Find Research Outputs

Search in all content

Filters for Research Output

Search concepts
Selected Filters

Publication Year

  • 2020
  • 2019
  • 2018
  • 2017
  • 2016

Author

  • Jonathan A Eisen
2020

2019 Novel coronavirus (CoviD-19) pandemic: Built environment considerations to reduce transmission

Dietz, L., Horve, P. F., Coil, D. A., Fretz, M., Eisen, J. A. & van Den Wymelenberg, K., Jan 1 2020, In : mSystems. 5, 2, e00245-20.

Research output: Contribution to journalReview article

Open Access
29 Scopus citations

A phylogenetically novel cyanobacterium most closely related to Gloeobacter

Grettenberger, C. L., Sumner, D. Y., Wall, K., Brown, C. T., Eisen, J. A., Mackey, T. J., Hawes, I., Jospin, G. & Jungblut, A. D., Jan 1 2020, (Accepted/In press) In : ISME Journal.

Research output: Contribution to journalArticle

Open Access

Bacterial community sequences of submerged aquatic vegetation in the Potomac River

Alexiev, A., Vann, L. E., Lang, J. M. & Eisen, J. A., Jan 2 2020, In : Microbiology Resource Announcements. 9, 1, e01175-19.

Research output: Contribution to journalArticle

Open Access

Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica

Dillon, M. L., Hawes, I., Jungblut, A. D., Mackey, T. J., Eisen, J. A., Doran, P. T. & Sumner, D. Y., Feb 1 2020, In : FEMS microbiology ecology. 96, 2

Research output: Contribution to journalArticle

Open Access

Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica

Dillon, M. L., Hawes, I., Jungblut, A. D., MacKey, T. J., Eisen, J. A., Doran, P. T. & Sumner, D. Y., Apr 2020, In : PloS one. 15, 4, e0231053.

Research output: Contribution to journalArticle

Open Access
Open Access

Erratum: 2019 novel coronavirus (Covid-19) pandemic: Built environment considerations to reduce transmission (mSystems (2020)5: 3(e00375-20)Doi: 10.1128/mSystems.00245-20)

Dietz, L., Horve, P. F., Coil, D. A., Fretz, M., Eisen, J. A. & van Den Wymelenberg, K., Jan 1 2020, In : mSystems. 5, 3, e00375-20.

Research output: Contribution to journalComment/debate

Open Access
1 Scopus citations

Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina

Ettinger, C. L. & Eisen, J. A., 2020, In : PloS one. 15, 7, p. e0236135

Research output: Contribution to journalArticle

Open Access

Reply to McDonald, "protections against the risk of airborne SARS-CoV-2 infection"

Dietz, L., Horve, P. F., Coil, D. A., Fretz, M., Fretz, M., Eisen, J. A., Eisen, J. A., Eisen, J. A., Van Den Wymelenberg, K. & Van Den Wymelenberg, K., Jun 2020, In : mSystems. 5, 3, e00435-20.

Research output: Contribution to journalComment/debate

Open Access

Roadmap for naming uncultivated Archaea and Bacteria

Murray, A. E., Freudenstein, J., Gribaldo, S., Hatzenpichler, R., Hugenholtz, P., Kämpfer, P., Konstantinidis, K. T., Lane, C. E., Papke, R. T., Parks, D. H., Rossello-Mora, R., Stott, M. B., Sutcliffe, I. C., Thrash, J. C., Venter, S. N., Whitman, W. B., Acinas, S. G., Amann, R. I., Anantharaman, K., Armengaud, J. & 44 others, Baker, B. J., Barco, R. A., Bode, H. B., Boyd, E. S., Brady, C. L., Carini, P., Chain, P. S. G., Colman, D. R., DeAngelis, K. M., de los Rios, M. A., Estrada-de los Santos, P., Dunlap, C. A., Eisen, J. A., Emerson, D., Ettema, T. J. G., Eveillard, D., Girguis, P. R., Hentschel, U., Hollibaugh, J. T., Hug, L. A., Inskeep, W. P., Ivanova, E. P., Klenk, H. P., Li, W. J., Lloyd, K. G., Löffler, F. E., Makhalanyane, T. P., Moser, D. P., Nunoura, T., Palmer, M., Parro, V., Pedrós-Alió, C., Probst, A. J., Smits, T. H. M., Steen, A. D., Steenkamp, E. T., Spang, A., Stewart, F. J., Tiedje, J. M., Vandamme, P., Wagner, M., Wang, F. P., Hedlund, B. P. & Reysenbach, A. L., Jan 1 2020, (Accepted/In press) In : Nature Microbiology.

Research output: Contribution to journalReview article

Open Access

Teredinibacter waterburyi sp. Nov., a marine, cellulolytic endosymbiotic bacterium isolated from the gills of the wood-boring mollusc bankia setacea (bivalvia: Teredinidae) and emended description of the genus teredinibacter

Altamia, M. A., Reuben Shipway, J., Stein, D., Betcher, M. A., Fung, J. M., Jospin, G., Eisen, J., Haygood, M. G. & Distel, D. L., Jan 1 2020, In : International Journal of Systematic and Evolutionary Microbiology. 70, 4, p. 2388-2394 7 p., 004049.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

The emergence of microbiome centres

Martiny, J. B. H., Whiteson, K. L., Bohannan, B. J. M., David, L. A., Hynson, N. A., McFall-Ngai, M., Rawls, J. F., Schmidt, T. M., Abdo, Z., Blaser, M. J., Bordenstein, S., Bréchot, C., Bull, C. T., Dorrestein, P., Eisen, J. A., Garcia-Pichel, F., Gilbert, J., Hofmockel, K. S., Holtz, M. L., Knight, R. & 8 others, Mark Welch, D. B., McDonald, D., Methé, B., Mouncey, N. J., Mueller, N. T., Pfister, C. A., Proctor, L. & Sachs, J. L., Jan 1 2020, In : Nature Microbiology. 5, 1, p. 2-3 2 p.

Research output: Contribution to journalComment/debate

Open Access

Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus

Brown, C. L., Garner, E., Jospin, G., Coil, D. A., Schwake, D. O., Eisen, J. A., Mukhopadhyay, B. & Pruden, A. J., Jan 2020, In : PloS one. 15, 1, e0223033.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
2019

Bacteria isolated from Bengal cat (Felis catus × Prionailurus bengalensis) anal sac secretions produce volatile compounds potentially associated with animal signaling

Yamaguchi, M. S., Ganz, H. H., Cho, A. W., Zaw, T. H., Jospin, G., McCartney, M. M., Davis, C. E., Eisen, J. A. & Coil, D. A., Jan 1 2019, In : PloS one. 14, 9, e0216846.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
Open Access

Comparison of Whole-Genome Sequences of Legionella pneumophila in Tap Water and in Clinical Strains, Flint, Michigan, USA, 2016

Garner, E., Brown, C. L., Schwake, D. O., Rhoads, W. J., Arango-Argoty, G., Zhang, L., Jospin, G., Coil, D. A., Eisen, J. A., Edwards, M. A. & Pruden, A., Nov 1 2019, In : Emerging infectious diseases. 25, 11, p. 2013-2020 8 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Early-career scientists shaping the world

Cristea, I. M., Dorrestein, P. C., Eisen, J. A., Gilbert, J. A., Huber, J. A., Jansson, J. K., Knight, R., Pollard, K. S., Raes, J., Silver, P. A., Webster, N. S. & Xu, J., May 1 2019, In : mSystems. 4, 3, e00196-19.

Research output: Contribution to journalEditorial

Open Access

Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment

CoilID, D. A., Jospin, G., Darling, A. E., Wallis, C., Davis, I. J., Harris, S., Eisen, J. A., Holcombe, L. J. & O'Flynn, C., Jun 1 2019, In : PloS one. 14, 6, e0214354.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Host-associated microbiomes drive structure and function of marine ecosystems

Wilkins, L. G. E., Leray, M., O'Dea, A., Yuen, B., Peixoto, R. S., Pereira, T. J., Bik, H. M., Coil, D. A., Duffy, J. E., Herre, E. A., Lessios, H. A., Lucey, N. M., Mejia, L. C., Rasher, D. B., Sharp, K. H., Sogin, E. M., Thacker, R. W., Vega Thurber, R., Wcislo, W. T., Wilbanks, E. G. & 1 others, Eisen, J. A., Nov 1 2019, In : PLoS biology. 17, 11, p. e3000533

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia

Wilkins, L. G. E., Ettinger, C. L., Jospin, G. & Eisen, J. A., Dec 1 2019, In : Scientific Reports. 9, 1, 3059.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria

Bik, H. M., Alexiev, A., Aulakh, S. K., Bharadwaj, L., Flanagan, J., Haggerty, J. M., Hird, S. M., Jospin, G., Lang, J. M., Sauder, L. A., Neufeld, J. D., Shaver, A., Sethi, A., Eisen, J. A. & Coil, D. A., Feb 20 2019, In : mSphere. 4, 1

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Network analysis to evaluate the impact of research funding on research community consolidation

Hicks, D. J., Coil, D. A., Stahmer, C. G. & Eisen, J. A., Jun 1 2019, In : PloS one. 14, 6, e0218273.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Prospecting Microbial Strains for Bioremediation and Probiotics Development for Metaorganism Research and Preservation

Villela, H. D. M., Vilela, C. L. S., Assis, J. M., Varona, N., Burke, C., Coil, D. A., Eisen, J. A. & Peixoto, R. S., Oct 31 2019, In : Journal of visualized experiments : JoVE. 152

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
2018

Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment

Dahlhausen, K. E., Doroud, L., Firl, A. J., Polkinghorne, A. & Eisen, J. A., Jan 1 2018, In : PeerJ. 2018, 3, 4452.

Research output: Contribution to journalArticle

10 Scopus citations

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893)

Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., Eloe-Fadrosh, E. A., Tringe, S. G., Ivanova, N. N., Copeland, A., Clum, A., Becraft, E. D., Malmstrom, R. R., Birren, B., Podar, M., Bork, P., Weinstock, G. M. & 34 others, Garrity, G. M., Dodsworth, J. A., Yooseph, S., Sutton, G., Glöckner, F. O., Gilbert, J. A., Nelson, W. C., Hallam, S. J., Jungbluth, S. P., Ettema, T. J. G., Tighe, S., Konstantinidis, K. T., Liu, W. T., Baker, B. J., Rattei, T., Eisen, J. A., Hedlund, B., Mcmahon, K. D., Fierer, N., Knight, R., Finn, R., Cochrane, G., Karsch-Mizrachi, I., Tyson, G. W., Rinke, C., Lapidus, A., Meyer, F., Yilmaz, P., Parks, D. H., Eren, A. M., Schriml, L., Banfield, J. F., Hugenholtz, P. & Woyke, T., Jul 6 2018, In : Nature Biotechnology. 36, 7, 1 p.

Research output: Contribution to journalComment/debate

3 Scopus citations

Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota

Horng, K. R., Ganz, H. H., Eisen, J. A. & Marks, S. L., Jan 1 2018, In : PeerJ. 2018, 5, e4827.

Research output: Contribution to journalArticle

7 Scopus citations

Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation

Rosado, P. M., Leite, D. C. A., Duarte, G. A. S., Chaloub, R. M., Jospin, G., Nunes da Rocha, U., P. Saraiva, J., Dini-Andreote, F., Eisen, J. A., Bourne, D. G. & Peixoto, R. S., Jan 1 2018, (Accepted/In press) In : ISME Journal.

Research output: Contribution to journalArticle

46 Scopus citations

Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota

Van Deynze, A., Zamora, P., Delaux, P. M., Heitmann, C., Jayaraman, D., Rajasekar, S., Graham, D., Maeda, J., Gibson, D., Schwartz, K. D., Berry, A. M., Bhatnagar, S., Jospin, G., Darling, A., Jeannotte, R., Lopez, J., Weimer, B. C., Eisen, J. A., Shapiro, H. Y., Ané, J. M. & 1 others, Bennett, A. B., Aug 7 2018, In : PLoS Biology. 16, 8, e2006352.

Research output: Contribution to journalArticle

39 Scopus citations

The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status

Hird, S. M., Ganz, H., Eisen, J. A. & Boyce, W. M., Sep 1 2018, In : mSphere. 3, 5, e00382-18.

Research output: Contribution to journalArticle

5 Scopus citations
2017

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

Mukherjee, S., Seshadri, R., Varghese, N. J., Eloe-Fadrosh, E. A., Meier-Kolthoff, J. P., Göker, M., Coates, R. C., Hadjithomas, M., Pavlopoulos, G. A., Paez-Espino, D., Yoshikuni, Y., Visel, A., Whitman, W. B., Garrity, G. M., Eisen, J. A., Hugenholtz, P., Pati, A., Ivanova, N. N., Woyke, T., Klenk, H. P. & 1 others, Kyrpides, N. C., Jul 1 2017, In : Nature Biotechnology. 35, 7, p. 676-683 8 p.

Research output: Contribution to journalArticle

93 Scopus citations

A microbial survey of the International Space Station (ISS)

Lang, J. M., Coil, D. A., Neches, R. Y., Brown, W. E., Cavalier, D., Severance, M., Hampton-Marcell, J. T., Gilbert, J. A. & Eisen, J. A., Jan 1 2017, In : PeerJ. 2017, 12, e4029.

Research output: Contribution to journalArticle

22 Scopus citations

Community-level differences in the microbiome of healthy wild mallards and those infected by influenza A viruses

Ganz, H. H., Doroud, L., Firl, A. J., Hird, S. M., Eisen, J. A. & Boyce, W. M., Jan 1 2017, In : mSystems. 2, 1, e00188.

Research output: Contribution to journalArticle

16 Scopus citations

Complete genome sequence of a Paenalcaligenes hominis strain isolated from a paraplegic patient with neurogenic bladder using single-molecule real-time sequencing technology

Mukhopadhyay, R., Joaquin, J., Hogue, R., Kilaru, A., Jospin, G., Mars, K., Eisen, J. A. & Chaturvedi, V., 2017, In : Genome Announcements. 5, 17, e00252-17.

Research output: Contribution to journalArticle

3 Scopus citations

Complete genome sequence of Dolosigranulum pigrum from a patient with interstitial lung disease using single-molecule real-time sequencing technology

Mukhopadhyay, R., Joaquin, J., Hogue, R., Fitzgerald, S., Jospin, G., Mars, K., Eisen, J. A. & Chaturvedi, V., 2017, In : Genome Announcements. 5, 18, e00317-17.

Research output: Contribution to journalArticle

Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds

Jiao, J. Y., Carro, L., Liu, L., Gao, X. Y., Zhang, X. T., Hozzein, W. N., Lapidus, A., Huntemann, M., Reddy, T. B. K., Varghese, N., Hadjithomas, M., Ivanova, N. N., Göker, M., Pillay, M., Eisen, J. A., Woyke, T., Klenk, H. P., Kyrpides, N. C. & Li, W. J., Feb 3 2017, In : Standards in Genomic Sciences. 12, 1, 21.

Research output: Contribution to journalArticle

3 Scopus citations

Draft Genome Sequence of Arthrobacter sp. Strain UCD-GKA (Phylum Actinobacteria)

Kincheloe, G. N., Eisen, J. A. & Coil, D. A., 2017, In : Genome Announcements. 5, 6, e01599-16.

Research output: Contribution to journalArticle

1 Scopus citations

Draft genome sequence of Propionibacterium avidum strain UCD-PD2 isolated from a feline anal sac

Dahms, P. A., Martin, A. L., Ganz, H. H., Eisen, J. A. & Coil, D. A., 2017, In : Genome Announcements. 5, 12, e00034-17.

Research output: Contribution to journalArticle

3 Scopus citations

Draft genome sequences of Dermacoccus nishinomiyaensis strains UCD-KPL2534 and UCD-KPL2528 isolated from an indoor track facility

Klein, B. A., Lemon, K. P., Gajare, P., Jospin, G., Eisen, J. A. & Coil, D. A., 2017, In : Genome Announcements. 5, 8, e01652-16.

Research output: Contribution to journalArticle

2 Scopus citations
3 Scopus citations
3 Scopus citations

Genomic attributes of extended-spectrum β-lactamase-producing Escherichia coli isolated from patients in Lebanon

Tokajian, S., Salloum, T., Eisen, J. A., Jospin, G., Farra, A., Mokhbat, J. E. & Coil, D. A., Mar 1 2017, In : Future Microbiology. 12, 3, p. 213-226 14 p.

Research output: Contribution to journalArticle

6 Scopus citations

Globalscale structure of the eelgrass microbiome

Fahimipour, A. K., Kardish, M. R., Lang, J. M., Green, J. L., Eisen, J. A. & Stachowicz, J. J., Jun 1 2017, In : Applied and Environmental Microbiology. 83, 12, e03391-16.

Research output: Contribution to journalArticle

33 Scopus citations

Gut Check: The evolution of an educational board game

Coil, D. A., Ettinger, C. L. & Eisen, J. A., Apr 28 2017, In : PLoS Biology. 15, 4, e2001984.

Research output: Contribution to journalArticle

13 Scopus citations

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

Ettinger, C. L., Voerman, S. E., Lang, J. M., Stachowicz, J. J. & Eisen, J. A., 2017, In : PeerJ. 2017, 4, e3246.

Research output: Contribution to journalArticle

26 Scopus citations

Microbiome succession during ammonification in eelgrass bed sediments

Ettinger, C. L., Williams, S. L., Abbott, J. M., Stachowicz, J. J. & Eisen, J. A., 2017, In : PeerJ. 2017, 8, 3674.

Research output: Contribution to journalArticle

3 Scopus citations

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

The Genome Standards Consortium, Aug 8 2017, In : Nature Biotechnology. 35, 8, p. 725-731 7 p.

Research output: Contribution to journalReview article

227 Scopus citations

Research priorities for harnessing plant microbiomes in sustainable agriculture

Busby, P. E., Soman, C., Wagner, M. R., Friesen, M. L., Kremer, J., Bennett, A., Morsy, M., Eisen, J. A., Leach, J. E. & Dangl, J. L., Mar 28 2017, In : PLoS Biology. 15, 3, e2001793.

Research output: Contribution to journalArticle

176 Scopus citations

Rokubacteria: Genomic giants among the uncultured bacterial phyla

Becraft, E. D., Woyke, T., Jarett, J., Ivanova, N., Godoy-Vitorino, F., Poulton, N., Brown, J. M., Brown, J., Lau, M. C. Y., Onstott, T., Eisen, J. A., Moser, D. & Stepanauskas, R., Nov 28 2017, In : Frontiers in Microbiology. 8, NOV, 2264.

Research output: Contribution to journalArticle

22 Scopus citations

The green berry consortia of the Sippewissett salt marsh: Millimeter-sized aggregates of diazotrophic unicellular cyanobacteria

Wilbanks, E. G., Salman-Carvalho, V., Jaekel, U., Humphrey, P. T., Eisen, J. A., Buckley, D. H. & Zinder, S. H., Sep 4 2017, In : Frontiers in Microbiology. 8, SEP, 1623.

Research output: Contribution to journalArticle

1 Scopus citations