Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes

Peng, Xuefeng; Wilken, St. Elmo; Lankiewicz, Thomas S.; Gilmore, Sean P.; Brown, Jennifer L.; Henske, John K.; Swift, Candice L.; Salamov, Asaf; Barry, Kerrie; Grigoriev, Igor V.; Theodorou, Michael K.; Valentine, David L.; O’Malley, Michelle A.

doi:10.1038/s41564-020-00861-0

Title: Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes

Journal Article · Mon Feb 01 00:00:00 EST 2021 · Nature Microbiology

DOI:https://doi.org/10.1038/s41564-020-00861-0· OSTI ID:1763851

Peng, Xuefeng; Wilken, St. Elmo; Lankiewicz, Thomas S.; Gilmore, Sean P.; Brown, Jennifer L.; Henske, John K.;

; Salamov, Asaf; Barry, Kerrie;

; Theodorou, Michael K.;

;

Abstract The herbivore digestive tract is home to a complex community of anaerobic microbes that work together to break down lignocellulose. These microbiota are an untapped resource of strains, pathways and enzymes that could be applied to convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities. We assembled 719 high-quality metagenome-assembled genomes (MAGs) that are unique at the species level. More than 90% of these MAGs are from previously unidentified herbivore gut microorganisms. Microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in terms of both methane production and extent of cellulose degradation, which indicates that fungi have an important role in methane release. Metabolic pathway reconstructions from MAGs of 737 bacteria, archaea and fungi suggest that cross-domain partnerships between fungi and methanogens enabled production of acetate, formate and methane, whereas bacterially dominated consortia mainly produced short-chain fatty acids, including propionate and butyrate. Analyses of carbohydrate-active enzyme domains present in each anaerobic consortium suggest that anaerobic bacteria and fungi employ mostly complementary hydrolytic strategies. The division of labour among herbivore anaerobes to degrade plant biomass could be harnessed for industrial bioprocessing.

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Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0010352; AC02-05CH11231

OSTI ID:: 1763851

Alternate ID(s):: OSTI ID: 1810823

Journal Information:: Nature Microbiology, Journal Name: Nature Microbiology Vol. 6 Journal Issue: 4; ISSN 2058-5276

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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