Culture-independent phylogenetic analysis of the faecal flora of the rat

被引:14
作者
Brooks, SPJ
McAllister, M
Sandoz, M
Kalmokoff, ML
机构
[1] Hlth Canada, Bur Microbial Hazards, Food Directorate,Hlth Prod & Foods Branch, Banting Res Ctr PL2204A2, Ottawa, ON K1A 0L2, Canada
[2] Hlth Canada, Nutr Res Div, Food Directorate,Hlth Prod & Foods Branch, Banting Res Ctr PL2203C, Ottawa, ON K1A 0L2, Canada
关键词
rat; faeces; 16S rDNA; phylogenetic; cultured bacteria;
D O I
10.1139/W03-075
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The dominant faecal flora of the rat was determined using randomly cloned 16S rDNA comparative sequence analysis. A total of 109 near full-length 16S rDNA clones were sequenced, representing 69 unique 16S rRNA phylotypes or operational taxonomic units (OTUs). Estimates of species richness indicated that approximately 338 species were present in the faeces, suggesting that only 20% of species were identified. Only two of 39 Gram-negative clones aligned with previously cultured species, the remainder fell into a separate lineage within the Bacteroides-Cytophaga phylum. Several clones within this new group were related to 16S rDNA sequences previously identified from mouse faeces. Lactobacilli were the most abundant Gram-positive species, representing 23% of the total clones but only 7% of OTUs. The remaining Gram-positive clones were distributed among the Clostridium coccoides group (9%), the Clostridium leptum subgroup (18%), and throughout the low GC Gram-positive bacteria (13%). The majority of OTUs (63/69 or 91%) were less than 97% homologous to previously cultured bacteria. Faecal samples were also cultured using a variety of anaerobic media. With the exception of the lactobacilli, the cultured isolates demonstrated low species diversity and poorly reflected the population, as defined through comparative sequence analysis.
引用
收藏
页码:589 / 601
页数:13
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