Project Overview

Bifido

   metagenomes   project metadata

VisibilityPublic
Static Linkhttp://metagenomics.anl.gov/linkin.cgi?project=329

Description

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 allow 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.

Funding Source

-

Contact

Administrative


Technical

Additional Data

includes_timeseries0
sff_completey
study_aliasPATCH
qiime_idqiime:967
sample_count20
study_titleImproved detection of bifidobacteria with optimised 16S rRNA gene based pyrosequencing
metadata_completey
miens_complianty
study_centerImperial College London
study_descriptionImprovement of 16S rRNA primers for bifidobacterial detection
investigation_typemimarks-survey

Metagenomes