title: Design of species-specific oligonucleotide probes for the detection of Bacteroides and Parabacteroides by fluorescence in situ hybridization and their application to the analysis of mouse caecal Bacteroides-Parabacteroides microbiota.
abstract: OBJECTIVE
  To develop species-specific monitoring techniques for rapid detection of Bacteroides and Parabacteroides inhabiting the mouse intestine by fluorescence in situ hybridization.
  
  
  RESULTS
  The specificity of oligonucleotide probes was evaluated by fluorescence whole-cell hybridization. Oligonucleotide probes specific for each species hybridized only with the target bacteria. Using these probes, caecal Bacteroides-Parabacteroides microbiota of conventional mice and specific pathogen-free (SPF) mice from three different breeders were analysed. It was shown that Bacteroides acidifaciens Group-1, Group-2 and Group-3 were dominant in conventional mice and SPF mice from two out of three breeders. Bacteroides vulgatus and Parabacteroides distasonis were detected in one of these two SPF breeding colonies in addition to Bact. acidifaciens. SPF mice of the remaining breeder harboured characteristic Bacteroides-Parabacteroides microbiota, consisting of Bacteroides sp. ASF519 and Bacteroides caccae.
  
  
  CONCLUSIONS
  Bacteroides acidifaciens is the dominant and most typical species in the mouse Bacteroides-Parabacteroides microbiota. The Group-3 was identified as a novel group and revealed to occupy a major niche together with Bact. acidifaciens Group-1 and Group-2.
  
  
  CONCLUSIONS
  The species-specific probe set developed in this study was the efficient tool for rapid detection of target bacterial groups inhabiting the mouse intestine. The results of this study provide important new information on the mouse Bacteroides-Parabacteroides community.
authors.affiliation: Laboratory of Veterinary Public Health, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Momose
authors.forename: S H
authors.initials: SH
authors.lastname: Park
authors.forename: Y
authors.initials: Y
authors.lastname: Miyamoto
authors.forename: K
authors.initials: K
authors.lastname: Itoh
mesh_terms: D000818:Animals; D001431:Bacteriological Techniques / Q000379:methods*; D041963:Bacteroidetes / Q000235:genetics / Q000302:isolation & purification*; D002432:Cecum / Q000382:microbiology*; D005243:Feces / Q000382:microbiology; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D051379:Mice; D008807:Mice, Inbred BALB C; D015345:Oligonucleotide Probes / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013045:Species Specificity; D013047:Specific Pathogen-Free Organisms
chemical_list: D015345:Oligonucleotide Probes; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S