Evolution, ecology and function of microbiomes and interactions therein

We are interested in general in the evolution, ecology and function of microbial communities and microbiomes and in the interactions that occur among microbes as well as between microbes and hosts.  In particular we are interested in learning the rules that apply across such systems.  Therefore we tend to not focus on one and of microbiome but rather compare across microbiomes.  Example projects we have worked on in the past include those listed below.

Plant Systems

  • 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 CL, Williams SL, Abbott JM, Stachowicz JJ, Eisen JA. 2017. Microbiome succession during ammonification in eelgrass bed sediments. PeerJ 5: e3674. Doi: 10.7717/peerj.3674. PMID: 28828269. PMCID: PMC5563154.
  • 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.  PMID: 28462046 PMCID: PMC5410140 DOI: 10.7717/peerj.3246.
  • 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. Doi: 10.1371/journal.pbio.2001793. PMID: 28350798. PMCID: PMC5370116.
  • Fahimipour AK, Kardish MR, Lang JM, Green JL, Eisen JA, Stachowicz JJ. 2017. Global-scale structure of the eelgrass microbiome. AEM 83(12): e03391-16. PMCID: PMC5452814.
  • Mousa WK, Shearer C, Limay-Rios V, Ettinger CL, Eisen JA, Raizada MN. 2016. Root-hair endophyte stacking in finger millet creates a physicochemical barrier to trap the fungal pathogen Fusarium graminearum. Nature Microbiology 1: 16167. PMID: 27669453. Posted to BioRXiv.
  • Shehata HR, Ettinger CL, Eisen JA and Raizada MN. 2016. Genes required for the anti-fungal activity of a bacterial endophyte isolated from a corn landrace grown continuously by subsistence farmers since 1000 BC. Frontiers in Microbiology 7: 1548. doi: 10.3389/fmicb.2016.01548
  • 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(8): E911-20. PMID: 25635017.

Animal Systems

  • 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.
  • McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, The American Gut Consortium, Knight R. 2018. American Gut: an open platform for citizen science microbiome research. mSystems 3:e00031-18. https://doi.org/10.1128/mSystems.00031-18. (Note – Eisen JA a coauthor as part of the American Gut Consortium).
  • 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. https://doi.org/10.1128/mSphere.00382-18.
  • Horng KR, Ganz HH, Eisen JA, Marks SL. 2018. Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota. PeerJ 6: e4827. https://doi.org/10.7717/peerj.4827.
  • 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 https://doi.org/10.7717/peerj.4452.
  • 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. PMID: 28293681. PMCID: PMC5347185.
  • 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. PMID: 25538865. PMCID: PMC4266855.
  • O’Flynn C, Deusch O, Darling A, Eisen JA, Wallis C, Davis I, Harris S. 2015. Comparative genomics of the genus Porphyromonas identifies adaptations for heme synthesis within the prevalent canine oral species Porphyromonas cangingivalis. Genome Biology and Evolution. doi:10.1093/gbe/evv220.  PMID: 26568374. PMCID: PMC4700951.
  • Martin ME, Bhatnagar S, George MD, Paster BJ, Canfield DR, Eisen JA, Solnick JS. 2013. The impact of Helicobacter pylori infection on the gastric microbiota of the rhesus macaque. PLOS ONE 8: e76375. PMID: 24116104. PMCID: PMC3792980.
  • 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. PMID: 21966276.
  • Hartman A, Lough D, Fiehn O, Barupal D, 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. PMID: 19805153. PDF.
  • Newton ILG, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM. 2007. The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315: 998-1000. PMID: 17303757. PDF. Supplement PDF.
  • Wu D, Daugherty SC, van Aken S, Pai G, Watkins K, Khouri H, Tallon L, Zaborsky J, Dunbar H, Tran P, Moran NA, Eisen JA. 2006. Metabolic complementarity and genomics of the dual symbiosis of sharpshooters. PLoS Biology 4: e188. PMID: 16729848. PDF.
  • Penn K, Wu D, Eisen JA, Ward N. 2006. Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Applied and Environmental Microbiology 72: 1680-1683. PMID: 16461727. PDF.
  • Schmidt EW, Nelson JT, Rakso D, Sudek S, Eisen JA, Haygood MG, Ravel J. 2005. Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the obligate cyanobacterial symbiont of Lissoclinum patella (ascidia). Proceedings of the National Academy of Sciences USA 102: 7315-7320.  PMID: 15883371. PDF.
  • Wu M, Sun L, Vamathevan J, Riegler M, Deboy R, Brownlie J, McGraw E, Mohamoud Y, Lee P, Berry K, Khouri HM, Paulsen IT, Nelson KE, Martin W, Esser C, Ahmadinejad N, Wiegand C, Durkin AS, Nelson WC, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Gwinn M, Kolonay JF, Madupu R, Craven MB, Utterback T, Weidman J, Nierman WC, Aken SV, Tettelin H, O’Neill S, Eisen JA. 2004. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome massively infected with mobile genetic elements. PLoS Biology 2: 327-341. PMID: 15024419. PDF.

Marine and Aquatic Systems

  • Wilbanks EG, Salman-Carvalho V, Jaekel U, Humphrey PT, Eisen JA, Buckley DH and Zinder SH. 2017. The green berry consortia of the Sippewissett Salt Marsh: millimeter-sized aggregates of diazotrophic unicellular cyanobacteria. Frontiers in Microbiology 8: 1623. PMID: 28928719. PMCID: PMC5591377.
  • Jungblut AD, Hawes I, Mackey TJ, Krusor M, Doran PT, Sumner DY, Eisen JA, Hillman C, Goroncy A. 2016. Microbial mat communities along an oxygen gradient in a perennially ice-covered Antarctic lake. Applied and Environmental Microbiology 82 (2): 620-630. doi:10.1128/AEM.02699-15. PMID: 26567300. PMCID: PMC4711149.
  • Hasan NA, Grim CJ, Lipp EK, Rivera IN, Chun J, Haley BJ, Taviani E, Choi SY, Hoq M, Munk AC, Brettin TS, Bruce D, Challacombe JF, Detter JC, Han CS, Eisen JA, Huq A, Colwell RR. 2015. Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species. Proceedings of the National Academy of Sciences USA 112(21): E2813-9. PMID: 25964331. PMCID: PMC4450432.
  • Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling AE, Facciotti MT. 2014. Phylogenetically driven sequencing of extremely halophilic Archaea reveals strategies for static and dynamic osmo-response. PLOS Genetics 10: e1004784. PMID: 25393412. PMCID: PMC4230888.
  • Castelle C, Hug LA, Wrighton KC, Thgomas, BC, Williams KH, Wu D, Tringe SG, Singer S, Eisen JA, Banfield JF. 2013. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications 4: 2120. PMID: 23979677. PMCID: PMC3903129.
  • Jiang X, Langille MGI, Neches RY, Elliot MA, Levin SA, Eisen JA, Weitz JS, Dushoff J. 2012. Functional biogeography of ocean microbes: dimension reduction of metagenomic data identifies biological patterns across scales. PLoS ONE 7: e43866. PMID: 23049741. PMCID: PMC3445553. PDF.
  • Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R. 2009. Assembling the marine metagenome, one cell at a time. PLoS ONE 4: e5299. PMID: 19390573. PDF.
  • Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC. 2007. The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families. PLoS Biology 5: e16 . PMID: 17355171. PDF.
  • Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcon LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC. 2007. The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through Eastern tropical pacific. PLoS Biology 5: e77. PMID: 17355176. PDF.
  • Penn K, Wu D, Eisen JA, Ward N. 2006. Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Applied and Environmental Microbiology 72: 1680-1683. PMID: 16461727. PDF.
  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Paulsen IT, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson JD, Hoffman J, Parsons R, Baden-Tillson H, Pfannkock C, Rogers Y-H, and Smith HO. 2004. Environmental whole genome shotgun sequencing: the Sargasso Sea. Science 304: 66-74. PMID: 15001713.
  • Shank T, Fornari D, Yoerger S, Humphries S, Bradley A, Hammond S, Lupton J, Schierer D, Collier R, Reysenbach A-L, Ding K, Seyfried W, Butterfield D, Olson E, Lilley M, Ward N, Eisen JA. 2003. Deep submergence synergy: Alvin and ABE explore the Galápagos Rift at 86°W. EOS 84: 425, 432-433. PDF.
  • Béjà O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, Hamada T, Eisen JA, Fraser CM, DeLong EF. 2002. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415: 630-633. PMID: 11832943. PDF.

Microbiomes of the Built Environment

  • Adams RI, Bhangar S, Dannemiller KC, Eisen JA, Fierer N, Gilbert JA, Green JL, Marr LC, Miller SL, Siegel JA, Stephens B. 2016. Ten questions concerning the microbiomes of buildings. Building and Environment 109: 224-234.
  • 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. https://doi.org/10.7717/peerj.4029.
  • Adams RI, Bhangar S, Dannemiller KC, Eisen JA, Fierer N, Gilbert JA, Green JL, Marr LC, Miller SL, Siegel JA, Stephens B. 2016. Ten questions concerning the microbiomes of buildings. Building and Environment 109: 224-234.
  • Coil DA, Flanagan JC, Stump A, Alexiev A, Lang JM, Eisen JA. 2015.Porphyrobacter mercurialis sp. nov., isolated from a stadium seat and emended description of the genus Porphyrobacter.PeerJ 3: e1400. PMID: 26587357. PMCID: PMC4647569.
  • Lax S, Hampton-Marcell JT, Gibbons SM, Barguil G, Smith D, Eisen JA, Gilbert JA. 2015. Forensic analysis of the microbiome of phones and shoes. Microbiome 3: 21. PMID: 25969737. PMCID: PMC4427962.
  • 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. https://peerj.com/articles/659/.  PMID: 25538865. PMCID: PMC4266855.
  • Bik HM, Coil DA, Eisen JA. 2014. microBEnet: lessons learned from building an interdisciplinary scientific community in the online sphere. PLOS Biology 12: e1001884. PMID: 24937755. PMCID: PMC4060986.