Adjusting microbiome profiles for differences in microbial load by spike-in bacteria.

ABSTRACT:

Background

Next-generation 16S ribosomal RNA gene sequencing is widely used to determine the relative composition of the mammalian gut microbiomes. However, in the absence of a reference, this does not reveal alterations in absolute abundance of specific operational taxonomic units if microbial loads vary across specimens.

Results

Here we suggest the spiking of exogenous bacteria into crude specimens to quantify ratios of absolute bacterial abundances. We use the 16S rDNA read counts of the spike-in bacteria to adjust the read counts of endogenous bacteria for changes in total microbial loads. Using a series of dilutions of pooled faecal samples from mice containing defined amounts of the spike-in bacteria Salinibacter ruber, Rhizobium radiobacter and Alicyclobacillus acidip

SUBMITTER: Stammler F 

PROVIDER: S-EPMC4915049 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature