{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T18:37:27Z","timestamp":1784831847884,"version":"3.55.0"},"reference-count":41,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,1,26]],"date-time":"2026-01-26T00:00:00Z","timestamp":1769385600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Main livestock and poultry molecular breeding platform","award":["2021YFYZ0009"],"award-info":[{"award-number":["2021YFYZ0009"]}]},{"name":"China Agriculture Research System","award":["CARS-43-A-3"],"award-info":[{"award-number":["CARS-43-A-3"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>This study systematically characterized functional compartmentalization along the intestinal tract of New Zealand rabbits by analyzing mucosal tissue and luminal contents from distinct segments, including the duodenum, jejunum, ileum, cecum, and colon, using RNA-seq and 16S rRNA sequencing. Transcriptomic analysis revealed that differentially expressed genes identified between the small and large intestines were mainly enriched in digestion, absorption, and immune functions. Genes associated with the transport of amino acids, sugars, vitamins, and bile salts showed significantly higher expression in the small intestine, whereas genes related to water absorption, short-chain fatty acids (SCFAs), nucleotides, and metal ion transport were preferentially expressed in the large intestine. From an immunological perspective, genes involved in fungal responses were enriched in the small intestine, while bacterial response pathways and pattern recognition receptor (PRR) signaling genes were upregulated in the large intestine. Microbiota analysis demonstrated significantly greater diversity and abundance in the large intestine compared with the small intestine. Specifically, Proteobacteria and Actinobacteria were enriched in the small intestine, whereas Firmicutes, Verrucomicrobia, and Bacteroidetes dominated the large intestine. Correlation analysis further identified significant associations between gut microbiota composition and host genes involved in nutrient digestion and absorption. Together, these findings provide transcriptome-based evidence for regional specialization of nutrient transport, immune responses, and microbial ecology along the rabbit intestine.<\/jats:p>","DOI":"10.3390\/ani16030390","type":"journal-article","created":{"date-parts":[[2026,1,26]],"date-time":"2026-01-26T15:48:30Z","timestamp":1769442510000},"page":"390","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["The Analysis of Transcriptomes and Microorganisms Reveals Differences Between the Intestinal Segments of New Zealand Rabbits"],"prefix":"10.3390","volume":"16","author":[{"given":"Die","family":"Tang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuangshuang","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chuang","family":"Tang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangyu","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8681-7684","authenticated-orcid":false,"given":"Mingzhou","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuewei","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Zhang","sequence":"additional","affiliation":[{"name":"Sichuan Academy of Grassland Sciences, Chengdu 611743, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jideng","family":"Ma","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1038\/s41385-021-00389-4","article-title":"Human gut-associated lymphoid tissues (GALT): Diversity, structure, and function","volume":"14","author":"Mrbe","year":"2021","journal-title":"Mucosal Immunol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1146\/annurev.cellbio.042308.113344","article-title":"Vertebrate endoderm development and organ formation","volume":"25","author":"Zorn","year":"2009","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e20191130","DOI":"10.1084\/jem.20191130","article-title":"Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine","volume":"217","author":"Wang","year":"2020","journal-title":"J. Exp. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1038\/nature11552","article-title":"Functional interactions between the gut microbiota and host metabolism","volume":"489","author":"Tremaroli","year":"2012","journal-title":"Nature"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1038\/nature05484","article-title":"Gut hormones and the regulation of energy homeostasis","volume":"444","author":"Murphy","year":"2006","journal-title":"Nature"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1038\/sj.embor.7400731","article-title":"The gut flora as a forgotten organ","volume":"7","author":"Shanahan","year":"2006","journal-title":"EMBO Rep."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Diether, N.E., and Willing, B.P. (2019). Microbial fermentation of dietary protein: An important factor in diet\u2013microbe\u2013host interaction. Microorganisms, 7.","DOI":"10.3390\/microorganisms7010019"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.1038\/s41385-021-00420-8","article-title":"Intestinal immune compartmentalization: Implications of tissue specific determinants in health and disease","volume":"14","author":"Brown","year":"2021","journal-title":"Mucosal Immunol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"G341","DOI":"10.1152\/ajpgi.00046.2013","article-title":"Studies of mucus in mouse stomach, small intestine, and colon. I. Gastrointestinal mucus layers have different properties depending on location as well as over the Peyer\u2019s patches","volume":"305","author":"Ermund","year":"2013","journal-title":"AJP Gastrointest. Liver Physiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/nri3608","article-title":"Intestinal epithelial cells: Regulators of barrier function and immune homeostasis","volume":"14","author":"Peterson","year":"2014","journal-title":"Nat. Rev. Immunol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1038\/nri3738","article-title":"Regional specialization within the intestinal immune system","volume":"14","author":"Mowat","year":"2014","journal-title":"Nat. Rev. Immunol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/s41579-018-0036-x","article-title":"Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier","volume":"16","author":"Martens","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_13","first-page":"28","article-title":"Isolation of Clostridium butyricum from pigs and its effects on intestinal villus development","volume":"30","author":"Ouyang","year":"2016","journal-title":"J. Qilu Univ. Technol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1016\/j.chom.2014.03.006","article-title":"Plasmacytoid dendritic cells mediate anti-inflammatory responses to a gut commensal molecule via both innate and adaptive mechanisms","volume":"15","author":"Dasgupta","year":"2014","journal-title":"Cell Host Microbe"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"12204","DOI":"10.1073\/pnas.0909122107","article-title":"Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota","volume":"107","author":"Round","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1038\/nature12331","article-title":"Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota","volume":"500","author":"Atarashi","year":"2013","journal-title":"Nature"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1126\/science.1198469","article-title":"Induction of colonic regulatory T cells by indigenous Clostridium species","volume":"331","author":"Atarashi","year":"2011","journal-title":"Science"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/nrmicro3050","article-title":"The abundance and variety of carbohydrate-active enzymes in the human gut microbiota","volume":"11","author":"Kaoutari","year":"2013","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/j.chom.2019.08.011","article-title":"Regional Diversity of the Gastrointestinal Microbiome","volume":"26","author":"Leone","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1124\/dmd.117.077313","article-title":"RNA-Seq Profiling of Intestinal Expression of Xenobiotic Processing Genes in Germ-Free Mice","volume":"45","author":"Fu","year":"2017","journal-title":"Drug Metab. Dispos. Biol. Fate Chem."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.4049\/jimmunol.172.2.1118","article-title":"Role of commensal bacteria in development of gut-associated lymphoid tissues and preimmune antibody repertoire","volume":"172","author":"Rhee","year":"2004","journal-title":"J. Immunol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1152\/ajplegacy.1959.197.6.1345","article-title":"Development of cecal distention in germ-free baby rats","volume":"197","author":"Wostmann","year":"1959","journal-title":"Am. J. Physiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"176","DOI":"10.4161\/gmic.28203","article-title":"Association of germ-free mice with a simplified human intestinal microbiota results in a shortened intestine","volume":"5","author":"Slezak","year":"2014","journal-title":"Gut Microbes"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1002\/ame2.12022","article-title":"The role of the gut microbiota on animal model reproducibility","volume":"1","author":"Turner","year":"2018","journal-title":"Anim. Model. Exp. Med."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1016\/j.immuni.2017.04.004","article-title":"Regionalized development and maintenance of the intestinal adaptive immune landscape","volume":"46","author":"Agace","year":"2017","journal-title":"Immunity"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1554","DOI":"10.1016\/j.jcmgh.2022.02.007","article-title":"A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics","volume":"13","author":"Burclaff","year":"2022","journal-title":"Cell. Mol. Gastroenterol. Hepatol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Chen, L., Zhang, Y., Pan, X., Liu, M., Wang, S., Huang, T., and Cai, Y.-D. (2018). Tissue expression difference between mRNAs and lncRNAs. Int. J. Mol. Sci., 19.","DOI":"10.3390\/ijms19113416"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/s00125-014-3451-1","article-title":"GLUT2, glucose sensing and glucose homeostasis","volume":"58","author":"Thorens","year":"2015","journal-title":"Diabetologia"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1016\/j.mam.2012.05.010","article-title":"The SLC37 family of phosphate-linked sugar phosphate antiporters","volume":"34","author":"Chou","year":"2013","journal-title":"Mol. Asp. Med."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.mam.2012.11.002","article-title":"Glucose transport families SLC5 and SLC50","volume":"34","author":"Wright","year":"2013","journal-title":"Mol. Asp. Med."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1111\/j.1748-1716.2010.02167.x","article-title":"Dietary fructose, salt absorption and hypertension in metabolic syndrome: Towards a new paradigm","volume":"201","author":"Soleimani","year":"2011","journal-title":"Acta Physiol."},{"key":"ref_32","first-page":"207","article-title":"Glutamine transporters as pharmacological targets: From function to drug design","volume":"15","author":"Scalise","year":"2020","journal-title":"Asian J. Pharm. Sci."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1017\/S1751731118001404","article-title":"Rabbit SLC15A1, SLC7A1 and SLC1A1 genes are affected by site of digestion, stage of development and dietary protein content","volume":"13","author":"Liu","year":"2019","journal-title":"Animal"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1007\/s00726-014-1905-x","article-title":"The many faces of interferon tau","volume":"47","author":"Bazer","year":"2015","journal-title":"Amino Acids"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1194\/jlr.R054114","article-title":"Intestinal transport and metabolism of bile acids","volume":"56","author":"Dawson","year":"2015","journal-title":"J. Lipid Res."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e00261-19","DOI":"10.1128\/mSystems.00261-19","article-title":"Age- and sex-dependent patterns of gut microbial diversity in human adults","volume":"4","author":"Kelley","year":"2019","journal-title":"mSystems"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1038\/ni.2608","article-title":"Control of pathogens and pathobionts by the gut microbiota","volume":"14","author":"Kamada","year":"2013","journal-title":"Nat. Immunol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"3213","DOI":"10.1111\/j.1462-2920.2010.02294.x","article-title":"High temporal and inter-individual variation detected in the human ileal microbiota","volume":"12","author":"Booijink","year":"2010","journal-title":"Environ. Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1016\/j.tibtech.2015.06.011","article-title":"Proteobacteria: Microbial signature of dysbiosis in gut microbiota","volume":"33","author":"Shin","year":"2015","journal-title":"Trends Biotechnol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1016\/j.dld.2018.02.012","article-title":"Actinobacteria: A relevant minority for the maintenance of gut homeostasis","volume":"50","author":"Binda","year":"2018","journal-title":"Dig. Liver Dis."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1007\/BF03402075","article-title":"Butyrate switches the pattern of chemokine secretion by intestinal epithelial cells through histone acetylation","volume":"5","author":"Fusunyan","year":"1999","journal-title":"Mol. Med."}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/3\/390\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,26]],"date-time":"2026-01-26T16:02:17Z","timestamp":1769443337000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/3\/390"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,26]]},"references-count":41,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,2]]}},"alternative-id":["ani16030390"],"URL":"https:\/\/doi.org\/10.3390\/ani16030390","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,26]]}}}