Just an abstract I enjoyed....
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.
Introduction
The remarkable diversity of the human colonic microbiota at the level of bacterial species and phylotypes has become apparent from 16S rRNA-based analyses. Not only are hundreds of phylotypes typically estimated to be present in the human colonic microbiota from a given faecal sample (Suau et al., 1999; Eckburg et al., 2005), but samples from different individuals have been reported to show limited overlap in the phylotypes present (Ley et al., 2006; Turnbaugh et al., 2008). A recent study (Tap et al., 2009), however, has indicated that certain phylotypes occur more commonly than others among the dominant faecal bacteria of different individuals. Identifying the dominant bacterial species that colonize the large intestine and the extent to which these are influenced by diet and host factors is of key importance in uncovering the impact of the colonic microbiota upon human health (Flint et al., 2007; Sokol et al., 2008).
A few studies to date have examined temporal changes, and these suggest a degree of stability in the colonic microbiota of individuals consuming their normal diets (Franks et al., 1998; Zoetendal et al., 1998; Costello et al., 2009). In contrast, little is known about the impact of dietary change upon microbial community composition. There is evidence that dietary supplementation with prebiotics such as fructo-oligosaccharides and inulin can promote specific groups of bacteria, including bifidobacteria (Bouhnik et al., 2004; Ramirez-Farias et al., 2009). It has also been shown that reductions in total carbohydrate content, in weight loss (WL) diets for obese subjects, have major effects upon the composition and metabolic outputs of the bacterial community in the colon (Duncan et al., 2007, 2008; Brinkworth et al., 2009). These changes are assumed to reflect the fermentation of non-digestible (ND) carbohydrate components (mainly non-starch polysaccharides (NSPs), resistant starch (RS) and certain oligosaccharides) that reach the large intestine. The impact upon the colonic microbiota of controlled changes in the main types of ND carbohydrate normally present in the diet (RS and NSP) has not however been examined in any detail. The ND carbohydrate content of the human diet is considered to influence health. For example, diets high in RS have been shown to benefit insulin sensitivity, possibly mediated by bacterial fermentative activity in the colon (Robertson et al., 2005). Diets containing RS and NSP offer potential benefits in prevention of colorectal cancer through the delivery of fermentation acids, in particular butyrate, to the distal colon (McIntyre et al., 1993; Duncan et al., 2007). Microbial breakdown of NSP also releases bound phytochemicals into the colon (Gill and Rowland, 2002). These health benefits may be particularly important in obese and overweight subjects who are at increased risk of developing colorectal cancer and diabetes (Polednak, 2003; Cani et al., 2007).
This study asks to what extent changes in the major type of ND carbohydrate in the diet influence the dominant bacterial phylotypes present in an individual. It also explores the dynamics of such changes, including their reversibility, for the first time through the use of detailed time courses and a cross-over design. A necessary supplementary question is whether the same dietary change elicits similar changes in the gut microbiota of different individuals. Our results reveal rapid and marked changes in the colonic microbiota of a group of overweight volunteers after a shift in the main type of ingested fermentable carbohydrate (RS or NSP). We also find that these changes can be highly specific to the individual, with potentially important implications for the design of fibre-enriched diets.