{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T16:51:59Z","timestamp":1791305519324,"version":"4.3.1"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:00:00Z","timestamp":1789084800000},"content-version":"vor","delay-in-days":253,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"US Department of Energy, Office of Science, Biological and Environmental Research Program","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"https:\/\/ror.org\/00mmn6b08","id-type":"ROR","asserted-by":"crossref"}]},{"name":"US Department of Energy, Office of Science","award":["DE-SC0022142"],"award-info":[{"award-number":["DE-SC0022142"]}],"id":[{"id":"https:\/\/ror.org\/00mmn6b08","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Anaerobic fermentation with microbial communities is an emerging platform for converting lignocellulosic biomass to biofuels and bioproducts. The process relies on diverse anaerobic microbes that interact to deconstruct and convert lignocellulosic biomass into a range of products, such as volatile fatty acids (VFAs), through arresting methanogenesis during fermentation. However, defining the distinct functional roles played by various fungi and bacteria during anaerobic biodegradation remains poorly understood. Here, we performed parallel enrichment experiments from cow feces, goat feces, and anaerobic digester sludge, selecting for fungal- or bacterial-dominated communities that convert sorghum biomass into VFAs. Subsequently, we reconstructed metabolic networks across these enrichments using recovered bacterial metagenome-assembled genomes (MAGs), fungal isolate genomes, and genome-centric metatranscriptomics. This enabled direct comparison of the carbohydrate-active enzymes and fermentation pathways expressed by bacterial and fungal communities during lignocellulose conversion to VFAs. Our findings implicate diverse bacteria affiliated with the Bacteroidales and Lachnospiraceae in the direct conversion of lignocellulosic biomass to propionate and butyrate, respectively, whereas Neocallimastix-dominated fungal enrichments converted lignocellulose to lactate, acetate, and formate. Analysis of carbohydrate-active enzymes revealed that bacterial and fungal communities primarily targeted the same dominant lignocellulosic substrates while employing distinct enzyme repertoires and multidomain carbohydrate-active enzyme architectures, highlighting complementary enzymatic strategies for accessing and deconstructing lignocellulosic biomass. We anticipate that these findings will help inform efforts to develop synthetic consortia with tailored functionality for low-cost conversion of lignocellulosic biomass to fuels and bio-based chemicals.<\/jats:p>","DOI":"10.1093\/ismeco\/ycag262","type":"journal-article","created":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T11:51:30Z","timestamp":1789041090000},"source":"Crossref","is-referenced-by-count":0,"title":["Carbohydrate-active enzyme architectures reflect distinct fungal and bacterial strategies for lignocellulose conversion to volatile fatty acids"],"prefix":"10.1093","volume":"6","author":[{"given":"Christopher E","family":"Lawson","sequence":"first","affiliation":[{"name":"Joint BioEnergy Institute , 5885 Hollis St 4th Floor, Emeryville, CA 94608 ,","place":["United States"]},{"name":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Rd, Berkeley, CA 94720 ,","place":["United States"]},{"name":"Department of Chemical Engineering and Applied Chemistry, University of Toronto , 200 College Street, Toronto, ON M5S 3E5 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel P","family":"Howard","sequence":"additional","affiliation":[{"name":"Department of Chemical Engineering and Applied Chemistry, University of Toronto , 200 College Street, Toronto, ON M5S 3E5 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas S","family":"Lankiewicz","sequence":"additional","affiliation":[{"name":"Joint BioEnergy Institute , 5885 Hollis St 4th Floor, Emeryville, CA 94608 ,","place":["United States"]},{"name":"Department of Chemical Engineering, University of California, Santa Barbara , 3357 Engrg II UCSB, Santa Barbara, CA 93106 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James B","family":"Brown","sequence":"additional","affiliation":[{"name":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Rd, Berkeley, CA 94720 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven W","family":"Singer","sequence":"additional","affiliation":[{"name":"Joint BioEnergy Institute , 5885 Hollis St 4th Floor, Emeryville, CA 94608 ,","place":["United States"]},{"name":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Rd, Berkeley, CA 94720 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H\u00e9ctor Garc\u00eda","family":"Mart\u00edn","sequence":"additional","affiliation":[{"name":"Joint BioEnergy Institute , 5885 Hollis St 4th Floor, Emeryville, CA 94608 ,","place":["United States"]},{"name":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Rd, Berkeley, CA 94720 ,","place":["United States"]},{"name":"DOE Agile BioFoundry , Emery Station East, 5885 Hollis Street, Emeryville, CA 94608 ,","place":["United States"]},{"name":"BCAM, Basque Center for Applied Mathematics , Mazarredo Zumarkalea, 14, Abando, 48009 Bilbao, Bizkaia ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6065-8491","authenticated-orcid":false,"given":"Michelle A","family":"O\u2019Malley","sequence":"additional","affiliation":[{"name":"Joint BioEnergy Institute , 5885 Hollis St 4th Floor, Emeryville, CA 94608 ,","place":["United States"]},{"name":"Department of Chemical Engineering, University of California, Santa Barbara , 3357 Engrg II UCSB, Santa Barbara, CA 93106 ,","place":["United States"]},{"name":"Department of Bioengineering, University of California , Santa Barbara, Bioengineering Building, Room 1101494 UCEN Rd, Santa Barbara, CA 93106-5170 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,11]]},"reference":[{"key":"2026100612015046800_ref1","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1016\/j.biortech.2014.09.103","article-title":"Anaerobic digestion of lignocellulosic biomass: challenges and opportunities","volume":"178","author":"Sawatdeenarunat","year":"2015","journal-title":"Bioresour Technol"},{"key":"2026100612015046800_ref2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2023008118","article-title":"Toward net-zero sustainable aviation fuel with wet waste\u2013derived volatile fatty acids, physical sciences","volume":"118","author":"Huq","year":"2021","journal-title":"Proc Natl Acad Sci"},{"key":"2026100612015046800_ref3","doi-asserted-by":"publisher","first-page":"1249","DOI":"10.1080\/21655979.2021.1996044","article-title":"A glimpse of the world of volatile fatty acids production and application: a review","volume":"13","author":"Agnihotri","year":"2022","journal-title":"Bioengineered"},{"key":"2026100612015046800_ref4","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1038\/s41564-020-00861-0","article-title":"Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes","volume":"6","author":"Peng","year":"2021","journal-title":"Nat Microbiol"},{"key":"2026100612015046800_ref5","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.00961","article-title":"Substrate-driven convergence of the microbial community in lignocellulose-amended enrichments of gut microflora from the Canadian beaver (Castor canadensis) and north American moose (Alces americanus)","volume":"7","author":"Wong","year":"2016","journal-title":"Front Microbiol"},{"key":"2026100612015046800_ref6","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1016\/j.tim.2017.05.012","article-title":"Ecological insights into the dynamics of 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F1 in monoculture and co-culture with a syntrophic methanogen","volume":"10","author":"Li","year":"2019","journal-title":"Front Microbiol"},{"key":"2026100612015046800_ref32","doi-asserted-by":"publisher","article-title":"Engineering anaerobic fungal-bacterial consortia for direct conversion of lignocellulosic biomass into medium-chain fatty acids","author":"Kim","DOI":"10.1101\/2025.08.19.670934"},{"key":"2026100612015046800_ref33","doi-asserted-by":"publisher","first-page":"jkaf137","DOI":"10.1093\/g3journal\/jkaf137","article-title":"Genomic and transcriptomic characterization of carbohydrate-active enzymes in the anaerobic fungus Neocallimastix cameroonii var. constans","volume":"15","author":"Blair","year":"2025","journal-title":"G3 (Bethesda)"},{"key":"2026100612015046800_ref34","doi-asserted-by":"publisher","volume":"14","journal-title":"Biotechnol 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