Modulation of the human gut microbiota by dietary fibres occurs at the species level

Abstract

BackgroundDietary intake of specific non-digestible carbohydrates (including prebiotics) is increasingly seen as a highly effective approach for manipulating the composition and activities of the human gut microbiota to benefit health. Nevertheless, surprisingly little is known about the global response of the microbial community to particular carbohydrates. Recent in vivo dietary studies have demonstrated that the species composition of the human faecal microbiota is influenced by dietary intake. There is now potential to gain insights into the mechanisms involved by using in vitro systems that produce highly controlled conditions of pH and substrate supply.ResultsWe supplied two alternative non-digestible polysaccharides as energy sources to three different human gut microbial communities in anaerobic, pH-controlled continuous-flow fermentors. Community analysis showed that supply of apple pectin or inulin resulted in the highly specific enrichment of particular bacterial operational taxonomic units (OTUs; based on 16S rRNA gene sequences). Of the eight most abundant Bacteroides OTUs detected, two were promoted specifically by inulin and six by pectin. Among the Firmicutes, Eubacterium eligens in particular was strongly promoted by pectin, while several species were stimulated by inulin. Responses were influenced by pH, which was stepped up, and down, between 5.5, 6.0, 6.4 and 6.9 in parallel vessels within each experiment. In particular, several experiments involving downshifts to pH 5.5 resulted in Faecalibacterium prausnitzii replacing Bacteroides spp. as the dominant sequences observed. Community diversity was greater in the pectin-fed than in the inulin-fed fermentors, presumably reflecting the differing complexity of the two substrates.ConclusionsWe have shown that particular non-digestible dietary carbohydrates have enormous potential for modifying the gut microbiota, but these modifications occur at the level of individual strains and species and are not easily predicted a priori. Furthermore, the gut environment, especially pH, plays a key role in determining the outcome of interspecies competition. This makes it crucial to put greater effort into identifying the range of bacteria that may be stimulated by a given prebiotic approach. Both for reasons of efficacy and of safety, the development of prebiotics intended to benefit human health has to take account of the highly individual species profiles that may result.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-015-0224-3) contains supplementary material, which is available to authorized users.

Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate

“…In Figure 2, the microbial dynamics within the range of the studied dilution rates is presented on three taxonomic levels, phylum, family, and species, while differences can be seen mainly below the family level as also shown by Chung et al [9] The main phylum in both inocula, Firmicutes, remained dominant throughout the cultivation experiments. In De-stat cultures, the proportion of Bacteroidetes was higher at low dilution rates ( D  < 0.1 1/h) but not significantly in the NW culture on AP, while decrease was observed in the OW cultures on this substrate.…”

“…Various in vitro models of the gut microbiota have been used to examine the effects of prebiotics [9,10], probiotics [11], and dietary modulations [12] on the gut microbiota and its metabolites. In vitro models facilitate frequent sampling and increased reproducibility [13].…”

Modulation of Gut Microbiota of Overweight Mice by Agavins and Their Association with Body Weight Loss

“…This might be mediated by selected supplement addition for specific bacterial taxa that tolerate more acidic pH [33], since direct effect of probiotic supplements on the microbiota have not been demonstrated [14,34,35]. Also, acetic acid suppresses appetite [36] and propionate and butyrate acids modulate hormones such as GLP-1 and PYY, involved in satiety [5−7].…”

The human gut microbiome as source of innovation for health: Which physiological and therapeutic outcomes could we expect?

“…It was recently shown that the response to a probiotic mix may be modulated by the initial microbiota configuration, the latter driving the permissivity to fermented food lactic acid bacteria [106,107]. Similarly, work by Chung et al indicates that depending on the presence/absence of specific fiber degraders, the microbiota may be totally irresponsive to specific fibers [108]. This will have to be documented further if we want to determine the degree of personalization made possible by nutritionbased strategies of modulation of the ecology of the human intestinal microbiota.…”