Selective plating underestimates abundance and shows differential recovery of bifidobacterial species from human feces

Abstract

The aim of the present work was to compare the efficacies and levels of selectivity of different culture-dependent and -independent methods for analyzing bifidobacteria in human stool samples. The three different culture media used here significantly differed from each other, particularly with regard to the recovery of Bifidobacterium adolescentis. Bifidobacterium medium failed to recover B. adolescentis; Beerens medium recovered some B. adolescentis organisms (17% of total bifidobacteria), whereas tomato-Eugon medium recovered mainly B. adolescentis organisms (58% of total bifidobacteria). A culture-independent method that combines GC fractionation of bacterial community DNA and 16S rRNA sequencing indicated that B. adolescentis organisms accounted for 85% of all bifidobacteria. Methodological biases, such as those described in this paper, should be taken into account in interpreting earlier studies and designing future experiments.

FIG. 1.

Effect of method on observed number of major bifidobacteria in human feces. BFM, BS medium, and TE medium are different bifidoselective media. GC-16S values are based on direct extraction of DNA from feces, percent G+C fractionation, and 16S rRNA sequencing as described in detail previously (1, 3).