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Background  Identification of unexpected taxa in 16S rRNA surveys of low-density microbiota, diluted mock communities and cultures demonstrated that a variable fraction of sequence reads originated from exogenous DNA. The sources of these contaminants are reagents used in DNA extraction, PCR, and next-generation sequencing library preparation, and human (skin, oral and respiratory) microbiota from the investigators.    Results  For  in silico  removal of reagent contaminants, a pipeline was used which combines the relative abundance of operational taxonomic units (OTUs) in V3–4 16S rRNA gene amplicon datasets with bacterial DNA quantification based on qPCR targeting of the V3 segment of the 16S rRNA gene. Serially diluted cultures of  Escherichia coli  and  Staphylococcus aureus  were used for 16S rDNA profiling, and DNA from each of these species was used as a qPCR standard. OTUs assigned to  Escherichia  or  Staphylococcus  were virtually unaffected by the decontamination procedure, whereas OTUs from  Pseudomonas , which is a major reagent contaminant, were completely or nearly completely removed. The decontamination procedure also attenuated the trend of increase in OTU richness in serially diluted cultures.    Conclusions  Removal of contaminant sequences derived from reagents based on use of qPCR data may improve taxonomic representation in samples with low DNA concentration. Using the described pipeline, OTUs derived from cross-contamination of negative extraction controls were not recognized as contaminants and not removed from the sample dataset.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-016-0689-4) contains supplementary material, which is available to authorized users.

Decontamination of 16S rRNA gene amplicon sequence datasets based on bacterial load assessment by qPCR