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Laboratory of Jonathan A. Eisen

The Eisen Lab research focuses on understanding the genomic basis for the origin of novelty (new functions and processes) in microorganisms. For many years, studies in this area were of limited scope. However, the advent of genome sequencing has allowed one to study the origin of novelty on a more global level. The Eisen lab's main location is in the U. C. Davis Genome Center. Dr. Eisen has appointments in the Section of Evolution and Ecology and the Department of Medical Microbiology at U. C. Davis and an Adjunct Appointment at the Joint Genome Institute.

Dr. Eisen is also a strong proponent of the Open Access movement in scientific publishing and is Academic Editor in Chief of PLoS Biology. Dr. Eisen is also an active and award winning science blogger (see his Tree of Life blog here). More detail is available Here.

General research areas -- Phylogenomics and the Origin of Novelty

• Mechanisms of novelty generation. A major component of our work involves using genome sequences to better understand the mechanisms by which new processes originate in microbes.
• Evolvability. We are particularly interested in constraints and biases in these novelty generating mechanisms that differ within and between species.
• Predicting organisms biology from their genome sequences. We make use of information on novelty generation to improve predictions of the biology of organisms from their genome sequences.
• Phylogenomic methods development. 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)

Current projects and model systems for studying novelty

• Improving phylogenetic coverage of 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 and GEBA (A Genomic Encyclopedia of Bacteria and Archaea) here.
• The evolution of intracellular symbioses. One of the simplest ways for organisms to acquire new functions is to engage in symbioses with other species. We use genomic sequencing of a diversity of such symbioses to better understand what the rules are for these symbioses to evolve. Examples of our projects include studies of symbionts of the glassy winged sharpshooter here, chemosynthetic symbionts (e.g., here), Wolbachia (wMel genome, BAC from Brugia Wolbachia, letter about Wolbachia classification).
• The functioning of communities of microbes in nature. 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 analyzing metagenomic data. 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 for more detail) and a collaboration with Simon Levin and Josh Weitz as part of the DARPA Fundamental laws of Biology program.
• 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).
• Other genome projects. The sequencing the genome of Tetrahymena thermophila a model ciliate here.

Recent Publications

• Amber L. Hartman, Denver M. Lough, Dinesh K. Barupal, Oliver Fiehn, Thomas Fishbein, Michael Zasloff, and Jonathan A. Eisen. Human gut microbiome adopts an alternative state following small bowel transplantation. . PNAS 2009 : 0904847106v1-pnas.0904847106
  • UPI Story about this
  • Press release
• Wu D, Hartman A, Ward N, Eisen JA (2008) An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP) . PLoS ONE 3(7): e2566. doi:10.1371/journal.pone.0002566
  • Blogged about by Genome Technology and Jonathan Eisen and Bora
  • Download here
• Wu M and Eisen JA. A simple, fast, and accurate method of phylogenomic inference Genome Biology 2008, 9:R151
  • Blogged about by Larry Moran

Software and Downloads

• AMPHORA - automated phylogenomic analysis for genomes and metagenomics http://bobcat.genomecenter.ucdavis.edu/AMPHORA/
• Compost Bin - Metagenomic Binning by PCA. Download http://bobcat.genomecenter.ucdavis.edu/souravc/compostbin/
• STAP - rRNA alignment and taxonomy pipeline. Download http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/STAP_download
• WATERS - a Workflow for the Alignment, Taxonomy and Ecology of Ribosomal Sequences: http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/WATERS

Social Media and Such

• For other sciency information about the lab see Jonathan Eisen's Work Blog
• For non sciency things see Jonathan's Davis, CA blog
• To follow Jonathan Eisen on Twitter go to http://twitter.com/phylogenomics
• To follow Jonathan Eisen on FriendFeed go to http://friendfeed.com/treeoflife
• Jonathan Eisen's Linked In profile is here: http://www.linkedin.com/in/jonathaneisen