{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T14:29:13Z","timestamp":1774621753738,"version":"3.50.1"},"reference-count":175,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2015,1,14]],"date-time":"2015-01-14T00:00:00Z","timestamp":1421193600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Computation"],"abstract":"<jats:p>A large and growing body of research implicates aberrant immune response and compositional shifts of the intestinal microbiota in the pathogenesis of many intestinal disorders. The molecular and physical interaction between the host and the microbiota, known as the host-microbiota interactome, is one of the key drivers in the pathophysiology of many of these disorders. This host-microbiota interactome is a set of dynamic and complex processes, and needs to be treated as a distinct entity and subject for study. Disentangling this complex web of interactions will require novel approaches, using a combination of data-driven bioinformatics with knowledge-driven computational modeling. This review describes the computational approaches for investigating the host-microbiota interactome, with emphasis on the human intestinal tract and innate immunity, and highlights open challenges and existing gaps in  the computation methodology for advancing our knowledge about this important facet of  human health.<\/jats:p>","DOI":"10.3390\/computation3010002","type":"journal-article","created":{"date-parts":[[2015,1,14]],"date-time":"2015-01-14T10:33:15Z","timestamp":1421231595000},"page":"2-28","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Computational Studies of the Intestinal  Host-Microbiota Interactome"],"prefix":"10.3390","volume":"3","author":[{"given":"Scott","family":"Christley","sequence":"first","affiliation":[{"name":"Department of Surgery, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA"}]},{"given":"Chase","family":"Cockrell","sequence":"additional","affiliation":[{"name":"Department of Surgery, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA"}]},{"given":"Gary","family":"An","sequence":"additional","affiliation":[{"name":"Department of Surgery, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA"}]}],"member":"1968","published-online":{"date-parts":[[2015,1,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nature11209","article-title":"A framework for human microbiome research","volume":"486","author":"Consortium","year":"2012","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","author":"Consortium","year":"2012","journal-title":"Nature"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature08821","article-title":"A human gut microbial gene catalogue established by metagenomic sequencing","volume":"464","author":"Qin","year":"2010","journal-title":"Nature"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1038\/nature11550","article-title":"Diversity, stability and resilience of the human gut microbiota","volume":"489","author":"Lozupone","year":"2012","journal-title":"Nature"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"R50","DOI":"10.1186\/gb-2011-12-5-r50","article-title":"Moving pictures of the human microbiome","volume":"12","author":"Caporaso","year":"2011","journal-title":"Genome Biol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1038\/ismej.2010.161","article-title":"Spatial organization of intestinal microbiota in the mouse ascending colon","volume":"5","author":"Nava","year":"2011","journal-title":"ISME J."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1038\/ismej.2013.185","article-title":"Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota","volume":"8","author":"Zhang","year":"2013","journal-title":"ISME J."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"4578","DOI":"10.1073\/pnas.1000081107","article-title":"Succession of microbial consortia in the developing infant gut microbiome","volume":"108","author":"Koenig","year":"2011","journal-title":"Proc. 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