Dairy genomes: Good example of the power of reference genomes for particular environments

Quick post here.  Just got alerted to this paper by automated searches from PubchaseConstruction of a dairy microbial genome catalog opens new perspect… – PubMed – NCBI.  This paper provides a really good example of how researchers interested in microbial ecology of a particular system (in this case, dairies and cheese) can use culturing and genome sequencing of select taxa to then help inform microbial ecology studies of that system.  It would be great to do this from more ecosystems, including, especially in my mind, built environments where we right now have only a limited number of reference genomes for cultured isolates.  This is one of the reasons we started on “Built Environment Reference Genomes” project at microBEnet as an undergraduate research activity.  Stay tuned for more information about this as we are also developing tools and methods and course materials to hopefully have anyone (and,well, everyone) do things like this.  (For example see our Swabs to Genomes workflow preprint).


One thought on “Dairy genomes: Good example of the power of reference genomes for particular environments

  1. Goes well with Ben Wolfe’s work at Tufts (fresh out of Rachel Dutton’s lab at Harvard last year). Where and when each of the species is introduced will be interesting to know. Several of the species named used to be thought of as strictly ‘milk spoiling agents’ or not present at all on cheese; can’t wait to see what causes them to either not ruin the cheese or the regulation of how they effect macroscopic phenotypes.

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Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.