Abstract
Next-generation sequencing of marker genes such as 16S ribosomal RNA is widely used to survey microbial communities. The abundance distribution (AD) of Operational Taxonomic Units (OTUs) in a sample is typically summarized by alpha diversity metrics, e.g. richness and entropy, discarding information about the AD shape. In this work, we describe octave plots, histograms which visualize the shape of microbial ADs by binning on a logarithmic scale with base 2. Optionally, histogram bars are colored to indicate possible spurious OTUs due to sequence error and cross-talk. Octave plots enable assessment of (a) the shape and completeness of the distribution, (b) the effects of noise on measured diversity, (c) whether low-abundance OTUs should be discarded, (d) whether alpha diversity metrics and estimators are reliable, and (e) the additional sampling effort (i.e., read depth) required to obtain a complete census of the community. The utility of octave plots is illustrated in a re-analysis of a prostate cancer study showing that the reported core microbiome is most likely an artifact of experimental error.
Info
Journal Article, 2018
UN SDG Classification
DK Main Research Area
Science/Technology
