Integrated analyses of the intestinal microbiome and transcriptome in NingXiang piglets

Integrated analyses of the intestinal microbiome and transcriptome in NingXiang piglets | 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 Article Integrated analyses of the intestinal microbiome and transcriptome in NingXiang piglets Zhenguo Hu, Yuezhou Yao, Feiyue Chen, Luya Feng, Zian Yuan, Junhao Deng, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3888036/v2 This work is licensed under a CC BY 4.0 License Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Abstract NingXiang (NX) pig has been recognized as one of the most famous Chinese indigenous breeds due to its characteristics in high fertility and stress resistance. However, the global intestinal gene expression profiling and the feature of gut microorganisms in NX piglets have not been studied. Here, we compared the intestinal microbiome and transcriptome between NX and Duroc × Landrace × Large white (DLY) piglets and found the high enrichment of several colonic Bacteroides, Prevotella and Clostridium species in NX piglets than DLY piglets. Further functional analyses of these microbes revealed their predominant function in methane, glycolysis and gluconeogenesis metabolism. Our mRNA-sequencing data unraveled the distinct colonic gene expression between these two pig breeds. In particular, NX piglets exhibited improved intestinal barrier function and cellulose digestibility, as well as varied immune features than DLY piglets. Finally, by integrating metagenomic and transcriptomic analyses, we further showed that the improved intestinal function in NX piglets may be determined by intestinal genes through modulating the composition of the gut microbes. Together, our study revealed the intestinal characteristics of NX piglets, providing their potential application in improving breeding strategies and developing dietary interventions. Indigenous Piglets Microbiota Stress resistance Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Full Text Additional Declarations The authors declare no competing interests. Supplementary Files SupplementalFile.docx Cite Share Download PDF Status: Posted Version 2 posted You are reading this latest preprint version Show more versions 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. 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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-3888036","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":269859598,"identity":"47682f11-a862-4a35-8bbf-d08381ae5a84","order_by":0,"name":"Zhenguo Hu","email":"","orcid":"","institution":"Institute of Subtropical Agriculture","correspondingAuthor":false,"prefix":"","firstName":"Zhenguo","middleName":"","lastName":"Hu","suffix":""},{"id":269859599,"identity":"46edd7a3-3820-4384-b954-d3dad547b7e7","order_by":1,"name":"Yuezhou Yao","email":"","orcid":"","institution":"Hunan Agricultural 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13:24:39","currentVersionCode":2,"declarations":{"humanSubjects":false,"vertebrateSubjects":false,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false},"doi":"10.21203/rs.3.rs-3888036/v2","doiUrl":"https://doi.org/10.21203/rs.3.rs-3888036/v2","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":55384954,"identity":"43923dca-9b8f-4ae4-93be-320990a7ab0e","added_by":"auto","created_at":"2024-04-26 14:32:26","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":1739941,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003ePig breeds exhibit distinct colonic microbial characteristics.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e(A)\u003c/strong\u003eComparison of the colonic microbial composition and diversity using Chao1, Simpson and Shannon indices between NX and DLY piglets. \u003cstrong\u003e(B)\u003c/strong\u003e Principal coordinate analysis of microbial compositional similarity between NX and DLY piglets. \u003cstrong\u003e(C-D)\u003c/strong\u003e Comparison of the abundance of colonic microorganisms between NX and DLY piglets at the Genus \u003cstrong\u003e(C)\u003c/strong\u003e and Species \u003cstrong\u003e(D)\u003c/strong\u003elevels.\u003c/p\u003e","description":"","filename":"Figure1.png","url":"https://assets-eu.researchsquare.com/files/rs-3888036/v2/9c91fcbeba4d1a84744af516.png"},{"id":55386190,"identity":"733349a6-c12e-4b05-a927-eb8ca96f41fe","added_by":"auto","created_at":"2024-04-26 14:48:26","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":2896441,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eNX and DLY piglets colonize different microbial species in the colon.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e(A) \u003c/strong\u003eVenn plot of the number of differentially colonized microbial (DCMs) species between NX and DLY piglets. \u003cstrong\u003e(B)\u003c/strong\u003e Heatmap cluster analysis of the top 30 DCMs at the species levels between NX and DLY piglets. \u003cstrong\u003e(C-D)\u003c/strong\u003eComparison of the abundance of colonic archaea \u003cstrong\u003e(C)\u003c/strong\u003e species between NX and DLY piglets. \u003cstrong\u003e(D)\u003c/strong\u003e Identification of the unique bacterial species between NX and DLY piglets, using the Linear discriminate analysis effect size (LEfSe).\u003c/p\u003e","description":"","filename":"Figure2.png","url":"https://assets-eu.researchsquare.com/files/rs-3888036/v2/07152c7111d53b509b954462.png"},{"id":55384957,"identity":"032eb5c0-87c0-41b8-8c01-1ff7f418b61a","added_by":"auto","created_at":"2024-04-26 14:32:27","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":1616164,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eNX piglets-enriched microbes modulate several metabolic functions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e(A-D)\u003c/strong\u003e Functional analyses of colonic microbiome between NX and DLY piglets using Kyoto Encyclopedia of Genes and Genomes (KEGG) \u003cstrong\u003e(A)\u003c/strong\u003e, Cazy \u003cstrong\u003e(B)\u003c/strong\u003e, BacMet\u003cstrong\u003e (C)\u003c/strong\u003e, and Swissprot \u003cstrong\u003e(D)\u003c/strong\u003e, respectively. (E-F) Comparison of the microbial-mediated functional categories \u003cstrong\u003e(E) \u003c/strong\u003eand the enrichment of glycoside hydrolases (GHs) and polysaccharide lyases (PLs) \u003cstrong\u003e(F)\u003c/strong\u003e between NX and DLY piglets. \u003cstrong\u003e(G-H)\u003c/strong\u003e Correlations between KEGG \u003cstrong\u003e(G)\u003c/strong\u003e or Cazy \u003cstrong\u003e(H)\u003c/strong\u003edata and differentially colonized bacterial species between NX and DLY piglets, using the Linear Discriminate Analysis.\u003c/p\u003e","description":"","filename":"Figure3.png","url":"https://assets-eu.researchsquare.com/files/rs-3888036/v2/f5af1aa77cdfef19af068c1d.png"},{"id":55386191,"identity":"63429823-715e-42a6-8f82-c6c7740a32eb","added_by":"auto","created_at":"2024-04-26 14:48:27","extension":"tif","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":926307,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eNX piglets manifest improved cellulose digestibility than DLY piglets\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e(A) \u003c/strong\u003eThe distribution of gut bacterial species involved in cellulose degradation between DLY and NX piglets. \u003cstrong\u003e(B)\u003c/strong\u003eThe expression level of colonic cellulases between DLY and NX piglets. \u003cstrong\u003e(C) \u003c/strong\u003eThe correlation analysis of cellulases and gut bacterial species in DLY and NX piglets.\u003c/p\u003e","description":"","filename":"Figure4.tif","url":"https://assets-eu.researchsquare.com/files/rs-3888036/v2/094477f14afc4dd85943520b.tif"},{"id":55385324,"identity":"fabd8386-2b76-4794-a8b7-ee2f0c31f979","added_by":"auto","created_at":"2024-04-26 14:40:26","extension":"tif","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":2758973,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eNX piglets exhibit better intestinal barrier function than DLY piglets\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e(A)\u003c/strong\u003e (Left) Heatmap analysis of differentially expressed intestinal barrier related genes from mRNAseq data between NX and DLY piglets. (Right) Validation of the mRNA expression of \u003cem\u003eE-cadherin\u003c/em\u003e, \u003cem\u003eTAD1\u003c/em\u003e, \u003cem\u003eWAS\u003c/em\u003e and \u003cem\u003eHCLS\u003c/em\u003e in the colon of NX and DLY piglets by RT-qPCR experiment. Asterisks denote statistically significant differences (*p\u0026lt;0.05, **p\u0026lt;0.01). \u003cstrong\u003e(B-C) \u003c/strong\u003eGene ontology (GO) \u003cstrong\u003e(B) \u003c/strong\u003eand Kyoto Encyclopedia of Genes and Genomes (KEGG) \u003cstrong\u003e(C) \u003c/strong\u003eanalyses of significantly upregulated intestinal barrier related genes in the colon of NX piglets compared to DLY piglets. \u003cstrong\u003e(D-E)\u003c/strong\u003e Gene ontology (GO) \u003cstrong\u003e(D)\u003c/strong\u003e and Kyoto Encyclopedia of Genes and Genomes (KEGG) \u003cstrong\u003e(E)\u003c/strong\u003e analyses of significantly downregulated intestinal barrier related genes in the colon of NX piglets compared to DLY piglets.\u003c/p\u003e","description":"","filename":"Figure5.tif","url":"https://assets-eu.researchsquare.com/files/rs-3888036/v2/913d57c5dbb92a0896fd797f.tif"},{"id":55384956,"identity":"9db056ad-f0d8-4e5e-af88-765bc0e5bb43","added_by":"auto","created_at":"2024-04-26 14:32:27","extension":"tif","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":3442535,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eVaried intestinal immune reactions between NX and DLY piglets\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e(A)\u003c/strong\u003e(Top) Heatmap analysis of differentially expressed intestinal antimicrobial peptide genes from mRNAseq data between NX and DLY piglets. (Bottom) Validation of the mRNA expression of Reg-Ⅲ-γ, Myod88, PBD-1 and PR39 in the colon of NX and DLY piglets by RT-qPCR experiment. Asterisks denote statistically significant differences (**p\u0026lt;0.01,***P\u0026lt;0.001). \u003cstrong\u003e(B)\u003c/strong\u003e (Top) Heatmap analysis of differentially expressed intestinal inflammatory genes from mRNAseq data between NX and DLY piglets. (Bottom) Validation of the mRNA expression of IL2, IL17F, IL-18, IL-8 and IL-22 in the colon of NX and DLY piglets by RT-qPCR experiment. Asterisks denote statistically significant differences (*p\u0026lt;0.05,**P\u0026lt;0.01). \u003cstrong\u003e(C-D)\u003c/strong\u003e Gene ontology (GO)\u003cstrong\u003e (C)\u003c/strong\u003e and Kyoto Encyclopedia of Genes and Genomes (KEGG) \u003cstrong\u003e(D)\u003c/strong\u003e analyses of significantly upregulated intestinal immune responsive genes in the colon of NX piglets compared to DLY piglets. \u003cstrong\u003e(E-F)\u003c/strong\u003eGene ontology (GO) \u003cstrong\u003e(D)\u003c/strong\u003e and Kyoto Encyclopedia of Genes and Genomes (KEGG) \u003cstrong\u003e(E)\u003c/strong\u003e analyses of significantly downregulated immune responsive genes in the colon of NX piglets compared to DLY piglets.\u003c/p\u003e","description":"","filename":"Figure6.tif","url":"https://assets-eu.researchsquare.com/files/rs-3888036/v2/4d3fb1621e7643ee612b5ef3.tif"},{"id":55384960,"identity":"6490e46a-630d-4ffe-a590-4e6db6fc97bb","added_by":"auto","created_at":"2024-04-26 14:32:27","extension":"tif","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":6369703,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eIntestinal gene affects intestinal function via modulating the composition of the gut microbiota\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e(A-B) \u003c/strong\u003eThe association analysis of gut bacterial species and intestinal barrier genes \u003cstrong\u003e(A)\u003c/strong\u003e and immune responsive genes \u003cstrong\u003e(B)\u003c/strong\u003e in NX and DLY piglets.\u003cstrong\u003e (C)\u003c/strong\u003e The comparison of the colonic microbial characteristics and intestinal gene expression pattern between NX and DLY piglets. Briefly, NX piglets preferentially colonize\u003cem\u003e Prevotella, Clostridium and Lactobacillus \u003c/em\u003especies that play critical roles in regulating nutrients metabolism including cellulose digestion. While the abundance of \u003cem\u003eStreptococcus\u003c/em\u003especies is largely enriched in DLY piglets. Additionally, NX piglets exhibit improved intestinal barrier function and varied immune reactions than DLY piglets. A subset of immune responsive genes including antimicrobial peptides genes as well as inflammatory genes are dysregulated between NX and DLY piglets. It is noted that the Th17 cells-mediated secretion of IL17F signaling pathway may determine the immune characteristics of these two breeds.\u003c/p\u003e","description":"","filename":"Figure7.tif","url":"https://assets-eu.researchsquare.com/files/rs-3888036/v2/e7ada32d06bfcee76ad68bc4.tif"},{"id":55385328,"identity":"12603a2d-868a-4152-aff1-7074667f68fc","added_by":"auto","created_at":"2024-04-26 14:40:27","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":6594627,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementalFile.docx","url":"https://assets-eu.researchsquare.com/files/rs-3888036/v2/0133b57fd2b3d22cd4da3a9d.docx"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003e\u003cstrong\u003eIntegrated analyses of the intestinal microbiome and transcriptome in NingXiang piglets\u003c/strong\u003e\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"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":"Indigenous Piglets, Microbiota, Stress resistance","lastPublishedDoi":"10.21203/rs.3.rs-3888036/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3888036/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eNingXiang (NX) pig has been recognized as one of the most famous Chinese indigenous breeds due to its characteristics in high fertility and stress resistance. However, the global intestinal gene expression profiling and the feature of gut microorganisms in NX piglets have not been studied. Here, we compared the intestinal microbiome and transcriptome between NX and Duroc × Landrace × Large white (DLY) piglets and found the high enrichment of several colonic \u003cem\u003eBacteroides, Prevotella\u003c/em\u003e and \u003cem\u003eClostridium\u003c/em\u003e species in NX piglets than DLY piglets. Further functional analyses of these microbes revealed their predominant function in methane, glycolysis and gluconeogenesis metabolism. Our mRNA-sequencing data unraveled the distinct colonic gene expression between these two pig breeds. In particular, NX piglets exhibited improved intestinal barrier function and cellulose digestibility, as well as varied immune features than DLY piglets. Finally, by integrating metagenomic and transcriptomic analyses, we further showed that the improved intestinal function in NX piglets may be determined by intestinal genes through modulating the composition of the gut microbes. Together, our study revealed the intestinal characteristics of NX piglets, providing their potential application in improving breeding strategies and developing dietary interventions.\u003c/p\u003e","manuscriptTitle":"Integrated analyses of the intestinal microbiome and transcriptome in NingXiang piglets","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2024-04-26 14:32:22","doi":"10.21203/rs.3.rs-3888036/v2","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}},{"code":1,"date":"2024-01-29 11:07:17","doi":"10.21203/rs.3.rs-3888036/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":"133c6e24-0de3-4c1d-8ae1-e438775420a1","owner":[],"postedDate":"April 26th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2024-03-18T17:29:50+00:00","versionOfRecord":[],"versionCreatedAt":"2024-04-26 14:32:22","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v2","identity":"rs-3888036","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-3888036","identity":"rs-3888036","version":["v2"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}