In vivo selection to identify bacterial strains with enhanced ecological performance in synbiotic applications

Abstract

One strategy for enhancing the establishment of probiotic bacteria in the human intestinal tract is via the parallel administration of a prebiotic, which is referred to as a synbiotic. Here we present a novel method that allows a rational selection of putative probiotic strains to be used in synbiotic applications: in vivo selection (IVS). This method consists of isolating candidate probiotic strains from fecal samples following enrichment with the respective prebiotic. To test the potential of IVS, we isolated bifidobacteria from human subjects who consumed increasing doses of galactooligosaccharides (GOS) for 9 weeks. A retrospective analysis of the fecal microbiota of one subject revealed an 8-fold enrichment in Bifidobacterium adolescentis strain IVS-1 during GOS administration. The functionality of GOS to support the establishment of IVS-1 in the gastrointestinal tract was then evaluated in rats administered the bacterial strain alone, the prebiotic alone, or the synbiotic combination. Strain-specific quantitative real-time PCR showed that the addition of GOS increased B. adolescentis IVS-1 abundance in the distal intestine by nearly 2 logs compared to rats receiving only the probiotic. Illumina 16S rRNA sequencing not only confirmed the increased establishment of IVS-1 in the intestine but also revealed that the strain was able to outcompete the resident Bifidobacterium population when provided with GOS. In conclusion, this study demonstrated that IVS can be used to successfully formulate a synergistic synbiotic that can substantially enhance the establishment and competitiveness of a putative probiotic strain in the gastrointestinal tract.

Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Figures

FIG 1

In vivo selection to identify putative probiotic strains to be used in synbiotic applications. (A) Concept of in vivo selection. (B) Proportion of fecal bifidobacteria in a human individual consuming GOS (included in chews) in four increasing doses (0, 2.5, 5, and 10 g) during a human feeding trial (25), as determined by 454 pyrosequencing of 16S rRNA tags. (C) Proportion of Bifidobacterium lineage species II in the same individual, as determined by pyrosequencing. (D) Cell numbers of B. adolescentis IVS-1 in the same individual, as quantified by strain-specific qRT-PCR.

FIG 2

Test of a synbiotic combination of B. adolescentis IVS-1 and GOS in a high-fat-diet rat model. (A) Experimental design of the rat study. Rats were fed either a standard diet or a high-fat diet for 8 weeks, supplemented with or without a probiotic (IVS-1), a prebiotic (GOS), or a synbiotic (IVS-1 plus GOS) for the last 4 weeks. (B) Quantification of absolute cell numbers of bifidobacteria in colonic and cecal contents by genus-specific qRT-PCR. (C) Strain-specific qRT-PCR was used to quantify absolute numbers of B. adolescentis IVS-1 in colonic and cecal contents.

FIG 3

Characterization of the rat colonic microbiota composition by Illumina sequencing of 16S rRNA tags. (A) Analysis of colonic microbiota at the OTU level. OTUs representing at least 1% of total sequences are shown individually, while OTUs representing

FIG 4

Correlation analysis of colonic taxa present in rats fed a high-fat diet supplemented with or without a probiotic (IVS-1), a prebiotic (GOS), or a synbiotic (IVS-1 plus GOS) or a standard diet. Bacterial quantities are expressed as percent abundances of total bacteria as determined by 16S rRNA sequencing. Spearman's correlations between Bifidobacteriaceae and Clostridiaceae (A), Bifidobacterium and Lactococcus (B), Bifidobacterium and Akkermansia (C), Bifidobacterium adolescentis IVS-1 and Lactococcus lactis (D), Bifidobacterium adolescentis IVS-1 and Bifidobacterium pseudolongum (E), and Bifidobacterium and Blautia (F) were determined.