{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T23:38:17Z","timestamp":1789601897343,"version":"build-2803163510"},"reference-count":68,"publisher":"National Academy of Sciences","issue":"35","license":[{"start":{"date-parts":[[2025,8,25]],"date-time":"2025-08-25T00:00:00Z","timestamp":1756080000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01AI049187"],"award-info":[{"award-number":["R01AI049187"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["RO1AI55O80"],"award-info":[{"award-number":["RO1AI55O80"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2025,9,2]]},"abstract":"<jats:p>\n                    The fungal species\n                    <jats:italic toggle=\"yes\">Candida albicans<\/jats:italic>\n                    and the bacterium\n                    <jats:italic toggle=\"yes\">Enterococcus faecalis<\/jats:italic>\n                    are members of the human gut microbiome. To explore the range of interactions between these two species, we utilized dual RNA-sequencing to transcriptionally profile both\n                    <jats:italic toggle=\"yes\">C. albicans<\/jats:italic>\n                    and\n                    <jats:italic toggle=\"yes\">E. faecalis<\/jats:italic>\n                    during coculture (compared with monoculture controls) under two conditions: 1) an in vitro setting that mimics certain features of the gut environment and 2) a gnotobiotic mouse gut model. RNA-seq analysis revealed a large number of gene expression changes induced by one species in the presence of the other. More specifically, both species highly upregulate citrate-metabolizing genes during coculture:\n                    <jats:italic toggle=\"yes\">C. albicans<\/jats:italic>\n                    upregulates\n                    <jats:italic toggle=\"yes\">CIT1<\/jats:italic>\n                    (citrate synthase) which produces citrate, while\n                    <jats:italic toggle=\"yes\">E. faecalis<\/jats:italic>\n                    upregulates its\n                    <jats:italic toggle=\"yes\">cit<\/jats:italic>\n                    operon, which breaks down citrate. In vitro analysis showed directly that citrate cross-feeding (production of citrate by\n                    <jats:italic toggle=\"yes\">C. albicans<\/jats:italic>\n                    and breakdown by\n                    <jats:italic toggle=\"yes\">E. faecalis)<\/jats:italic>\n                    enhances growth of\n                    <jats:italic toggle=\"yes\">E. faecalis<\/jats:italic>\n                    . A main byproduct of citrate metabolism in\n                    <jats:italic toggle=\"yes\">E. faecalis<\/jats:italic>\n                    is formate, a short chain fatty acid toxic to fungi. Our RNA profiling revealed that\n                    <jats:italic toggle=\"yes\">C. albicans<\/jats:italic>\n                    upregulates three formate dehydrogenases (FDHs) during coculture; we show that the FDH genes confer a growth advantage to\n                    <jats:italic toggle=\"yes\">C. albicans<\/jats:italic>\n                    when\n                    <jats:italic toggle=\"yes\">E. faecalis<\/jats:italic>\n                    (or simply formate) is present. These findings reveal a metabolically driven cycle between\n                    <jats:italic toggle=\"yes\">C. albicans<\/jats:italic>\n                    and\n                    <jats:italic toggle=\"yes\">E. faecalis<\/jats:italic>\n                    in the mouse gut and in vitro, where cross-feeding of citrate and detoxification of formate facilitates the growth of both species when they are cultured together.\n                  <\/jats:p>","DOI":"10.1073\/pnas.2504785122","type":"journal-article","created":{"date-parts":[[2025,8,25]],"date-time":"2025-08-25T19:06:57Z","timestamp":1756148817000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":5,"title":["Shared metabolism between a bacterial and fungal species that reside in the human gut"],"prefix":"10.1073","volume":"122","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9738-6808","authenticated-orcid":false,"given":"Haley","family":"Gause","sequence":"first","affiliation":[{"name":"TETRAD Graduate Program, Department of Biochemistry and Biophysics, University of California","place":["San Francisco"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4503-3327","authenticated-orcid":false,"given":"Alexander D.","family":"Johnson","sequence":"additional","affiliation":[{"name":"TETRAD Graduate Program, Department of Biochemistry and Biophysics, University of California","place":["San Francisco"]},{"name":"Department of Microbiology and Immunology, University of California","place":["San Francisco"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2025,8,25]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2016.11.008"},{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41522-022-00275-2"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2023.2296603"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13052-020-0781-0"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra1600266"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2021.1979882"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-18871-1"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/nm.4517"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.01575"},{"key":"e_1_3_4_10_2","first-page":"837","article-title":"Yeasts in the Gut","volume":"106","author":"Schulze J.","year":"2009","unstructured":"J. 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