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.T he mechanistic role of the gastrointestinal (GI) microbiota and its metabolites in maintaining human health has been well demonstrated (1-3). Gut microbes provide several important benefits for their host, including provision of nutrients, development and maturation of the immune system, and protection against pathogens via colonization resistance (4). However, the gut microbiota may also contribute to obesity, inflammatory and autoimmune diseases, and other chronic disease states (5-7). Such diseases are often associated with compositional alterations in the fecal microbiota, a condition referred to as "dysbiosis" (8). Given that the presence of specific types of bacteria and their relative abundance within the gut are considered to affect host health, there is much interest in devising strategies that modulate gut microbiota composition and potentially redress disease-related dysbiotic patterns (9).Dietary approaches currently available to modulate the gut microbiota include prebiotics (10-12), fermentable fibers (13, 14), probiotics (or live biotherapeutics) (15), and synbiotics, which are a combination of a probiotic and a prebiotic (11, 16). According to Kolida and Gibson (16), synbiotics can be either complementary or synergistic. Complementary synbiotics consist of a probiotic and a prebiotic selected to independently confer benefits to the host. In contrast, sy...

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

“…Aliquots (200 µl) of each sample were used for DNA extraction following procedures described elsewhere 52 . 16S rRNA gene tag sequencing (MiSeq, Illumina) of V5-V6 regions was performed at the University of Minnesota Genomics Center using primers 784F (5′-RGGATTAGATACCC′) and 1064R (5′-CGACRRCCATGCANCACCT) 53 . Raw sequence reads were processed using IMNGS (www.imngs.org) with a pipeline developed in-house based on UPARSE 54 .…”

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

“…Moreover, the ability of a probiotic strain to persist when specific niche-defining resources are available reinforces the potential of the symbiotic concept (Kolida and Gibson, 2011). If systematically developed based on ecological criteria (Krumbeck et al, 2015), synbiotics could ensure the provision of growth substrates (in the form of dietary carbohydrates or prebiotics) that enable longterm persistence of probiotic strains.…”

“…The fecal microbiota in samples collected during the baseline (of AH1206 treatment period), the last day of AH1206 consumption, the last day of placebo consumption, and 28 days of TOP was characterized by nextgeneration sequencing as described by Krumbeck et al (2015). WMS was performed with fecal samples obtained during baseline, the last day of consumption of the probiotic, and the 20 week follow-up sample using the Illumina HiSeq 2500 platform.…”

Designing synbiotics for improved human health

“…Most prebiotic compounds currently in use support the growth of many different bacteria indigenous to the host, so there must be some indication that a particular prebiotic specifically supports the growth of the introduced organism for the pair to be referred to as a synbiotic. One approach to the design of synbiotics is through in vivo enrichment with a prebiotic of interest and subsequent isolation of organisms whose abundance increases with the introduced prebiotic (Krumbeck et al ., 2015). This approach ensures that even in a competitive background, the isolated organisms will be the most likely to use the prebiotic compound of interest.…”