Improved Detection of Bifidobacteria with Optimised 16S rRNA-Gene Based Pyrosequencing
Author(s)
Type
Journal Article
Abstract
The 16S rRNA gene is conserved across all bacteria and as such is routinely targeted in PCR surveys of bacterial diversity. PCR primer design aims to amplify as many different 16S rRNA gene sequences from as wide a range of organisms as possible, though there are no suitable 100% conserved regions of the gene, leading to bias. In the gastrointestinal tract, bifidobacteria are a key genus, but are often under-represented in 16S rRNA surveys of diversity. We have designed modified, 'bifidobacteria-optimised' universal primers, which we have demonstrated detection of bifidobacterial sequence present in DNA mixtures at 2% abundance, the lowest proportion tested. Optimisation did not compromise the detection of other organisms in infant faecal samples. Separate validation using fluorescence in situ hybridisation (FISH) shows that the proportions of bifidobacteria detected in faecal samples were in agreement with those obtained using 16S rRNA based pyrosequencing. For future studies looking at faecal microbiota, careful selection of primers will be key in order to ensure effective detection of bifidobacteria.
Editor(s)
Ahmed, N
Date Issued
2012-03-28
Citation
PLoS One, 2012, 7 (3), pp.e32543-e32543
ISSN
1932-6203
Publisher
PUBLIC LIBRARY SCIENCE
Start Page
e32543
End Page
e32543
Journal / Book Title
PLoS One
Volume
7
Issue
3
Copyright Statement
© 2012 Sim et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original author and source are credite
use, distribution, and reproduction in any medium, provided the original author and source are credite
License URL
Description
28/10/14 meb. OA paper , Ok to add.
Identifier
http://www.ncbi.nlm.nih.gov/pubmed?term=sim%20k%5Bau%5D%20kroll%20js%5Bau%5D
Publication Status
Published
Article Number
e32543