title: Biomass utilization by gut microbiomes.
abstract: Mammals rely entirely on symbiotic microorganisms within their digestive tract to gain energy from plant biomass that is resistant to mammalian digestive enzymes. Especially in herbivorous animals, specialized organs (the rumen, cecum, and colon) have evolved that allow highly efficient fermentation of ingested plant biomass by complex anaerobic microbial communities. We consider here the two most intensively studied, representative gut microbial communities involved in degradation of plant fiber: those of the rumen and the human large intestine. These communities are dominated by bacteria belonging to the Firmicutes and Bacteroidetes phyla. In Firmicutes, degradative capacity is largely restricted to the cell surface and involves elaborate cellulosome complexes in specialized cellulolytic species. By contrast, in the Bacteroidetes, utilization of soluble polysaccharides, encoded by gene clusters (PULs), entails outer membrane binding proteins, and degradation is largely periplasmic or intracellular. Biomass degradation involves complex interplay between these distinct groups of bacteria as well as (in the rumen) eukaryotic microorganisms.
authors.affiliation: Department of Animal Sciences and Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; email: bwhite44@illinois.edu.
authors.forename: Bryan A
authors.initials: BA
authors.lastname: White
authors.forename: Raphael
authors.initials: R
authors.lastname: Lamed
authors.forename: Edward A
authors.initials: EA
authors.lastname: Bayer
authors.forename: Harry J
authors.initials: HJ
authors.lastname: Flint
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D018533:Biomass; D041981:Gastrointestinal Tract / Q000378:metabolism / Q000382:microbiology*; D006801:Humans; D064307:Microbiota
keywords: carbohydrate-active enzymes (CAZymes); carbohydrate-binding module (CBM); cohesin; dockerin; glycoside hydrolases; polysaccharide utilization loci (PULs)