{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T12:14:53Z","timestamp":1768479293510,"version":"3.49.0"},"posted":{"date-parts":[[2019,4,10]]},"group-title":"Bioinformatics","reference-count":37,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2019,4,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Indoles have been shown to play a significant role in cardiometabolic disorders. While some individual bacterial species are known to produce indole-adducts, to our best knowledge no studies have made use of publicly available genome data to identify prokaryotes, specifically those associated with the human gut microbiota, contributing to the indole metabolic network.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>\n                    Here, we propose a computational strategy, comprising the integration of KEGG and BLAST, to identify prokaryote-specific metabolic reactions relevant for the production of indoles, as well as to predict new members of the human gut microbiota potentially involved in these reactions. By identifying relevant prokaryotic species for further validation studies\n                    <jats:italic>in vitro<\/jats:italic>\n                    , this strategy represents a useful approach for those interrogating the metabolism of other gut-derived microbial metabolites relevant to human health.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Availability<\/jats:title>\n                  <jats:p>\n                    All R scripts and files (gut microbial dataset, FASTA protein sequences, BLASTP output files) are available from\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/AndreaRMICL\/Microbial_networks\">https:\/\/github.com\/AndreaRMICL\/Microbial_networks<\/jats:ext-link>\n                    .\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>\n                    ARM:\n                    <jats:email>andrea.rodriguez-martinez13@imperial.ac.uk<\/jats:email>\n                    ; LH:\n                    <jats:email>lesley.hoyles@ntu.ac.uk<\/jats:email>\n                    .\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/602458","type":"posted-content","created":{"date-parts":[[2019,4,10]],"date-time":"2019-04-10T18:38:01Z","timestamp":1554921481000},"source":"Crossref","is-referenced-by-count":0,"title":["A network-based data-mining approach to investigate indole-related microbiota-host co-metabolism"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7107-7211","authenticated-orcid":false,"given":"Ana Luisa","family":"Neves","sequence":"first","affiliation":[]},{"given":"Andrea","family":"Rodriguez-Martinez","sequence":"additional","affiliation":[]},{"given":"Rafael","family":"Ayala","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4971-9003","authenticated-orcid":false,"given":"Joram M","family":"Posma","sequence":"additional","affiliation":[]},{"given":"MR","family":"Abellona U","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0384-7317","authenticated-orcid":false,"given":"Julien","family":"Chilloux","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8123-8349","authenticated-orcid":false,"given":"Jeremy K","family":"Nicholson","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9523-7024","authenticated-orcid":false,"given":"Marc-Emmanuel","family":"Dumas","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6418-342X","authenticated-orcid":false,"given":"Lesley","family":"Hoyles","sequence":"additional","affiliation":[]}],"member":"54368","reference":[{"key":"2019041211351627000_602458v1.1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1990.9999"},{"key":"2019041211351627000_602458v1.2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2672.2006.02896.x"},{"key":"2019041211351627000_602458v1.3","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1128\/AEM.44.2.275-280.1982","article-title":"Mass spectrometric quantification of indole-3-acetic Acid in Rhizobium culture supernatants: relation to root hair curling and nodule initiation","volume":"44","year":"1982","journal-title":"Appl Environ Microbiol"},{"issue":"3","key":"2019041211351627000_602458v1.4","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1093\/clinchem\/30.3.426","article-title":"Use of high-resolution proton nuclear magnetic resonance spectroscopy for rapid multi-component analysis of urine","volume":"30","year":"1984","journal-title":"Clin Chem"},{"key":"2019041211351627000_602458v1.5","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.2215\/CJN.03980609","article-title":"Serum Indoxyl Sulfate Is Associated with Vascular Disease and Mortality in Chronic Kidney Disease Patients","volume":"4","year":"2009","journal-title":"Clin J Am Soc Nephro"},{"key":"2019041211351627000_602458v1.6","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0073076"},{"key":"2019041211351627000_602458v1.7","doi-asserted-by":"publisher","DOI":"10.1038\/nature17645"},{"key":"2019041211351627000_602458v1.8","unstructured":"Chamberlain, S. , et al. 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