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Firmicutes  and  Bacteroidetes  are the predominant bacterial phyla colonizing the healthy human large intestine. Whilst both ferment dietary fibre, genes responsible for this important activity have been analysed only in the  Bacteroidetes , with very little known about the  Firmicutes . This work investigates the carbohydrate-active enzymes (CAZymes) in a group of  Firmicutes ,  Roseburia  spp. and  Eubacterium rectale , which play an important role in producing butyrate from dietary carbohydrates and in health maintenance. Genome sequences of 11 strains representing  E. rectale  and four  Roseburia  spp. were analysed for carbohydrate-active genes. Following assembly into a pan-genome, core, variable and unique genes were identified. The 1840 CAZyme genes identified in the pan-genome were assigned to 538 orthologous groups, of which only 26 were present in all strains, indicating considerable inter-strain variability. This analysis was used to categorize the 11 strains into four carbohydrate utilization ecotypes (CUEs), which were shown to correspond to utilization of different carbohydrates for growth. Many glycoside hydrolase genes were found linked to genes encoding oligosaccharide transporters and regulatory elements in the genomes of  Roseburia  spp. and  E. rectale , forming distinct polysaccharide utilization loci (PULs). Whilst PULs are also a common feature in  Bacteroidetes , key differences were noted in these  Firmicutes , including the absence of close homologues of  Bacteroides  polysaccharide utilization genes, hence we refer to Gram-positive PULs (gpPULs). Most CAZyme genes in the  Roseburia / E. rectale  group are organized into gpPULs. Variation in gpPULs can explain the high degree of nutritional specialization at the species level within this group.

Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes