Major research areas

The main overarching focus on the Eisen lab is on the mechanisms by which new functions original and in particular the causes and effects of variation in these mechanisms between taxa. Among our current research topics are:

Improving phylogenetic coverage of microbial genomes.

In order to get a full appreciation of microbial diversity and genomics we needs to understand more about the poorly studied branches in the tree of life. Examples of our work on this include:

• A past NSF Tree of Life project see here
• GEBA (A Genomic Encyclopedia of Bacteria and Archaea) here
• Microbial Dark Matter (project run by Tanja Woyke at DOE-JGI).  See for example a 2013 paper on this project here.
• Genealogy of Life project – PI Ramunas Stepanauskas

The evolution and ecology of the interactions between microbes and multicellular organisms.

Interactions with microbes play critical roles in the evolution, ecology, and function of multicellular organisms.  The Eisen lab has been studying the evolution and ecology of such interactions using primarily DNA sequencing of the microbes in such interactions.

One aspect of our work in this area has been genomic studies of mutualistic interactions between a host and endosymbionts.  Exampes of projects in this area include

• A collaboration with JGI and the lab of Colleen Cavanaugh (my undergraduate advisor) on the chemosynthetic symbionts found in the giant clam Calyptogena magnifica. See paper here
• A collaboration with the lab of Scott O’Neill on the first Wolbachia genome. See paper here: wMel genome as well as a few other Wolbachia papers BAC from Brugia Wolbachia, letter about Wolbachia classification.
• A collaboration with Nancy Moran’s lab on studying the genomes of the symbionts inside the glassy winged sharpshooter. See PLoS Biology paper here

We have also done some work on the genomics and evolution of pathogens that are have detrimental affects of various hosts.  Examples of our work in this area include:

Finally, much of our work now focuses on “microbiome” studies – the studies of entire communities of microbes found in association with a host.  Examples of the “hosts” that we are or have studied include Drosophila, coral, humans, rice and corn.  We also have a new program in this area on the “Seagrass Microbiome“.

The functioning of communities of microbes.
For many years, we focused on studies of microbes grown in pure culture in the laboratory. Recently, we have shifted much of our focus to using genome sequencing to study microbes directly in their natural habitats. See for example

• Review
• GOS Proteins
• GOS Survey
• Sargasso metagenomics
• Phototroph metagenomics.

Computational methods for carrying out phylogenomic and metagenomic analyses. We are currently working on multiple projects focusing on designing methods for analyzing metagenomic data. Our work on this includes

• iSEEM (a collaboration with the labs of Jessica Green and Katherine Pollard; see http://openwetware.org/wiki/ISEEM for more detail)
• a collaboration with Simon Levin and Josh Weitz as part of the DARPA Fundamental laws of Biology program.

Embedded within all our work is the development of computational approaches in which evolutionary reconstructions and genome analyses are combined into a composite phylogenomic approach (e.g., Eisen1995; Eisen1997, Eisen1998 Eisen2002, Wu2005, EisenWu2002)

The genomics and evolution of carbon fixation.
We use the evolution of carbon fixation as a model for studying the origin and evolution and processes and pathways. Our work includes genomic studies of the reverse TCA cycle (e.g., here, here and here), methylotrophy (here), Carboxydotrophs (e.g., here), plastid evolution and/or the Calvin cycle (e.g., here, here, here, here, and here), and chemosynthetic symbionts (here, here).