Original Article

Subject Category: Microbe-microbe and microbe-host interactions

The ISME Journal (2011) 5, 220–230; doi:10.1038/ismej.2010.118; published online 5 August 2010

Dominant and diet-responsive groups of bacteria within the human colonic microbiota

Alan W Walker1, Jennifer Ince2, Sylvia H Duncan2, Lucy M Webster2, Grietje Holtrop3, Xiaolei Ze2, David Brown2, Mark D Stares1, Paul Scott1, Aurore Bergerat2, Petra Louis2, Freda McIntosh2, Alexandra M Johnstone2, Gerald E Lobley2, Julian Parkhill1 and Harry J Flint2

  1. 1Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, UK
  2. 2Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
  3. 3Biomathematics and Statistics Scotland, Aberdeen, UK

Correspondence: HJ Flint, Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen AB21 9SB, UK. E-mail: H.Flint@abdn.ac.uk

Received 25 January 2010; Revised 11 May 2010; Accepted 21 June 2010; Published online 5 August 2010.



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.


human colon; resistant starch; 16S rRNA; phylotypes; Ruminococcus; temporal change