Core microbiome investigation
Karl Cottenie (IB)
The core microbiome is a crucial concept in microbiome studies. Recently, Risely (2020) (https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2656.13229?af=R) identified 5 types of “core” definitions used in the literature. Each of these definitions have different implications on the study of microbiomes in general. At the same time, Gloor et al. (2017) advocated for using different statistical techniques to analyse microbiome data due to their compositional nature. However, it is possible that a study focusing on core OTUs might interfere with the common statistical analyses for compositional data.
The objective of this research project is to 1) investigate the implications of the different definitions of what constitutes a “core” microbiome community, and 2) whether the compositional statistical method is the optimal approach for these data. The student will use a combination of different types of existing data sets. The Earth Microbiome Project (https://www.nature.com/articles/nature24621) sampled over a 100 microbial communities across the globe in a standardized fashion. A second type of data is data collected for the Kluane Red Squirrel project that has both a temporal and spatial component.