The Phylogenomic Diversity of Herbivore-Associated Fibrobacter spp. Is Correlated to Lignocellulose-Degrading Potential

Journal Article · Wed Dec 26 00:00:00 EST 2018 · mSphere

DOI:https://doi.org/10.1128/mSphere.00593-18· OSTI ID:1630236

Neumann, Anthony P.  ^[1]; Suen, Garret  ^[1]; Rodrigues, ed., Jorge M.

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1. Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA

ABSTRACT Members of the genusFibrobacterare cellulose-degrading bacteria and common constituents of the gastrointestinal microbiota of herbivores. Although considerable phylogenetic diversity is observed among members of this group, few functional differences explaining the distinct ecological distributions of specific phylotypes have been described. In this study, we sequenced and performed a comparative analysis of whole genomes from 38 novelFibrobacterstrains against the type strains for the two formally describedFibrobacterspeciesF. succinogenesstrain S85 andF. intestinalisstrain NR9. Significant differences in the number of genes encoding carbohydrate-active enzyme families involved in plant cell wall polysaccharide degradation were observed amongFibrobacterphylotypes.F. succinogenesgenomes were consistently enriched in genes encoding carbohydrate-active enzymes compared to those ofF. intestinalisstrains. Moreover, genomes ofF. succinogenesphylotypes that are dominant in the rumen had significantly more genes annotated to major families involved in hemicellulose degradation (e.g., CE6, GH10, and GH43) than did the genomes ofF. succinogenesphylotypes typically observed in the lower gut of large hindgut-fermenting herbivores such as horses. Genes encoding a putative urease were also identified in 12 of theFibrobactergenomes, which were primarily isolated from hindgut-fermenting hosts. Screening for growth on urea as the sole source of nitrogen provided strong evidence that the urease was active in these strains. These results represent the strongest evidence reported to date for specific functional differences contributing to the ecology ofFibrobacterspp. in the herbivore gut. IMPORTANCEThe herbivore gut microbiome is incredibly diverse, and a functional understanding of this diversity is needed to more reliably manipulate this community for specific gain, such as increased production in ruminant livestock. Microbial degraders of plant cell wall polysaccharides in the herbivore gut, particularlyFibrobacterspp., are of fundamental importance to their hosts for digestion of a diet consisting primarily of recalcitrant plant fibers. Considerable phylogenetic diversity exists among members of the genusFibrobacter, but much of this diversity remains cryptic. Here, we used comparative genomics, applied to a diverse collection of recently isolatedFibrobacterstrains, to identify a robust association between carbohydrate-active enzyme gene content and theFibrobacterphylogeny. Our results provide the strongest evidence reported to date for functional differences amongFibrobacterphylotypes associated with either the rumen or the hindgut and emphasize the general significance of carbohydrate-active enzymes in the evolution of fiber-degrading bacteria.

• Research Organization: Univ. of Wisconsin, Madison, WI (United States); Univ. of California, Oakland, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: AC02-05CH11231; SC0008104
• OSTI ID: 1630236
• Alternate ID(s): OSTI ID: 1611013
• Journal Information: mSphere, Journal Name: mSphere Vol. 3 Journal Issue: 6; ISSN 2379-5042
• Publisher: American Society for Microbiology
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Fibrobacter
carbohydrate-active enzymes
cellulose
fiber
genomics
gut microbiota
herbivores