title: Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonicFirmicutes.
abstract: FirmicutesandBacteroidetesare 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 theBacteroidetes, with very little known about theFirmicutes. This work investigates the carbohydrate-active enzymes (CAZymes) in a group ofFirmicutes,Roseburiaspp. andEubacterium rectale, which play an important role in producing butyrate from dietary carbohydrates and in health maintenance. Genome sequences of 11 strains representingE. rectaleand fourRoseburiaspp. 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 ofRoseburiaspp. andE. rectale, forming distinct polysaccharide utilization loci (PULs). Whilst PULs are also a common feature inBacteroidetes, key differences were noted in theseFirmicutes, including the absence of close homologues ofBacteroidespolysaccharide utilization genes, hence we refer to Gram-positive PULs (gpPULs). Most CAZyme genes in theRoseburia/E. rectalegroup are organized into gpPULs. Variation in gpPULs can explain the high degree of nutritional specialization at the species level within this group.
authors.affiliation: 1​ Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: O Sheridan
authors.affiliation: 1​ Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK.
authors.forename: Jennifer C
authors.initials: JC
authors.lastname: Martin
authors.affiliation: 2​ Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
authors.forename: Trevor D
authors.initials: TD
authors.lastname: Lawley
authors.affiliation: 2​ Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
authors.forename: Hilary P
authors.initials: HP
authors.lastname: Browne
authors.affiliation: 3​ Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
authors.forename: Hugh M B
authors.initials: HMB
authors.lastname: Harris
authors.affiliation: 4​ Unité de Microbiologie INRA, Centre de Recherche de Clermont-Ferrand/Theix, 63122 Saint Genès Champanelle, France.
authors.forename: Annick
authors.initials: A
authors.lastname: Bernalier-Donadille
authors.affiliation: 1​ Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK.
authors.forename: Sylvia H
authors.initials: SH
authors.lastname: Duncan
authors.affiliation: 3​ Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
authors.forename: Paul W
authors.initials: PW
authors.lastname: O'Toole
authors.affiliation: 1​ Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK.
authors.forename: Karen
authors.initials: K
authors.lastname: P Scott
authors.affiliation: 1​ Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK.
authors.forename: Harry
authors.initials: H
authors.lastname: J Flint
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D002087:Butyrates / Q000378:metabolism; D003106:Colon / Q000382:microbiology*; D004040:Dietary Carbohydrates / Q000378:metabolism; D004798:Enzymes / Q000235:genetics* / Q000378:metabolism; D000068536:Bacillota / Q000201:enzymology* / Q000235:genetics* / Q000378:metabolism; D016680:Genome, Bacterial; D006801:Humans; D011134:Polysaccharides / Q000378:metabolism*; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins; D002087:Butyrates; D004040:Dietary Carbohydrates; D004798:Enzymes; D011134:Polysaccharides
keywords: Carbohydrate; Lachnospiraceae; Roseburia; comparative genomics; gut microbiota; obligate anaerobe