Low sequencing efforts bias analyses of shared taxa in microbial communities.

Folia Microbiologica
Leandro N LemosLuiz F W Roesch

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

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Citations

Dec 25, 2012·Applied and Environmental Microbiology·Stephanie YarwoodDavid Myrold
Mar 25, 2014·Microbial Ecology·Carla R TaddeiMarina B Martinez
Jan 13, 2015·Water Research·Natalie M HullNorman R Pace
Oct 10, 2013·FEMS Microbiology Ecology·Tatiana A VishnivetskayaTullis C Onstott
Apr 3, 2019·PloS One·Karina ColonettiLuiz Fernando Wurdig Roesch
Oct 25, 2016·Microbes and Environments·Camilla KristoffersenKnut Rudi
Feb 26, 2013·Poultry Science·S WeiZ Yu
Feb 28, 2020·Biochimie·Gustavo Mottin RizowyIda Vanessa Doederlein Schwartz

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