Low sequencing efforts bias analyses of shared taxa in microbial communities.
Abstract
The potential for comparing microbial community population structures has been greatly enhanced by developments in next generation sequencing methods that can generate hundreds of thousands to millions of reads in a single run. Conversely, many microbial community comparisons have been published with no more than 1,000 sequences per sample. These studies have presented data on levels of shared operational taxonomic units (OTUs) between communities. Due to lack of coverage, that approach might compromise the conclusions about microbial diversity and the degree of difference between environments. In this study, we present data from recent studies that highlight this problem. Also, we analyzed datasets of 16 rRNA sequences with small and high sequence coverage from different environments to demonstrate that the level of sequencing effort used for analyzing microbial communities biases the results. We randomly sampled pyrosequencing-generated 16S rRNA gene libraries with increasing sequence effort. Sequences were used to calculate Good's coverage, the percentage of shared OTUs, and phylogenetic distance measures. Our data showed that simple counts of presence/absence of taxonomic unities do not reflect the real similarity in member...Continue Reading
References
Citations
Commercial DNA extraction kits impact observed microbial community composition in permafrost samples
Related Concepts
Related Feeds
Biodiversity Data
Biodiversity refers to the variety and variability of life on Earth. Biodiversity is typically a measure of variation at the genetic, species, and ecosystem level.Discover the latest research on biodiversity data here.