Microbiome source tracking using single nucleotide variants

Recently Leah Briscoe, Eran, Halperin, and Nandita Garud posted a preprint to bioRxiv on source tracking in the microbiome with single nucleotide variants.

In short, remember when this happened?

We wondered whether microbes could traverse oceans. To answer this question, we modified the input to a popular source tracking method called FEAST such that it takes in SNVs instead of speices. SNVs are known to provide higher resolution information than species about transmissions from sources to sinks, yet never have been incorporated in a source tracking algorithm. We found, surprisingly, that with SNVs but not speices there is a distance decay relationship between ocecans around the world!


We confirm the ability of SNVs over species in simualtions and applications to mother-infant data as well.


Please check out the paper and let us know what you think!