{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T03:42:48Z","timestamp":1790826168831,"version":"4.1.0"},"reference-count":41,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2020,4,14]],"date-time":"2020-04-14T00:00:00Z","timestamp":1586822400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Seventh Framework Programme","award":["311794"],"award-info":[{"award-number":["311794"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>The composition of the intestinal microbiota plays an important role in the digestion and utilization of nutrients and for gut health. Low-fiber diets stimulate digestion and absorption processes, predominantly in the upper region of the gastrointestinal tract, thereby increasing the conversion of feed into body weight. As a consequence, the chemical composition of digesta after duodenal and jejunal absorption processes and passage has a limited complexity affecting colonization and molecular profiles of enterocytes in the hind gut. To decipher ileal and caecal microbial ecosystems and host transcriptional profiles that are beneficial for effective use of the remaining nutrients, pigs differing in feeding efficiency were studied. Biological functions that were consistently enriched at both the gene and microbiota levels comprise immunity-related processes, which ensure the integrity of the gastrointestinal tract. In addition, the differential abundance of certain genera, including Rothia, Subdoligranulu, Leeia and Cellulosilyticum, reflects the establishment of a microbial profile that supports the digestion of endogenously indigestible dietary components in highly feed-efficient pigs. Overall, the results indicate the potential to promote these beneficial functions and further improve feed efficiency through manipulation of dietary and probiotic strategies.<\/jats:p>","DOI":"10.3390\/microorganisms8040563","type":"journal-article","created":{"date-parts":[[2020,4,15]],"date-time":"2020-04-15T04:01:46Z","timestamp":1586923306000},"page":"563","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Host-Microbiota Interactions in Ileum and Caecum of Pigs Divergent in Feed Efficiency Contribute to Nutrient Utilization"],"prefix":"10.3390","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6470-0434","authenticated-orcid":false,"given":"Henry","family":"Reyer","sequence":"first","affiliation":[{"name":"Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6835-7562","authenticated-orcid":false,"given":"Michael","family":"Oster","sequence":"additional","affiliation":[{"name":"Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ursula M.","family":"McCormack","sequence":"additional","affiliation":[{"name":"Animal and Grassland Research and Innovation Centre, Teagasc Pig Development Department, Moorepark, Fermoy, Co. Cork P61 C996, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3939-6255","authenticated-orcid":false,"given":"Eduard","family":"Mur\u00e1ni","sequence":"additional","affiliation":[{"name":"Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0262-395X","authenticated-orcid":false,"given":"Gillian E.","family":"Gardiner","sequence":"additional","affiliation":[{"name":"Department of Science, Waterford Institute of Technology, Waterford, Co. Waterford X91 K0EK, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4714-1057","authenticated-orcid":false,"given":"Siriluck","family":"Ponsuksili","sequence":"additional","affiliation":[{"name":"Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peadar G.","family":"Lawlor","sequence":"additional","affiliation":[{"name":"Animal and Grassland Research and Innovation Centre, Teagasc Pig Development Department, Moorepark, Fermoy, Co. Cork P61 C996, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9523-6790","authenticated-orcid":false,"given":"Klaus","family":"Wimmers","sequence":"additional","affiliation":[{"name":"Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany"},{"name":"Faculty of Agricultural and Environmental Sciences, University Rostock, 18059 Rostock, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,4,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2973","DOI":"10.1038\/ismej.2016.77","article-title":"Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits","volume":"10","author":"Mach","year":"2016","journal-title":"ISME J."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"McCormack, U.M., Curi\u00e3o, T., Buzoianu, S.G., Prieto, M.L., Ryan, T., Varley, P., Crispie, F., Magowan, E., Metzler-Zebeli, B.U., and Berry, D. (2017). Exploring a possible link between the intestinal microbiota and feed efficiency in pigs. Appl. Environ. Microbiol., 83.","DOI":"10.1128\/AEM.00380-17"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1778","DOI":"10.1093\/jas\/sky109","article-title":"Microbiome profiling of commercial pigs from farrow to finish","volume":"96","author":"Youmans","year":"2018","journal-title":"J. Anim. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1673","DOI":"10.1007\/s10482-018-1057-1","article-title":"Differences in gut microbiota composition in finishing landrace pigs with low and high feed conversion ratios","volume":"111","author":"Tan","year":"2018","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"4536","DOI":"10.1038\/s41598-018-22692-0","article-title":"A global comparison of the microbiome compositions of three gut locations in commercial pigs with extreme feed conversion ratios","volume":"8","author":"Quan","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"18933","DOI":"10.1073\/pnas.1007028107","article-title":"Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors","volume":"107","author":"Benson","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/j.vetimm.2005.02.001","article-title":"The expanding role of microarrays in the investigation of macrophage responses to pathogens","volume":"105","author":"McGuire","year":"2005","journal-title":"Vet. Immunol. Immunopathol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.vetmic.2009.08.014","article-title":"Transcriptomics of enterotoxigenic escherichia coli infection. Individual variation in intestinal gene expression correlates with intestinal function","volume":"141","author":"Niewold","year":"2010","journal-title":"Vet. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2709","DOI":"10.1093\/jn\/137.12.2709","article-title":"The novel porcine lactobacillus sobrius strain protects intestinal cells from enterotoxigenic escherichia coli k88 infection and prevents membrane barrier damage","volume":"137","author":"Roselli","year":"2007","journal-title":"J. Nutr."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"6821","DOI":"10.1021\/acs.jafc.7b01925","article-title":"Possible molecular mechanisms by which an essential oil blend from star anise, rosemary, thyme, and oregano and saponins increase the performance and ileal protein digestibility of growing broilers","volume":"65","author":"Reyer","year":"2017","journal-title":"J. Agric. Food Chem."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"3237","DOI":"10.1080\/10408398.2018.1486284","article-title":"Modulation of gastrointestinal barrier and nutrient transport function in farm animals by natural plant bioactive compounds\u2014A comprehensive review: Plant bioactive compounds and gastrointestinal functions","volume":"59","author":"Patra","year":"2019","journal-title":"Crit. Rev. Food Sci. Nutr."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1080\/1040841X.2017.1373062","article-title":"Alternatives to antibiotics in poultry feed: Molecular perspectives","volume":"44","author":"Suresh","year":"2018","journal-title":"Crit. Rev. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1186\/s13059-015-0614-4","article-title":"Site-specific programming of the host epithelial transcriptome by the gut microbiota","volume":"16","author":"Sommer","year":"2015","journal-title":"Genome Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1093\/nutrit\/nuy009","article-title":"Relationship between the gut microbiome and brain function","volume":"76","author":"Mohajeri","year":"2018","journal-title":"Nutr. Rev."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"McCormack, U.M., Curi\u00e3o, T., Metzler-Zebeli, B.U., Magowan, E., Berry, D.P., Reyer, H., Prieto, M.L., Buzoianu, S.G., Harrison, M., and Rebeiz, N. (2019). Porcine feed efficiency-associated intestinal microbiota and physiological traits: Finding consistent cross-locational biomarkers for residual feed intake. mSystems, 4.","DOI":"10.1128\/mSystems.00324-18"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Freeman, T.C., Ivens, A., Baillie, J.K., Beraldi, D., Barnett, M.W., Dorward, D., Downing, A., Fairbairn, L., Kapetanovic, R., and Raza, S. (2012). A gene expression atlas of the domestic pig. BMC Biol., 10.","DOI":"10.1186\/1741-7007-10-90"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Hadlich, F., Reyer, H., Oster, M., Trakooljul, N., Mur\u00e1ni, E., Ponsuksili, S., and Wimmers, K. (2020). Reprobe: Workflow for revised probe assignment and updated probe-set annotation in microarrays. bioRxiv.","DOI":"10.1101\/2020.03.10.985119"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1038\/nbt.2676","article-title":"Predictive functional profiling of microbial communities using 16s rrna marker gene sequences","volume":"31","author":"Langille","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Rohart, F., Gautier, B., Singh, A., and L\u00ea Cao, K.-A. (2017). Mixomics: An r package for \u2018omics feature selection and multiple data integration. PLoS Comp. Biol., 13.","DOI":"10.1101\/108597"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3123","DOI":"10.1093\/bioinformatics\/btu494","article-title":"Stamp: Statistical analysis of taxonomic and functional profiles","volume":"30","author":"Parks","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"4069","DOI":"10.2527\/jas.2012-6197","article-title":"Genetic parameters for different measures of feed efficiency and related traits in boars of three pig breeds","volume":"91","author":"Do","year":"2013","journal-title":"J. Anim. Sci."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1093\/ps\/86.8.1739","article-title":"Developmental regulation of nutrient transporter and enzyme mrna abundance in the small intestine of broilers","volume":"86","author":"Gilbert","year":"2007","journal-title":"Poult. Sci."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1007\/s00438-017-1325-1","article-title":"Exploring the genetics of feed efficiency and feeding behaviour traits in a pig line highly selected for performance characteristics","volume":"292","author":"Reyer","year":"2017","journal-title":"Mol. Genet. Genom."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/s40104-015-0031-2","article-title":"A review of feed efficiency in swine: Biology and application","volume":"6","author":"Patience","year":"2015","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2141","DOI":"10.2527\/jas.2012-6053","article-title":"Intestinal integrity, endotoxin transport and detoxification in pigs divergently selected for residual feed intake","volume":"91","author":"Mani","year":"2013","journal-title":"J. Anim. Sci."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1152\/physiolgenomics.00021.2018","article-title":"Feed-efficient pigs exhibit molecular patterns allowing a timely circulation of hormones and nutrients","volume":"50","author":"Reyer","year":"2018","journal-title":"Physiol. Genom."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Vigors, S., O\u2019Doherty, J.V., Kelly, A.K., O\u2019Shea, C.J., and Sweeney, T. (2016). The effect of divergence in feed efficiency on the intestinal microbiota and the intestinal immune response in both unchallenged and lipopolysaccharide challenged ileal and colonic explants. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0148145"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1038\/nbt1297","article-title":"Complete genome sequence of the erythromycin-producing bacterium saccharopolyspora erythraea nrrl23338","volume":"25","author":"Oliynyk","year":"2007","journal-title":"Nat. Biotechnol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1111\/j.1574-6976.2011.00313.x","article-title":"Streptomyces as symbionts: An emerging and widespread theme?","volume":"36","author":"Seipke","year":"2012","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.5713\/ajas.14.0001R","article-title":"Characterization of dietary energy in swine feed and feed ingredients: A review of recent research results","volume":"28","author":"Velayudhan","year":"2015","journal-title":"Asian Australas J. Anim. Sci."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/2049-1891-5-15","article-title":"Fiber effects in nutrition and gut health in pigs","volume":"5","author":"Lindberg","year":"2014","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.jff.2019.05.035","article-title":"Effects of the different dietary fibers on luminal microbiota composition and mucosal gene expression in pig colons","volume":"59","author":"Xu","year":"2019","journal-title":"J. Funct. Foods"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1848","DOI":"10.1017\/S1751731116000847","article-title":"Pigs that are divergent in feed efficiency, differ in intestinal enzyme and nutrient transporter gene expression, nutrient digestibility and microbial activity","volume":"10","author":"Vigors","year":"2016","journal-title":"Animal"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Zamakhchari, M., Wei, G., Dewhirst, F., Lee, J., Schuppan, D., Oppenheim, F.G., and Helmerhorst, E.J. (2011). Identification of rothia bacteria as gluten-degrading natural colonizers of the upper gastro-intestinal tract. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0024455"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Brown, C.T., Davis-Richardson, A.G., Giongo, A., Gano, K.A., Crabb, D.B., Mukherjee, N., Casella, G., Drew, J.C., Ilonen, J., and Knip, M. (2011). Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0025792"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e00004","DOI":"10.1128\/mSystems.00004-17","article-title":"Meta-analysis to define a core microbiota in the swine gut","volume":"2","author":"Holman","year":"2017","journal-title":"MSystems"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"877","DOI":"10.3389\/fmicb.2015.00877","article-title":"Responses in colonic microbial community and gene expression of pigs to a long-term high resistant starch diet","volume":"6","author":"Sun","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2357","DOI":"10.1128\/JB.00239-11","article-title":"Complete genome sequence of the cellulose-degrading bacterium cellulosilyticum lentocellum","volume":"193","author":"Miller","year":"2011","journal-title":"J. Bacteriol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2206","DOI":"10.3389\/fmicb.2017.02206","article-title":"Effect of dietary forage to concentrate ratios on dynamic profile changes and interactions of ruminal microbiota and metabolites in holstein heifers","volume":"8","author":"Zhang","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.bpg.2016.02.007","article-title":"Physiology of intestinal absorption and secretion","volume":"30","author":"Kiela","year":"2016","journal-title":"Best Pract. Res. Clin. Gastroenterol."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Metzler-Zebeli, B.U., Lawlor, P.G., Magowan, E., McCormack, U.M., Curi\u00e3o, T., Hollmann, M., Ertl, R., Aschenbach, J.R., and Zebeli, Q. (2017). Finishing pigs that are divergent in feed efficiency show small differences in intestinal functionality and structure. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0174917"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/8\/4\/563\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T13:21:10Z","timestamp":1760361670000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/8\/4\/563"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,4,14]]},"references-count":41,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2020,4]]}},"alternative-id":["microorganisms8040563"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms8040563","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,4,14]]}}}