title: Design and application of group-specific oligonucleotide probes for detecting and monitoring mouse clostridia.
abstract: Clostridia dominate the rodent intestinal bacterial community and play an important role in physiological functions of the host. However, their ecology and diversity are still unclear. In our previous report, we showed that phylogenetically novel groups of clostridia inhabit the mouse intestine and contribute to the normalization of germfree mice. In this study, five new oligonucleotide probes were designed and applied to detect these clostridial groups that are essential for the normalization of germfree mice. Faecal microbiota of conventional mouse strains and specific pathogen-free mice from different breeding colonies were analysed by fluorescence in situ hybridization using these five probes. Our results showed that the composition of clostridia differed among mouse strains and also among mouse groups of the same inbred strain from different breeding colonies. These five new probes for mouse clostridia were able to detect the difference in clostridial diversity in each mouse group. In addition to Clostridium, we also analysed Bacteroides and Lactobacillus using previously described probes and the number or the frequency of occurrence of Bacteroides was shown to be different among mouse groups analysed. The oligonucleotide probe set including our newly developed and previously described probes used in this study can be applied to monitoring of significant groups of mouse intestinal microbiota.
authors.affiliation: Laboratory of Veterinary Public Health, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657,  Japan.
authors.forename: Yoshika
authors.initials: Y
authors.lastname: Momose
authors.forename: Sang-Hee
authors.initials: SH
authors.lastname: Park
authors.forename: Hidekazu
authors.initials: H
authors.lastname: Niwa
authors.forename: Teruko
authors.initials: T
authors.lastname: Iwasaki
authors.forename: Aya
authors.initials: A
authors.lastname: Maruyama
authors.forename: Gerwin C
authors.initials: GC
authors.lastname: Raangs
authors.forename: Hermie J M
authors.initials: HJ
authors.lastname: Harmsen
authors.forename: Gjalt W
authors.initials: GW
authors.lastname: Welling
authors.forename: Kikuji
authors.initials: K
authors.lastname: Itoh
mesh_terms: D000818:Animals; D001431:Bacteriological Techniques / Q000379:methods*; D001439:Bacteroides / Q000235:genetics; D003013:Clostridium / Q000235:genetics* / Q000302:isolation & purification; D005243:Feces / Q000382:microbiology; D017404:In Situ Hybridization, Fluorescence; D007422:Intestines / Q000382:microbiology*; D007778:Lactobacillus / Q000235:genetics; D051379:Mice; D015345:Oligonucleotide Probes / Q000235:genetics*; D013045:Species Specificity; D013047:Specific Pathogen-Free Organisms
chemical_list: D015345:Oligonucleotide Probes