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

• DOI: 10.1186/s40168-016-0175-0
• Publication Date: 2016-06-22T06:17:37Z
• Authors: Frank Stämmler; Joachim Gläsner; Andreas Hiergeist; Ernst Holler; Daniela Weber; Peter J. Oefner; André Gessner; Rainer Spang
• Keywords: Medical microbiology

Next-generation 16S ribosomal RNA gene sequencing is widely used to determine the relative composition of mammalian gut microbiomes. However, in absence a reference, this does not reveal alterations absolute abundance specific operational taxonomic units if microbial loads vary across specimens.Here we suggest spiking exogenous bacteria into crude specimens quantify ratios bacterial abundances. We use rDNA read counts spike-in adjust endogenous for changes total loads. Using series dilutions pooled faecal samples from mice containing defined amounts Salinibacter ruber, Rhizobium radiobacter and Alicyclobacillus acidiphilus, demonstrate that spike-in-based calibration allows accurate estimation Applied stool patients undergoing allogeneic stem cell transplantation, were able both abundances various phyla, especially genus Enterococcus, response antibiotic treatment radio-chemotherapeutic conditioning.Exogenous microbiome studies enable OTU abundances, providing novel insights structure dynamics intestinal