Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes
Résumé
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 fr
om 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 uniqu
e 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 diffe
rent 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.
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