Research on the role of diet on gut and systemic health has led to considerable interest toward identifying novel therapeutic modulators of the gut microbiome, including the use of prebiotics and probiotics. However, various host responses have often been reported among many clinical trials. This is in part due to competitive exclusion as a result of the absence of ecological niches as well as host-mediated constraints via colonization resistance. In this research, we developed a novel in vitro enrichment (IVE) method for isolating autochthonous strains that can function as synergistic synbiotics and overcome these constraints. The method relied on stepwise in vitro fecal fermentations to enrich for and isolate Bifidobacterium strains that ferment the prebiotic xylooligosaccharide (XOS). We subsequently isolated Bifidobacterium longum subsp. longum CR15 and then tested its establishment in 20 unique fecal samples with or without XOS. The strain was established in up to 18 samples but only in the presence of XOS. Our findings revealed that the IVE method is suitable for isolating potential synergistic probiotic strains that possess the genetic and biochemical ability to ferment specific prebiotic substrates. The IVE method can be used as an initial high-throughput screen for probiotic selection and isolation prior to further characterization and in vivo tests. IMPORTANCE This study describes an in vitro enrichment method to formulate synergistic synbiotics that have potential for establishing autochthonous strains across multiple individuals. The rationale for this approach—that the chance of survival of a bacterial strain is improved by providing it with its required resources—is based on classic ecological theory. From these experiments, a human-derived strain, Bifidobacterium longum subsp. longum CR15, was identified as a xylooligosaccharide (XOS) fermenter in fecal environments and displayed synergistic effects in vitro. The high rate of strain establishment observed in this study provides a basis for using synergistic synbiotics to overcome the responder/nonresponder phenomenon that occurs frequently in clinical trials with probiotic and prebiotic interventions. In addition, this approach can be applied in other protocols that require enrichment of specific bacterial populations prior to strain isolation.

Synbiotics, mixtures of live microbes and substrates selectively utilized by host organisms, are of considerable interest due to their ability to improve gastrointestinal health. However, formulating synbiotics remains challenging, due in part, to the absence of rational strategies to assess these products for synbiotic activities prior to clinical trials. Currently, synbiotics are formulated as either complementary or synergistic. Complementary synbiotics are made by combining probiotics and prebiotics, with each component acting independently and with the combination shown to provide a clinical health benefit. Most commercial synbiotics as well as those used in clinical trials have been of the complementary type. In contrast, synergistic synbiotics require that the added microbe is specifically stimulated or it’s persistence or activity are enhanced by the cognate substrate. Although several innovative examples have been described in the past few years based on this principle, in practice, relatively few synbiotic studies have tested for synergism. In this review, selected recent examples of complementary and synergistic synbiotics and the rationale for their formulation will be described. In addition, pre-clinical experimental approaches for identifying combinations that provide a basis for satisfying the requirements for synergism will be discussed.