Molecular diversity of Bacteroides spp. in human fecal microbiota as determined by group-specific 16S rRNA gene clone library analysis.
ABSTRACT Bacteroides spp. represent a prominent bacterial group in human intestinal microbiota with roles in symbiosis and pathogenicity; however, the detailed composition of this group in human feces has yet to be comprehensively characterized. In this study, the molecular diversity of Bacteroides spp. in human fecal microbiota was analyzed from a seven-member, four-generation Chinese family using Bacteroides spp. group-specific 16S rRNA gene clone library analysis. A total of 549 partial 16S rRNA sequences amplified by Bacteroides spp.-specific primers were classified into 52 operational taxonomic units (OTUs) with a 99% sequence identity cut-off. Twenty-three OTUs, representing 83% of all clones, were related to 11 validly described Bacteroides species, dominated by Bacteroides coprocola, B. uniformis, and B. vulgatus. Most of the OTUs did not correspond to known species and represented hitherto uncharacterized bacteria. Relative to 16S rRNA gene universal libraries, the diversity of Bacteroides spp. detected by the group-specific libraries was much higher than previously described. Remarkable inter-individual differences were also observed in the composition of Bacteroides spp. in this family cohort. The comprehensive observation of molecular diversity of Bacteroides spp. provides new insights into potential contributions of various species in this group to human health and disease.
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ABSTRACT: Extensive genetic diversity has been discovered in the microbial world, yet mechanisms that shape and maintain this diversity remain poorly understood. This thesis investigates to what extent populations of the gamma-proteobacterial family, Vibrionaceae, are ecologically specialized by investigating the distribution across a wide range of environmental categories, such as marine invertebrates or particles in the water column. Additionally, it seeks to determine whether in situ population distributions directly result from a competitive advantage over other Vibrio populations. This was investigated by in vitro competition assays on mixtures of native, sterilized particles. Generalist populations were found to dominate the associations with marine invertebrates, consistent with a model of high migration dominated population assembly. A majority of populations occurred broadly within and among the different types of invertebrates sampled, with one population being a near perfect generalist with regard to seasons, host taxa and body regions. High variability across host individuals, consistent with a scenario of stochastic clonal expansion, was especially pronounced in crab and zooplankton samples. Specialization, demonstrated by specific and reproducible association with different particle types in the water column, is more common than specialization within invertebrate hosts.
- Journal of Cystic Fibrosis 06/2009; 8. DOI:10.1016/S1569-1993(09)60178-8 · 3.82 Impact Factor
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ABSTRACT: Two anaerobic, Gram-negative, non-motile and non-spore-forming bacterial strains, designated MAJ27(T) and MAJ26, were isolated from human faeces. Both isolates grew optimally at 37 °C, were oxidase- and catalase-negative, were sensitive to bile and produced acid from fermentation of several substrates, including glucose. A study based on 16S rRNA gene sequences showed that both isolates were closely related to type strains of species of the genus Bacteroides. Comparisons of the isolates with Bacteroides thetaiotaomicron VPI 5482(T) and Bacteroides finegoldii JCM 13345(T) showed high levels of 16S rRNA gene sequence similarity (98.6-98.7 and 96.9-97.0 %, respectively), but low levels of DNA-DNA relatedness (≤22 %). The DNA G+C content (42.7±1 mol%) and the major fatty acid (anteiso-C(15 : 0), 39.3-42.5 %) supported the assignment of the isolates to the genus Bacteroides. Based on phenotypic, chemotaxonomic, genotypic and phylogenetic studies, we propose that strains MAJ27(T) and MAJ26 be classified as representing a novel species, Bacteroides faecis sp. nov. The type strain is MAJ27(T) (=KCTC 5823(T)=JCM 16478(T)).International Journal of Systematic and Evolutionary Microbiology 12/2009; 60(Pt 11):2572-6. DOI:10.1099/ijs.0.020024-0 · 2.80 Impact Factor