"auto","created_at":"2021-07-07 14:52:02","extension":"pdf","order_by":12,"title":"","display":"","copyAsset":false,"role":"supplement","size":269040,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryFig1.pdf","url":"https://assets-eu.researchsquare.com/files/rs-665224/v1/71e247bdd3b792ff46189527.pdf"},{"id":11212438,"identity":"453780e6-4685-4cf8-ac88-d51f3780333d","added_by":"auto","created_at":"2021-07-07 14:52:01","extension":"pdf","order_by":13,"title":"","display":"","copyAsset":false,"role":"supplement","size":5922371,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryFig2.pdf","url":"https://assets-eu.researchsquare.com/files/rs-665224/v1/54b7f54a097c0e206b9dc0f6.pdf"},{"id":11212471,"identity":"398a2b8d-e3ad-4446-96f2-dc8d400ce1e9","added_by":"auto","created_at":"2021-07-07 14:52:03","extension":"pdf","order_by":14,"title":"","display":"","copyAsset":false,"role":"supplement","size":17057826,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryFig3.pdf","url":"https://assets-eu.researchsquare.com/files/rs-665224/v1/2a164b4b11c90291355e5c79.pdf"}],"financialInterests":"","formattedTitle":"A reference gene catalogue of chicken gut antibiotic resistomes","fulltext":[{"header":"Full Text","content":"This preprint is available for \u003ca href='/article/rs-665224/latest.pdf' target='_blank'\u003edownload as a PDF\u003c/a\u003e."}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Antibiotic resistance genes, Metagenome, Chicken gut, Host-tracking, Mobile genetic elements","lastPublishedDoi":"10.21203/rs.3.rs-665224/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-665224/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eBackground: The chicken gut microbiota, as a reservoir of antibiotic resistance genes (ARGs), poses a high risk to humans and animals worldwide. Yet a comprehensive exploration of the chicken gut antibiotic resistomes remains incomplete. \u003c/p\u003e\u003cp\u003eResults: In this study, we established the largest chicken gut resistance gene catalogue to date through metagenomic analysis of 629 chicken gut samples. We found significantly higher abundance of ARGs in the Chinese chicken gut than that in the Europe. tetX, mcr, and blaNDM, the genes resistant to antibiotics of last resort for human and animal health, were frequently detected in the Chinese chicken gut. The abundance of ARGs was linearly correlated with that of mobile genetic elements (MGEs). The host-tracking analysis identified Escherichia, Enterococcus, Staphylococcus, Klebsiella, and Lactobacillus as the major ARG hosts. Especially, Lactobacillus, an intestinal probiotic, carried multiple drug resistance genes, and was proportional to ISLhe63, highlighting its potential risk in agricultural production processes. \u003c/p\u003e\u003cp\u003eConclusions: We first established a reference gene catalogue of chicken gut antibiotic resistomes. Our study help to improve the knowledge and understanding of chicken antibiotic resistomes for knowledge-based sustainable chicken meat production.\u003c/p\u003e","manuscriptTitle":"A reference gene catalogue of chicken gut antibiotic resistomes","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2021-07-07 14:51:52","doi":"10.21203/rs.3.rs-665224/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"4e493bf1-5242-4909-af13-e80fe7d71996","owner":[],"postedDate":"July 7th, 2021","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":5492315,"name":"General Microbiology"}],"tags":[],"updatedAt":"2021-09-09T16:35:01+00:00","versionOfRecord":[],"versionCreatedAt":"2021-07-07 14:51:52","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-665224","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-665224","identity":"rs-665224","version":["v1"]},"buildId":"WrCJVZZCHTDjtuVLN7oU0","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}