Article

Molecular diversity of Bacteroides spp. in human fecal microbiota as determined by group-specific 16S rRNA gene clone library analysis.

Laboratory of Molecular Microbial Ecology and Ecogenomics, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
Systematic and Applied Microbiology (Impact Factor: 3.29). 06/2009; 32(3):193-200. DOI: 10.1016/j.syapm.2009.02.001
Source: PubMed

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.

0 Bookmarks
 · 
137 Views
  • [Show abstract] [Hide abstract]
    ABSTRACT: Bacteroides molecular markers have been used to identify human fecal contamination in natural waters, but recent work in our laboratory confirmed cross-amplification of several human-specific Bacteroides spp. assays with fecal DNA from fish. For identification of unique molecular markers, Bacteroides from human (n = 4) and fish (n = 7) fecal samples were cultured and their identities were further confirmed using Rapid ID 32A API strips. The 16S rDNA from multiple isolates from each sample was PCR amplified, cloned, and sequenced to identify unique markers for development of more stringent human-specific assays. In human feces, Bacteroides vulgatus was the dominant species (75% of isolates), whereas in tilapia feces, Bacteroides eggerthii was dominant (66%). Bacteroides from grass carp, channel catfish, and blue catfish may include Bacteroides uniformis, Bacteroides ovatus, or Bacteroides stercoris. Phylogenic analyses of the 16S rRNA gene sequences showed distinct Bacteroides groupings from each fish species, while human sequences clustered with known B. vulgatus. None of the fish isolates showed significant similarity to Bacteroides sequences currently deposited in NCBI (National Center for Biotechnology Information). This study expands the current sequence database of cultured fish Bacteroides. Such data are essential for identification of unique molecular markers in human Bacteroides that can be utilized in differentiating fish and human fecal contamination in water samples.
    Canadian Journal of Microbiology 12/2013; 59(12):771-7. · 1.20 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: DNA restriction fragment polymorphism technologies such as amplified ribosomal DNA restriction analysis (ARDRA) and terminal restriction fragment length polymorphism (T-RFLP) have been widely used in investigating microbial community structures. However, these methods are limited due to either the low resolution or sensitivity. In this study, a fluorophore-ribosomal DNA restriction typing (f-DRT) approach is developed for structural profiling of microbial communities. 16S rRNA genes are amplified from the community DNA and digested by a single restriction enzyme Msp I. All restriction fragments are end-labeled with a fluorescent nucleotide Cy5-dCTP via a one-step extension reaction and detected with an automated DNA sequencer. All 50 predicted restriction fragments between 100 and 600 bp were detected when twelve single 16S rRNA gene sequences were analyzed using f-DRT approach; 92% of these fragments were determined with accuracy of ±2 bp. In the defined model communities containing five components with different ratios, relative abundance of each component was correctly revealed by this method. The f-DRT analysis also showed structural shifts of intestinal microbiota in carcinogen-treated rats during the formation of precancerous lesions in the colon, as sensitive as multiple digestion-based T-RFLP analysis. This study provides a labor and cost-saving new method for monitoring structural shifts of microbial communities.
    Archives of Microbiology 01/2011; 193(5):341-50. · 1.91 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    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. · 2.11 Impact Factor