Journal Article

Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis

Cunningham, Andrew C, Dawson, John A, Bramhacharya, Shanti, Suen, Garret, Weimer, Paul J, Kendziorski, Christina, Stevenson, David M, Christopherson, Melissa R

2014

Overview

Bacteria in the genus Ruminococcus are important and ubiquitous members of mammalian guts. In particular, ruminococci are key contributors to the rumen ecosystem because they are capable of digesting a wide range of plant cell wall polysaccharides. In bovines, Ruminococcus albus 7 is a primary cellulose degrader that ferments acetate, a nutrient usable by its host. Moreover, it is one of the few organisms that ferments cellulose to ethanol at mesophilic temperatures in vitro. The mechanism of cellulose degradation by R. albus 7 is not well-defined and is thought to involve pilin-like proteins, unique carbohydrate-binding domains, a thick glycocalyx, and cellulosomes. We compared the genome sequence for R. albus 7 with other Clostridiales known to utilize cellulosomes, in addition to other non-fibrolytic clostridia. We found that R. albus 7 does not encode for cellulosomal components. We further probed the fibrolytic capabilities of R. albus 7 using a combination of fermentation analyses and RNA-seq-based transcriptomics. We found that R. albus 7 is capable of fermenting a wide range of fibrous substrates into ethanol. When grown on cellulose in a chemostat, R. albus 7 utilized a carbohydrate-degrading strategy that involves overexpression of the rare CBM37 domain and the tryptophan biosynthetic operon. Our findings contribute to the understanding of carbohydrate degradation by this organism, which may enhance industrial cellulose fermentation efforts, in addition to providing insight into the role of ruminococci as key members of the mamalian gut microbiota.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,Springer
• Subject: 09 BIOMASS FUELS / acetates / Acetates - metabolism / alcoholic fermentation / Analysis / Animal Genetics and Genomics / Animals / Bacteria / Bacteriology / BASIC BIOLOGICAL SCIENCES / Biomedical and Life Sciences / Biosynthesis / carbohydrate binding / Carbohydrate Metabolism / Carbohydrates / cell walls / Cellulase / Cellulases - genetics / Cellulases - metabolism / Cellulose / Cellulose - metabolism / Cellulose utilization / Cellulosomes - metabolism / Chromosomes / Clostridium / Colleges & universities / Enzymes / Ethanol / Ethanol - metabolism / Ethanol production / Fermentation / Gastrointestinal tract / Gene Expression Profiling / gene overexpression / Genomes / Hydrolysis / in vitro studies / Life Sciences / Microarrays / Microbial Genetics and Genomics / microbial physiology / nucleotide sequences / operon / Phylogeny / Physiological aspects / Plant Genetics and Genomics / Prokaryote microbial genomics / Proteins / Proteomics / Research Article / Rumen / Rumen - microbiology / rumen bacteria / rumen fermentation / Ruminantia / Ruminococcus / Ruminococcus - classification / Ruminococcus - genetics / Ruminococcus - metabolism / Ruminococcus albus / Saccharides / Scholarships & fellowships / Substrate Specificity / temperature / Transcription, Genetic / Transcriptome / transcriptomics / tryptophan / Tryptophan - metabolism