An In Vitro Enrichment Strategy for Formulating Synergistic Synbiotics

Appl Environ Microbiol. 2019 Aug 1;85(16):e01073-19. doi: 10.1128/AEM.01073-19. Print 2019 Aug 15.


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.

Keywords: bifidobacteria; prebiotic; probiotic; synbiotic; xylooligosaccharide.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adult
  • Bacteria / classification
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Bifidobacterium / genetics
  • Bifidobacterium / growth & development
  • Bifidobacterium / isolation & purification*
  • Bifidobacterium / metabolism*
  • Feces / microbiology
  • Fermentation
  • Gastrointestinal Microbiome
  • Glucuronates / metabolism
  • Humans
  • Oligosaccharides / metabolism
  • Phylogeny
  • Synbiotics / analysis*
  • Young Adult


  • Glucuronates
  • Oligosaccharides
  • xylooligosaccharide