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Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem

Lookup NU author(s): Professor William Willats

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


Abstract

Because of their agricultural value, there is a great body of research dedicated to understanding the microorganisms responsible for rumen carbon degradation. However, we lack a holistic view of the microbial food web responsible for carbon processing in this ecosystem. Here, we sampled rumen-fistulated moose, allowing first of its kind access to rumen microbial communities actively degrading woody plant biomass in real-time. We resolved 1,193 viral contigs and unique, near-complete microbial metagenome-assembled genomes (MAGs), many of which lacked previous metabolic insights. Plant-derived metabolites were measured with NMR and carbohydrate microarrays to quantify the carbon nutrient landscape. Network analyses directly linked measured metabolites to expressed proteins from these unique MAGs, revealing a genome-resolved three-tiered carbohydrate fueled trophic system. This provided a glimpse into microbial specialization into functional guilds defined by specific metabolites. To validate our proteomic inferences, the catalytic activity of a polysaccharide utilization locus from a highly connected metabolic hub genome was confirmed using heterologous gene expression. Viral detected proteins and linkages to microbial hosts demonstrate that phage are active controllers of rumen ecosystem function. Our findings elucidate the microbial and viral members, as well as their metabolic interdependencies, that support in situ carbon degradation in the rumen ecosystem.


Publication metadata

Author(s): Solden LM, Naas AE, Roux S, Daly RA, Collins WB, Nicora CD, Purvine SO, Hoyt DW, Schückel J, Jorgensen B, Willats W, Spalinger DE, Firkins JL, Lipton MS, Sullivan MB, Pope PB, Wrighton KC

Publication type: Article

Publication status: Published

Journal: Nature Microbiology

Year: 2018

Volume: 3

Pages: 1274-1284

Online publication date: 24/10/2018

Acceptance date: 25/07/2018

Date deposited: 02/07/2018

ISSN (electronic): 2058-5276

Publisher: Nature Publishing Group

URL: https://doi.org/10.1038/s41564-018-0225-4

DOI: 10.1038/s41564-018-0225-4


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