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.

Figure 1

Culturability of 16S rRNA phylotypes in relation to their abundance. 16S rRNA sequences (5915) obtained from faecal samples of six volunteers (for all four diets) were classified into 320 phylotypes (defined at >98% sequence identity) (Supplementary Table S4). The % of phylotypes showing >98% sequence identity to a cultured bacterium is seen to increase with increasing phylotype abundance. The phylotype frequency distribution is shown as a percentage; actual numbers of phylotypes were 9 (>2% of all sequences), 17 (>1%<2%), 24 (>0.5%<1%) and 270 (<0.5%) (total 320). Data refer to volunteers 16, 20, 22 (diet order RS-NSP) and 19, 23, 24 (diet order NSP-RS).

Figure 2

Incidence of phylotypes in different individuals. The distribution of all 320 16S rRNA phylotypes was determined across the six volunteers (see Figure 1, Supplementary Table S4); the numbers of phylotypes found in all six individuals (32) and in five (25), four (20), three (36), two (62) or one (145) of the six are shown here according to bacterial phylum.

Figure 3

Impact of diet and individual variation upon faecal microbiota composition. A principal coordinates analysis (using Canberra distance matrix) based on 16S rRNA clone libraries from 26 faecal samples (obtained from six donors under four dietary conditions) (Supplementary Table S4). Colour code is based on donor (v16, v19, v20, v22, v23 and v24). Diets are indicated as M, maintenance; NSP, non-starch polysaccharide; RS, resistant starch; WL, weight loss. Two samples were analysed for v16 from the M and NSP diets.

Figure 4

Diet-driven changes in four groups of human colonic bacteria detected by qPCR. Abundance for each targeted group is expressed as a percentage of the signal obtained with a general bacterial primer set (see Supplementary Table S3 for primers and conditions used). All available time points are shown for the 14 volunteers: left-hand panels show the diet order M-NSP-RS-WL and right-hand panels M-RS-NSP-WL, (a and b) R-ruminococci (relatives of R. bromii); (c and d) relatives of E. rectale and Roseburia spp.; (e and f) Bifidobacterium spp.; (g and h) relatives of O. valericigenes.

Figure 5

Populations of three groups of potentially amylolytic bacteria on the RS (high-resistant starch) and NSP (low-resistant starch) diets. Populations, estimated by qPCR, are shown for R-ruminococci, E. rectale/Roseburia spp. and Bifidobacterium spp. for all 14 volunteers, according to diet order. Data are the mean values for each volunteer during the second and third week of the RS and NSP diets (overall means are given in Table 2).

Figure 6

Starch digestibilities. The whole tract % digestibility of resistant starch was determined after estimating resistant starch present in the supplied diet and in 24 h faecal samples (see Materials and Methods section). Results are shown only for the NSP and RS diet periods. The markedly reduced resistant starch digestibilities in v14 and v25 correspond with low R-ruminococcal numbers in these individuals (see text and Supplementary Table S5).