Bioinformatic correction of bacterial morphology-based extraction bias and chimeras in microbiome sequencing data

Abstract

IntroductionMicrobiome amplicon sequencing data are distorted by multiple protocol-dependent biases, originating from bacterial DNA extraction, contamination, sequence errors, and chimeras. In particular, extraction bias is a major confounder in sequencing-based microbiome analyses, with no correction method available to date. Here, we suggest using mock community controls to bioinformatically correct extraction bias based on morphological properties.MethodsWe compared dilution series of 3 mock communities with an even or staggered composition. DNA was extracted with 8 different extraction protocols (2 buffers, 2 extraction kits, 2 lysis conditions). Extracted DNA was sequenced (V1-V3 16S rRNA gene) together with corresponding DNA mocks. Sequences were denoised using DADA2, and annotated by matching against mock reference genomes.ResultsMicrobiome composition was significantly different between extraction kits and lysis conditions, but not between buffers. Independent of the extraction protocol, chimera formation increased with high input cell number. Contaminants originated mostly from buffers, and considerable cross-contamination was observed in low-input samples. Comparison of microbiome composition of the cell mocks to corresponding DNA mocks revealed taxon-specific protocol-dependent extraction bias. Strikingly, this extraction bias per species was predictable by bacterial cell morphology. Morphology-based bioinformatic correction of extraction bias significantly improved sample compositions when applied to different samples, even with different taxa.ConclusionsOur results indicate that higher DNA density increases chimera formation during PCR amplification. Furthermore, we show that bioinformatic correction of extraction bias is feasible based on bacterial cell morphology.