Jonathan Eisen, Ph.D.
GBSF Room 5311
Davis Campus

Our work focuses on genomic basis for the origin of novelty in microorganisms (how new processes and functions evolve). We are currently focusing on mutualistic symbioses involving microbes because such symbioses are one of the simplest and most important means for organisms to acquire new processes and functions. We are interested in the mechanisms through which such symbioses originate and are maintained and how symbionts communicate with their hosts or partners. We are studying a wide diversity of such symbioses ranging from single symbionts that live inside host cells to the thousands of microbes species that live inside the human digestive tract. Most of our research involves a combination of genome sequencing, bioinformatics and phylogenomic analysis, and high throughput environmental microbiology.

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Rosado PM, Leite DCA, Duarte GAS, Chaloub RM, Jospin G, Nunes da Rocha U, P Saraiva J, Dini-Andreote F, Eisen JA, Bourne DG, Peixoto RS. 2018. Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation. 2018. ISME J. doi: 10.1038/s41396-018-0323-6. PMID: 3051881.

Hird S, Ganz H, Eisen JA, Boyce WM. 2018. The cloacal microbiome of five wild duck species varies by species and influenza A virus infection status. mSphere 3:e00382-18.

Van Deynze A, Zamora P, Delaux PM, Heitmann C, Jayaraman D, Rajasekar S, Graham D, Maeda J, Gibson D, Schwartz KD, Berry AM, Bhatnagar S, Jospin G, Darling A, Jeannotte R, Lopez J, Weimer BC, Eisen JA, Shapiro HY, Ané JM, Bennett AB. 2018. Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLoS Biology 16(8):e2006352. doi: 10.1371/journal.pbio.2006352. PMID: 30086128. PMCID: PMC6080747.

Ettinger C, Wilkins L, Dahlhausen K, Ghose S, Oberbauer D, Eisen JA, Coil D. 2018 Even Superheroes Need Help Sometimes: Three Incredible Tales of Microbial Symbiosis. Frontiers in Young Minds 6: 50. doi: 10.3389/frym.2018.00050.

Grettenberger CL, Sumner D, Wall K, Brown CT, Eisen JA, Mackey T, Hawes I, Jungblut A. Insights into the evolution of oxygenic photosynthesis from a phylogenetically novel, low-light cyanobacterium. Submitted. Preprint on BioRXiv.

Horng KR, Ganz HH, Eisen JA, Marks SL. 2018. Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota. PeerJ 6: e4827.
Dahlhausen KE, Doroud L, Firl AJ, Polkinghorne A, Eisen JA. 2018. Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment. PeerJ 6: e4452

Lang JM, Coil DA, Neches RY, Brown WE, Cavalier D, Severance M, Hampton-Marcell JT, Gilbert JA, Eisen JA. 2017. A microbial survey of the International Space Station (ISS). PeerJ 5:e4029.

Coil DA, Ettinger CL, Eisen JA. 2017. Gut Check: The evolution of an educational board game. PLoS Biology 15(4): e2001984. 

Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Paez-Espino D, Yoshikuni Y, Visel A, Whitman WB, Garrity GM, Eisen JA, Hugenholtz P, Pati A, Ivanova NN, Woyke T, Klenk HP, Kyrpides NC. 2017. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nature Biotechnology 35: 676–683. PMID: 28604660.

Fahimipour AK, Kardish MR, Lang JM, Green JL, Eisen JA, Stachowicz JJ. 2017. Global-scale structure of the eelgrass microbiome. Applied and Environmental Microbiology. 83:e03391-16.

Ettinger CL, Voerman SE, Lang JM, Stachowicz JJ, Eisen JA. 2017. Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge. PeerJ 5: e3246.

Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, Morsy M, Eisen JA, Leach JE, Dangl JL. 2017. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biology 15(3): e2001793.

Ganz HH, Doroud L, Firl AJ, Hird SM, Eisen JA, Boyce WM. 2017. Community-level differences in the microbiome of healthy wild mallards and those infected by influenza A viruses. mSystems 2: e00188-16.

Dunitz MI, Lang JM, Jospin G, Darling AE, Eisen JA, Coil DA. 2015. Swabs to genomes: a comprehensive workflow. PeerJ 3: e960.

Edwards J, Johnson C, Santos-Medellin C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V. 2015. Structure, variation, and assembly of the root-associated microbiomes of rice. Proceedings of the National Academy of Sciences USA 12: E911-20

Lang JM, Eisen JA, Zivcovik A. 2014. The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of model meals. Peer J 2: e659.

Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. 2014. Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2:e415.

Darling AE; Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243.

Wu D, Jospin G, Eisen JA. 2013. Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups. PLOS ONE 8(10): e77033. doi:10.1371/journal.pone.0077033

Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. 2013. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications 4:2120. doi: 10.1038/ncomms3120. PMID: 23979677.

Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499(7459): 431-7. doi: 10.1038/nature12352.

Lang JM, Darling AE, Eisen JA. 2013. Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices. PLoS ONE 8(4): e62510. doi:10.1371/journal.pone.0062510.

Rands C, Darling AE, Fujita M, Kong L, Webster MT, Clabaut C, Emes RD, Heger A, Meader S, Hawkins MB, Eisen MB, Teiling C, Affourtit J, Boese B, Grant PR, Grant BR, Eisen JA, Abzhanov A, Ponting CP. 2013. Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics 2013, 14:95 doi:10.1186/1471-2164-14-95.