Statistical analysis of co-occurrence patterns in microbial presence-absence datasets.

ABSTRACT: Drawing on a long history in macroecology, correlation analysis of microbiome datasets is becoming a common practice for identifying relationships or shared ecological niches among bacterial taxa. However, many of the statistical issues that plague such analyses in macroscale communities remain unresolved for microbial communities. Here, we discuss problems in the analysis of microbial species correlations based on presence-absence data. We focus on presence-absence data because this information is more readily obtainable from sequencing studies, especially for whole-genome sequencing, where abundance estimation is still in its infancy. First, we show how Pearson's correlation coefficient (r) and Jaccard's index (J)-two of the most common metrics for correlation analysis of presence-absenc

SUBMITTER: Mainali KP 

PROVIDER: S-EPMC5689832 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature