title: Dominant and diet-responsive groups of bacteria within the human colonic microbiota.
abstract: The populations of dominant species within the human colonic microbiota can potentially be modified by dietary intake with consequences for health. Here we examined the influence of precisely controlled diets in 14 overweight men. Volunteers were provided successively with a control diet, diets high in resistant starch (RS) or non-starch polysaccharides (NSPs) and a reduced carbohydrate weight loss (WL) diet, over 10 weeks. Analysis of 16S rRNA sequences in stool samples of six volunteers detected 320 phylotypes (defined at >98% identity) of which 26, including 19 cultured species, each accounted for >1% of sequences. Although samples clustered more strongly by individual than by diet, time courses obtained by targeted qPCR revealed that 'blooms' in specific bacterial groups occurred rapidly after a dietary change. These were rapidly reversed by the subsequent diet. Relatives of Ruminococcus bromii (R-ruminococci) increased in most volunteers on the RS diet, accounting for a mean of 17% of total bacteria compared with 3.8% on the NSP diet, whereas the uncultured Oscillibacter group increased on the RS and WL diets. Relatives of Eubacterium rectale increased on RS (to mean 10.1%) but decreased, along with Collinsella aerofaciens, on WL. Inter-individual variation was marked, however, with >60% of RS remaining unfermented in two volunteers on the RS diet, compared to <4% in the other 12 volunteers; these two individuals also showed low numbers of R-ruminococci (<1%). Dietary non-digestible carbohydrate can produce marked changes in the gut microbiota, but these depend on the initial composition of an individual's gut microbiota.
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Alan W
authors.initials: AW
authors.lastname: Walker
authors.forename: Jennifer
authors.initials: J
authors.lastname: Ince
authors.forename: Sylvia H
authors.initials: SH
authors.lastname: Duncan
authors.forename: Lucy M
authors.initials: LM
authors.lastname: Webster
authors.forename: Grietje
authors.initials: G
authors.lastname: Holtrop
authors.forename: Xiaolei
authors.initials: X
authors.lastname: Ze
authors.forename: David
authors.initials: D
authors.lastname: Brown
authors.forename: Mark D
authors.initials: MD
authors.lastname: Stares
authors.forename: Paul
authors.initials: P
authors.lastname: Scott
authors.forename: Aurore
authors.initials: A
authors.lastname: Bergerat
authors.forename: Petra
authors.initials: P
authors.lastname: Louis
authors.forename: Freda
authors.initials: F
authors.lastname: McIntosh
authors.forename: Alexandra M
authors.initials: AM
authors.lastname: Johnstone
authors.forename: Gerald E
authors.initials: GE
authors.lastname: Lobley
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Harry J
authors.initials: HJ
authors.lastname: Flint
mesh_terms: D001105:Archaea / Q000235:genetics / Q000254:growth & development / Q000502:physiology; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism; D044822:Biodiversity; D003106:Colon / Q000382:microbiology*; D018592:Cross-Over Studies; D004032:Diet; D004038:Diet, Reducing; D004040:Dietary Carbohydrates / Q000378:metabolism; D004044:Dietary Proteins / Q000378:metabolism; D005243:Feces / Q000382:microbiology; D006801:Humans; D008297:Male; D054892:Metagenome / Q000235:genetics / Q000502:physiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013213:Starch / Q000378:metabolism
chemical_list: D004040:Dietary Carbohydrates; D004044:Dietary Proteins; D012336:RNA, Ribosomal, 16S; D013213:Starch