ABSTRACT
Molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with universal PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. Unfortunately both amplicon-based and shotgun sequencing approaches have significant shortcomings that limit the ability to study microbiome dynamics. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. This new method generates a quantitative, pan-Domain community profile with significantly less expenditure and sequencing effort than a shotgun metagenomic sequencing approach. Molecular microbial profiles were compared for antibiotic-amended soil samples using CaptureSeq, shotgun metagenomics, and amplicon-based techniques. The CaptureSeq method generated a microbial profile that provided a much greater depth and sensitivity than shotgun metagenomic sequencing while simultaneously mitigating the bias effects associated with amplicon-based methods. The resulting community profile provided quantitatively reliable information about all three Domains of life (Bacteria, Archaea, and Eukarya). The applications of CaptureSeq are globally impactful and will facilitate highly accurate studies of host-microbiome interactions for environmental, crop, animal and human health.
DNA sequencing data associated with this work has been deposited at NCBI under BioProject PRJNA406970 and SRA deposits SRX3181274-SRX3181276 and SRX3187583-SRX3187601.
