{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T11:23:22Z","timestamp":1773055402136,"version":"3.50.1"},"posted":{"date-parts":[[2026,2,2]]},"group-title":"Bioengineering","reference-count":41,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T00:00:00Z","timestamp":1769990400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01DK130815"],"award-info":[{"award-number":["R01DK130815"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01AT011618"],"award-info":[{"award-number":["R01AT011618"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,3,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Protein-bound uremic toxins are inefficiently cleared by dialysis and contribute to complications in chronic kidney disease, motivating approaches that target their gut-derived precursors. Here we investigate anaerobic\n                  <jats:italic>p<\/jats:italic>\n                  -cresol metabolism by the environmental denitrifier\n                  <jats:italic>Thauera aminoaromatica<\/jats:italic>\n                  S2, a pathway originally evolved for aromatic pollutant degradation. Proteomic stable isotope probing with\n                  <jats:sup>13<\/jats:sup>\n                  C-labeled\n                  <jats:italic>p<\/jats:italic>\n                  -cresol reveals strong incorporation of labeled carbon into\n                  <jats:italic>T. aminoaromatica<\/jats:italic>\n                  proteins, whereas parallel incubations with human fecal microbiomes show minimal incorporation, indicating limited intrinsic gut capacity for\n                  <jats:italic>p<\/jats:italic>\n                  -cresol utilization. Label-enriched proteins enable reconstruction of the anaerobic\n                  <jats:italic>p<\/jats:italic>\n                  -cresol degradation pathway and identification of key enzymes synthesized during growth on\n                  <jats:italic>p<\/jats:italic>\n                  -cresol. Moreover, hydrogel-encapsulated\n                  <jats:italic>T. aminoaromatica<\/jats:italic>\n                  remains active during co-incubation with the gut microbiome, achieving complete removal of 0.3 mM\n                  <jats:italic>p<\/jats:italic>\n                  -cresol in less than 10 hours, a timescale compatible with typical intestinal transit in the colon. Together, these findings establish a biochemical basis for repurposing environmental aromatic degradation pathways for gut-localized\n                  <jats:italic>p<\/jats:italic>\n                  -cresol removal.\n                <\/jats:p>","DOI":"10.64898\/2026.01.30.702948","type":"posted-content","created":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T21:30:13Z","timestamp":1770067813000},"source":"Crossref","is-referenced-by-count":0,"title":["Biochemical mechanism of\n                  <i>p<\/i>\n                  -cresol removal by\n                  <i>Thauera aminoaromatica<\/i>\n                  S2"],"prefix":"10.64898","author":[{"given":"Oishi","family":"Sen","sequence":"first","affiliation":[{"name":"Department of Civil and Environmental Engineering, University of Washington; Seattle, Washington"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pei-Hsin","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, University of Washington; Seattle, Washington"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Prakit","family":"Saingam","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, University of Washington; Seattle, Washington"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bruce J.","family":"Godfrey","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, University of Washington; Seattle, Washington"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonathan","family":"Himmelfarb","sequence":"additional","affiliation":[{"name":"Center for Kidney Disease Innovation, Icahn School of Medicine at Mount Sinai"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Xiong","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Oklahoma"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chongle","family":"Pan","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Oklahoma"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mari Karoliina Henriikka","family":"Winkler","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, University of Washington; Seattle, Washington"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"issue":"2","key":"2026030902151070000_2026.01.30.702948v2.1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.5430\/jbei.v3n2p1","article-title":"Extraction and purification of recombinant intact human Parathyroid Hormone (hPTH) from bacterial cell","volume":"3","year":"2017","journal-title":"Journal of Biomedical Engineering and Informatics"},{"key":"2026030902151070000_2026.01.30.702948v2.2","doi-asserted-by":"crossref","unstructured":"Bedmar, E. 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