Decontamination of 16S rRNA gene amplicon sequence datasets based on bacterial load assessment by qPCR.
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.
Genomic Research Laboratory, Department of Genetics and Laboratory Medicine, Department of Medical Specialties, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1211, Geneva, 14, Switzerland. vladimir.lazarevic@genomic.ch.
Vladimir
V
Lazarevic
Genomic Research Laboratory, Department of Genetics and Laboratory Medicine, Department of Medical Specialties, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1211, Geneva, 14, Switzerland.
Nadia
N
Gaïa
Genomic Research Laboratory, Department of Genetics and Laboratory Medicine, Department of Medical Specialties, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1211, Geneva, 14, Switzerland.
Myriam
M
Girard
Genomic Research Laboratory, Department of Genetics and Laboratory Medicine, Department of Medical Specialties, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1211, Geneva, 14, Switzerland.
Jacques
J
Schrenzel
D001419:Bacteria / Q000145:classification* / Q000235:genetics; D058491:Bacterial Load; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D059018:DNA Contamination; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D006801:Humans; D064307:Microbiota; D016133:Polymerase Chain Reaction / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
16S rRNA gene sequencing; Bacterial communities; Contaminant DNA; Microbiome