Abstract
Oligotyping is a computational method used to increase the resolution of marker gene microbiome studies. Although oligotyping can distinguish highly similar sequence variants, the resulting units are not necessarily phylogenetically and ecologically informative due to limitations of the selected marker gene. In this perspective, we examine how oligotyping data is interpreted in recent literature, and we illustrate some of the method’s constraints with a case study of the harmful bloom-forming cyanobacterium Microcystis. We identified three Microcystis oligotypes from a western Lake Erie bacterial community 16S rRNA gene (V4 region) survey that had previously clustered into one OTU. We found the same three oligotypes and two additional sequence variants in 46 Microcystis cultures isolated from Michigan inland lakes spanning a trophic gradient. In Lake Erie, shifts in Microcystis oligotypes corresponded to spatial nutrient gradients and temporal transitions in bloom toxicity. In the cultures, Microcystis oligotypes showed preferential distributions for different trophic states, but genomic data revealed that the oligotypes identified in Lake Erie did not correspond to toxin gene presence. Thus, oligotypes could not be used for inferring toxic ecotypes. Most strikingly, Microcystis oligotypes were not monophyletic. Our study supports the utility of oligotyping for distinguishing sequence types along certain ecological features, while it stresses that 16S rRNA gene sequence types may not reflect ecologically or phylogenetically cohesive populations. Therefore, we recommend that studies employing oligotyping or related tools consider these caveats during data interpretation.
Highlights
Reviewed by: Pier Luigi Buttigieg, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Germany Jean-Francois Humbert, Université Pierre et Marie Curie, France
We examine how oligotyping data is interpreted in recent literature, and we illustrate some of the method’s constraints with a case study of the harmful bloom-forming cyanobacterium Microcystis
We identified three Microcystis oligotypes from a western Lake Erie bacterial community 16S rRNA gene (V4 region) survey that had previously clustered into one operational taxonomic units (OTUs)
Summary
Microbiome studies using 16S rRNA gene amplicons typically aggregate sequences into operational taxonomic units (OTUs) based on a 97% sequence identity threshold. Due to the potential increase in ecological resolution, the oligotyping method has been broadly applied for studies in microbial biogeography (Schmidt et al, 2014; Buttigieg and Ramette, 2015; Cloutier et al, 2015; Newton and McLellan, 2015), host–microbe associations (Eren et al, 2014; Menke et al, 2014; Fisher et al, 2015), and links between microbes and disease (Eren et al, 2011). The points we raise in this perspective apply to the interpretation of oligotyping, MED, dada, and any other tools attempting to make ecotype inferences from 16S rRNA gene amplicons
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