Jonathan Eisen, Ph.D.
Distinguished Professor
GBSF Room 5311
Davis Campus
530-752-3498
e-mail
Lab Page | Blog | BlueSky
Other Links | Ted Talk on the Human Microbiome
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.
Selected Publications from Work at UC Davis
Rojas CA, Marks SL, Borras E, Lesea H, McCartney MM, Coil DA, Davis CE, Eisen JA. 2023. "Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics". Scientific Reports 13: 19382. DOI: 10.1038/s41598-023-45997-1.
De León ME, Wilson HS, Jospin G, Eisen JA. 2023. "Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein producing bacteria and non violacein producing close relatives". Microbial Genomes 9: 000971. DOI: 10.1099/mgen.0.000971.
Rojas CA, Holekamp KE, Viladomat MJ, Souza V, Eisen JA, Theis KR. 2022. "Taxonomic, genomic, and functional variation in the gut microbiomes of wild spotted hyenas across two decades of study". mSystems 19: e0096522. DOI: 10.1128/msystems.00965-22.
Wilbanks EG, Doré H, Ashby MH, Heiner C, Roberts RJ, Eisen JA. 2022. "Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity". ISME Journal 16: 1921-1931. DOI: 10.1038/s41396-022-01242-7.
Leray M, Wilkins LGE, Apprill A, Bik HM, Clever F, Connolly SR, De León ME, Duffy JE, Ezzat L, Gignoux-Wolfsohn S, Herre EA, Kaye JZ, Kline DI, Kueneman JG, McCormick MK, McMillan WO, O'Dea A, Pereira TJ, Petersen JM, Petticord DF, Torchin ME, Vega Thurber R, Videvall E, Wcislo WT, Yuen B, Eisen JA. 2021. "Natural experiments and long-term monitoring are critical to understand and predict marine host–microbe ecology and evolution". PLOS Biology 19: e3001322. DOI: 10.1371/journal.pbio.3001322.
Ettinger CL, Vann LE, Eisen JA. 2021. "Global diversity and biogeography of the Zostera marina mycobiome". Applied and Environmental Microbiology 87: e02795-20. DOI: 10.1128/AEM.02795-20.
Dietz L, Horve PF, Coil DA, Fretz M, Eisen JA, Van Den Wymelenberg K. 2020. "Novel coronavirus (COVID-19) pandemic: built environment considerations to reduce transmission". mSystems 5: e00245-20. DOI: 10.1128/mSystems.00245-20.
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". ISME Journal 13: 921-926. DOI: 10.1038/s41396-018-0323-6.
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. DOI: 10.7717/peerj.4452.
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. DOI: 10.1128/AEM.03391-16.
Dunitz MI, Lang JM, Jospin G, Darling AE, Eisen JA, Coil DA. 2015. "Swabs to genomes: a comprehensive workflow". PeerJ 3: e960. DOI: 10.7717/peerj.960.
Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA. 2013. "PhyloSift: phylogenetic analysis of genomes and metagenomes". PeerJ 2: e243. DOI: 10.7717/peerj.243.
Chandler JA, Lang JM, Bhatnagar S, Eisen JA, Kopp A. 2011. "Bacterial communities of diverse Drosophila species: ecological context of a host-microbe model system". PLOS Genetics 7: e1002272. DOI: 10.1371/journal.pgen.1002272.
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D’haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. 2009. "A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea". Nature 462: 1056-1060. DOI: 10.1038/nature08656.
Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, Eisen JA. 2009. "Human gut microbiome adopts an alternative state following small bowel transplantation". Proceedings of the National Academy of Sciences USA 106: 17187-17192. DOI: 10.1073/pnas.0904847106.
Wu M, Eisen JA. 2008. "A simple, fast, and accurate method of phylogenomic inference". Genome Biology 9: R151. DOI: 10.1186/gb-2008-9-10-r151.
Wu D, Daugherty SC, Van Aken SE, Pai GH, Watkins KL, Khouri H, Tallon LJ, Zaborsky JM, Dunbar HE, Tran PL, Moran NA, Eisen JA. 2006. "Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters". PLOS Biology 4: e188. DOI: 10.1371/journal.pbio.0040188.
