Jonathan Eisen, Ph.D.
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.
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.
Rojas CA, Entrolezo Z, Jarett JK, Jospin G, Kingsbury DD, Martin A, Eisen JA, Ganz HH. 2023. "Microbiome responses to fecal microbiota transplantation in cats with chronic digestive issues". Veterinary Sciences 10(9): 561. DOI: 10.3390/vetsci10090561.
Yu L, Khachaturyan M, Matschiner M, Healey A, Bauer D, Cameron B, Cusson M, Emmett Duffy J, Joel Fodrie F, Gill D, Grimwood J, Hori M, Hovel K, Hughes AR, Jahnke M, Jenkins J, Keymanesh K, Kruschel C, Mamidi S, Menning DM, Moksnes PO, Nakaoka M, Pennacchio C, Reiss K, Rossi F, Ruesink JL, Schultz ST, Talbot S, Unsworth R, Ward DH, Dagan T, Schmutz J, Eisen JA, Stachowicz JJ, Van De Peer Y, Olsen JL, Reusch TBH. 2023. "Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)". Nature Plants 9: 1207–1220. DOI: 10.1038/s41477-023-01464-3.
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.
Tran MT, Seuylemezian A, Wright A, Coil D, Eisen JA, Guan L. 2023. "Draft genome sequences of spacecraft-associated microbes isolated from six NASA missions". Microbiology Resource Announcements 12: e01011-22. DOI: 10.1128/mra.01011-22.
Perry LM, Cruz SM, Kleber KT, Judge SJ, Darrow MA, Jones LB, Basmaci UN, Joshi N, Settles ML, Durbin-Johnson BP, Gingrich AA, Monjazeb AM, Carr-Ascher J, Thorpe SW, Murphy WJ, Eisen JA, Canter RJ. 2023. "Human soft tissue sarcomas harbor an intratumoral viral microbiome which is linked with natural killer cell infiltrate and prognosis". Journal for Immunotherapy of Cancer 11: e004285. DOI: 10.1136/jitc-2021-004285.
Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C, Konnikova L, Lebeer S, Macpherson AJ, Massey RC, McHardy AC, Koren O, Lawley TD, Ley RE, O'Mahony L, O'Toole PW, Pamer EG, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda DM, Smith GCS, Sokol H, Spector TD, Surette MG, Tannock GW, Walker AW, Yassour M, Walter J. 2023. "Questioning the fetal microbiome and pitfalls of low biomass microbial studies". Nature Microbiology 613: 639-649. DOI: 10.1038/s41586-022-05546-8.
Kleber KT, Iranpur KR, Perry LM, Cruz SM, Razmara AM, Culp WTN, Kent MS, Eisen JA, Rebhun RB, Canter RJ. 2022. "Using the canine microbiome to bridge translation of cancer immunotherapy from pre-clinical murine models to human clinical trials". Frontiers in Immunology 13: 983344. DOI: 10.3389/fimmu.2022.983344.
Wu J, Danko D, Afshinnekoo E, Bezdan D, Bhattacharyya M, Castro-Nallar E, Chmielarczyk A, Hazrin-Chong NH, Deng Y, Dias-Neto E, Frolova A, Mason-Buck G, Iraola G, Jang S, Łabaj P, Lee PKH, Nieto-Caballero M, Osuolale OO, Ouzounis CA, Perlin MH, Prithiviraj B, Rascovan N, Różańska A, Schriml LM, Semmler T, Suzuki H, Ugalde JA, Young B, Werner J, Zambrano MM, Zhao Y, Mason C, Shi T; MetaSUB Consortium. 2022. "Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association." Environmental Research 207: 112183. DOI: 10.1016/j.envres.2021.112183.
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.
Ganz HH, Jospin G, Rojas CA, Martin AL, Dahlhausen K, Kingsbury DD, Osborne CX, Entrolezo Z, Redner S, Ramirez B, Eisen JA, Leahy M, Keaton C, Wong J, Gardy J, Jarett JK. 2022. "The Kitty Microbiome Project: defining the healthy fecal “Core Microbiome” in pet domestic cats". Veterinary Sciences 9: 635. DOI: 10.3390/vetsci9110635.
Coil DA, Pechacek R, Kaze M, Zuniga-Montanez R, Guerrero RG, Eisen JA, Shapiro K, Bischel HN. 2022. "SARS-CoV-2 RNA is readily detectable at least 8 months after shedding in an isolation facility". mSphere 11: e0017722. DOI: 10.1128/msphere.00177-22.
Clever F, Sourisse JM, Preziosi RF, Eisen JA, Guerra ECR, Scott JJ, Wilkins LGE, Altieri AH, McMillan WO, Leray M. 2022. "The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs". Nature Communications Biology 17: 50. DOI: 10.1038/s42003-022-03679-0.
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.
Zuniga-Montanez R, Coil DA, Eisen JA, Pechacek R, Guerrero RG, Kim M, Shapiro K, Bischel H. 2022. "The challenge of SARS-CoV-2 environmental monitoring in schools using floors and portable HEPA filtration units: Fresh or relic RNA?". PLOS ONE 17: e0267212. DOI: 10.1371/journal.pone.0267212.
