Barcoded Pyrosequencing Reveals That Consumption of Galactooligosaccharides Results in a Highly Specific Bifidogenic Response in Humans

Abstract

Prebiotics are selectively fermented ingredients that allow specific changes in the gastrointestinal microbiota that confer health benefits to the host. However, the effects of prebiotics on the human gut microbiota are incomplete as most studies have relied on methods that fail to cover the breadth of the bacterial community. The goal of this research was to use high throughput multiplex community sequencing of 16S rDNA tags to gain a community wide perspective of the impact of prebiotic galactooligosaccharide (GOS) on the fecal microbiota of healthy human subjects. Fecal samples from eighteen healthy adults were previously obtained during a feeding trial in which each subject consumed a GOS-containing product for twelve weeks, with four increasing dosages (0, 2.5, 5, and 10 gram) of GOS. Multiplex sequencing of the 16S rDNA tags revealed that GOS induced significant compositional alterations in the fecal microbiota, principally by increasing the abundance of organisms within the Actinobacteria. Specifically, several distinct lineages of Bifidobacterium were enriched. Consumption of GOS led to five- to ten-fold increases in bifidobacteria in half of the subjects. Increases in Firmicutes were also observed, however, these changes were detectable in only a few individuals. The enrichment of bifidobacteria was generally at the expense of one group of bacteria, the Bacteroides. The responses to GOS and the magnitude of the response varied between individuals, were reversible, and were in accordance with dosage. The bifidobacteria were the only bacteria that were consistently and significantly enriched by GOS, although this substrate supported the growth of diverse colonic bacteria in mono-culture experiments. These results suggest that GOS can be used to enrich bifidobacteria in the human gastrointestinal tract with remarkable specificity, and that the bifidogenic properties of GOS that occur in vivo are caused by selective fermentation as well as by competitive interactions within the intestinal environment.

In Vivo Selection To Identify Bacterial Strains with Enhanced Ecological Performance in Synbiotic Applications

“…3A). These findings confirm the highly specific bifidogenic response of GOS, which was previously demonstrated in humans (32).…”

“…In a previous study (25,32), we reported a significant and remarkably specific enrichment of Bifidobacterium populations in human subjects during dietary supplementation with GOS (as demonstrated by 454 sequencing, genus-specific qRT-PCR, and quantitative culture), which is in agreement with data from other GOS feeding studies (33)(34)(35)(36)(37)(38). Cultural enumeration of fecal samples during the human trial allowed us to identify individuals in which bifidobacteria were enriched by GOS and from whom strains likely to utilize GOS in vivo could be selected.…”

“…Based on 16S rRNA sequencing, IVS-1 had 98.4% identity (100% query coverage and an E value of zero) with the 16S rRNA gene of B. adolescentis ATCC 15703 T and was therefore allotted to this species. However, the strain belongs to a distinct phylogenetic cluster (Bifidobacterium species II cluster) detectable by using the V1-V3 region of the 16S rRNA gene (32). This cluster was significantly enriched by GOS in all subjects, including the individual from whom IVS-1 was isolated (Fig.…”

“…Based on the culture data, 454 sequencing (32), and the GOS fermentation tests, we selected one strain and designated it IVS-1. This strain originated from a subject who showed a strong bifidogenic response to GOS (Fig.…”

Human gut microbiota: does diet matter?

“…The best sources of naturally occurring prebiotics may be found in vegetables such as artichokes, onions, chicory, garlic and leeks (167) . There are numerous studies in which the bifidogenic properties of prebiotics are shown (121,122,166,(168)(169)(170)(171) . In addition, increase in abundance of lactobacilli (121,122) and F. prausnitzii (170,172) has been shown.…”