Improvement of the representation of bifidobacteria in fecal microbiota metagenomic libraries by application of the cpn60 universal primer cocktail.

Actinobacteria, particularly bifidobacteria, are widely observed to be underrepresented in metagenomic studies of microbial communities. We have compared human fecal microbiota clone libraries based on 16S rRNA and cpn60 PCR products. Taxonomic profiles were similar except that the cpn60 libraries contained large numbers of bifidobacterial sequences.