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 498% identity) of which 26, including 19 cultured species, each accounted for 41% 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 460% of RS remaining unfermented in two volunteers on the RS diet, compared to o4% in the other 12 volunteers; these two individuals also showed low numbers of R-ruminococci (o1%). 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.

Modulation of the gut microbiota by prebiotic fibres and bacteriocins

“…Moreover, R. bromii was suggested to be a keystone species in resistant starch degradation, particularly type 3, which is required for the other bacteria to utilize the products from resistant starch [57]. Concordantly to the other studies [16,55,56], the Ruminococcus genus (including R. bromii ) increased in relative abundance in growing pigs that were fed with a type 3 resistant starch-containing diet [30]. An alteration in gut microbiome and a predominance of beneficial bacterial populations were observed in these pigs compared to control pigs.…”

“…bromii , E. rectale and Roseburia spp. populations in the gut of different animal models and humans [16,55,56]. Moreover, R. bromii was suggested to be a keystone species in resistant starch degradation, particularly type 3, which is required for the other bacteria to utilize the products from resistant starch [57].…”

Human gut microbiota: does diet matter?

“…), resistant starch (stimulates bifidobacteria, Bacteroides spp., Ruminococcus bromii, E. rectale and Roseburia spp. ), β-glucan (stimulates bifidobacteria) and fructan (stimulates bifidobacteria, Bacteroides spp., lactobacilli and butyrate-producers) are well recognised (144,(154)(155)(156)(157)(158)(159)(160)(161) . In addition, arabinoxylan-oligosaccharides, which are enzymatic hydrolysis products of arabinoxylan, have been shown to stimulate the growth of bifidobacteria in some studies (156) .…”

Biome engineering‐2020

“…Why are the effects so small? One reason could be that the effect of the diet changes on the microbiota did not overcome the inter‐subject variations in the intestinal microbiota (Walker et al ., 2011; Wu et al ., 2011). Notably, only studies using a cross‐over design where both diets were given to the same subjects showed clear effects (David et al ., 2014).…”