Apr 23, 2016

New insights in host-associated microbial diversity with broad and accurate taxonomic resolution

BioRxiv : the Preprint Server for Biology
Matthew T AglerEric M Kemen

Abstract

Deep microbiome profiling has sparked a revolution in biology, recontextualizing mechanisms such as macroorganismal adaptation and evolution. Amplicon sequencing has been critical for characterization of highly diverse microbiomes, but several challenges still hinder their investigation: (1) Poor coverage of the full diversity, (2) Read depth losses and (3) Erroneous diversity inflation/distortion. We developed a modular approach to quickly profile at least 8 interchangeable loci in a single sequencing run, including a simple and cost-effective way to block amplification of non-targets (like host DNA). We further correct observed distortion in amplified diversity by phylogenetically grouping erroneous OTUs, creating a phylogeny-based unit we call OPUs.Our approach achieves full, accurate characterization of a mixed-kingdom mock community of bacteria, fungi and oomycetes at high depth even in non-target contaminated systems. The OPU concept enables much more accurate estimations of alpha and beta diversity trends than OTUs and overcomes disagreements between studies caused by methodology. Leveraging the approach in the Arabidopsis thaliana phyllosphere, we generated to our knowledge the most complete microbiome survey to date. M...Continue Reading

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Mentioned in this Paper

Study
Meta Analysis (Statistical Procedure)
Nucleic Acid Sequencing
Profile (Lab Procedure)
Mixed Neoplasm
Gene Amplification Technique
Etiology
Sequencing
Microbiome
Adaptation

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