title: 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.
authors.affiliation: Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, USA School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA.
authors.forename: Janina A
authors.initials: JA
authors.lastname: Krumbeck
authors.affiliation: Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, USA.
authors.forename: María X
authors.initials: MX
authors.lastname: Maldonado-Gomez
authors.affiliation: Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, USA Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
authors.forename: Inés
authors.initials: I
authors.lastname: Martínez
authors.affiliation: Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, USA.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Frese
authors.affiliation: Department of Animal Science, University of Nebraska, Lincoln, Nebraska, USA.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Burkey
authors.affiliation: Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA.
authors.forename: Karuna
authors.initials: K
authors.lastname: Rasineni
authors.affiliation: Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, USA.
authors.forename: Amanda E
authors.initials: AE
authors.lastname: Ramer-Tait
authors.affiliation: Department of Biochemistry, University of Nebraska, Lincoln, Nebraska, USA.
authors.forename: Edward N
authors.initials: EN
authors.lastname: Harris
authors.affiliation: Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, USA.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Hutkins
authors.affiliation: Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, USA Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada jwalter1@ualberta.ca.
authors.forename: Jens
authors.initials: J
authors.lastname: Walter
mesh_terms: D000818:Animals; D001644:Bifidobacterium / Q000187:drug effects* / Q000302:isolation & purification*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005243:Feces / Q000382:microbiology; D006801:Humans; D008969:Molecular Sequence Data; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D051381:Rats; D060888:Real-Time Polymerase Chain Reaction; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D058616:Synbiotics
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S