Weitz Group @ Georgia Tech Theoretical Ecology and Quantitative Biology



Functional biogeography of ocean microbes (collaborative paper in PLoS One)

Posted by jsweitz

Joshua Weitz teamed up with multiple scientists to investigate how microbial function, as found in metagenomic datasets, varies due to geographic and environmental factors. The paper Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization was published in PLoS One.

In doing so, our team has extended a method called "Non-negative Matrix Factorization" (NMF) to decompose functional profile matrices. These matrices represent the abundances of microbial function at distinct sample locations. The decomposition enables a dual representation of site and functional profiles. It differs from prior methods in that it does not classify a given site into a fixed category - reflecting the potential for intermediate types. We applied this NMF approach to the Global Ocean Survey data to show that environmental, rather than strictly geographic, effects are more strongly correlated to functional abundances. We also identify similar protein functions in several components and suggest that functional co-occurrence across metagenomic samples could lead to future methods for de-novo functional prediction.