Publications

74 publications

2020

Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Shulz, F., ... Eloe-Fadrosh, E. (2020). A genomic catalogue of Earth’s microbiomes. Nature Biotechnol (accepted; in press).
Petras, D., Minich, J. J., Kunselman, E., Wang, M., White, M. E., Allen, E. E., ... Dorrestein, P. C. (2020). Non-target tandem mass spectrometry enables the prioritization of anthropogenic pollutants in seawater along the northern San Diego coast. submitted to Analytical Chemistry – ChemRxiv. doi: 10.26434/chemrxiv.9817133.v2
Minich, J. J., Power, C., Melanson, M., Knight, R., Webber, C., Rough, K., ... Allen, E. E. (2020). The Southern Bluefin Tuna mucosal microbiome is influenced by husbandry method, net pen location, and anti-parasite treatment. Frontiers in Microbiology. doi: 10.1101/2020.05.19.105270
Allemann, M. N., & Allen, E. E. (2020). Genetic regulation of the bacterial omega-3 polyunsaturated fatty acid biosynthesis pathway. Journal of Bacteriology. doi: 10.1128/JB.00050-20
Podell, S., Blanton, J. M., Oliver, A., Schorn, M. A., Agarwal, V., Biggs, J. S., ... Allen, E. E. (2020). A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. Microbiome, 8. doi: 10.21203/rs.2.17204/v1
Fedarko, M. W., Martino, C., Morton, J. T., González, A., Rahman, G., Marotz, C. A., ... Knight, R. (2020). Visualizing ’omic feature rankings and log-ratios using Qurro. NAR Genomics and Bioinformatics, 2(2). doi: 10.1093/nargab/lqaa023
Schulhof, M. A., Allen, A. E., Allen, E. E., Mladenov, N., McCrow, J. P., Jones, N. T., ... Shurin, J. B. (2020). Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location. Molecular Ecology. doi: 10.1111/mec.15469
Minich, J. J., Jantawongsri, K., Johnston, C., Bowie, K., Bowman, J., Knight, R., ... Allen, E. (2020). Microbial ecology of Atlantic salmon (Salmo salar) hatcheries: Impacts of the built environment on fish mucosal microbiota. Applied and Environmental Microbiology, 86(12). doi: 10.1101/828749
Minich, J., Petrus, S., Michael, J. D., Michael, T. P., Knight, R., & Allen, E. (2020). Temporal, environmental, and biological drivers of the mucosal microbiome in a wild marine fish, Scomber japonicus. mSphere, 5. doi: 10.1128/mSphere.00401-20
Mohanty, I., Podell, S., Biggs, J. S., Garg, N., Allen, E. E., & Agarwal, V. (2020). Multi-omic profiling of melophlus sponges reveals diverse metabolomic and microbiome architectures that are non-overlapping with ecological neighbors. Marine Drugs, 18(2), 124. doi: 10.3390/md18020124

2019

Podell, S., Blanton, J. M., Neu, A., Agarwal, V., Biggs, J. S., Moore, B. S., & Allen, E. E. (2019). Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles. The ISME Journal. doi: 10.1038/s41396-018-0292-9
Kolody, B. C., McCrow, J. P., Allen, L. Z., Aylward, F. O., Fontanez, K. M., Moustafa, A., ... Allen, A. E. (2019). Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. The ISME Journal. doi: 10.1038/s41396-019-0472-2
Schorn, M. A., Jordan, P. A., Podell, S., Blanton, J. M., Agarwal, V., Biggs, J. S., ... Moore, B. S. (2019). Comparative genomics of cyanobacterial symbionts reveals distinct, specialized metabolism in tropical Dysideidae sponges. mBio, 10. doi: 10.1128/mBio.00821-19
Neu, A. T., Allen, E. E., & Roy, K. (2019). Diversity and composition of intertidal gastropod microbiomes across a major marine biogeographic boundary. Environmental Microbiology Reports, 11(3), 434-447. doi: 10.1111/1758-2229.12743
Allemann, M. N., Shulse, C. N., & Allen, E. E. (2019). Linkage of marine bacteria polyunsaturated fatty acid and long-chain hydrocarbon biosynthesis. Frontiers in Microbiology, 10(702). doi: 10.3389/fmicb.2019.00702
Peoples, L. M., Grammatopoulou, E., Pombrol, M., Xu, X. X., Osuntokun, O., Blanton, J., ... Bartlett, D. H. (2019). Microbial community diversity within sediments from two geographically separated hadal trenches. Frontiers in Microbiology, 10(347). doi: 10.3389/fmicb.2019.00347

2018

Minich, J. J., Humphrey, G., Benitez, R. A. S., Sanders, J., Swofford, A., Allen, E. E., & Knight, R. (2018). High-throughput miniaturized 16S rRNA amplicon library preparation reduces costs while preserving microbiome integrity. Msystems, 3(6). doi: 10.1128/mSystems.00166-18
Plominsky, A. M., Henriquez-Castillo, C., Delherbe, N., Podell, S., Ramirez-Flandes, S., Ugalde, J. A., ... Trefault, N. (2018). Distinctive archaeal composition of an artisanal crystallizer pond and functional insights into salt-saturated hypersaline environment adaptation. Frontiers in Microbiology, 9(1800). doi: 10.3389/fmicb.2018.01800
Minich, J. J., Zhu, Q., Xu, Z. Z., Amir, A., Ngochera, M., Simwaka, M., ... Knight, R. (2018). Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). MicrobiologyOpen, e00716. doi: 10.1002/mbo3.716
Guillemette, R., Kaneko, R., Blanton, J., Tan, J., Witt, M., Hamilton, S., ... Azam, F. (2018). Bacterioplankton drawdown of coral mass-spawned organic matter. The ISME Journal. doi: 10.1038/s41396-018-0197-7
Minich, J. J., Zhu, Q. Y., Janssen, S., Hendrickson, R., Amir, A., Vetter, R., ... Knight, R. (2018). KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. Msystems, 3(3). doi: 10.1128/mSystems.00218-17
Peoples, L. M., Donaldson, S., Osuntokun, O., Xia, Q., Nelson, A., Blanton, J., ... Bartlett, D. H. (2018). Vertically distinct microbial communities in the Mariana and Kermadec trenches. Plos One, 13(4). doi: 10.1371/journal.pone.0195102
Plominsky, A. M., Trefault, N., Podell, S., Blanton, J. M., De la Iglesia, R., Allen, E. E., ... Ulloa, O. (2018). Metabolic potential and in situ transcriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen and sulfur cycling in anoxic marine zones. Environmental Microbiology. doi: 10.1111/1462-2920.14109
Allemann, M. N., & Allen, E. E. (2018). Characterization and Application of Marine Microbial Omega-3 Polyunsaturated Fatty Acid Synthesis. Methods in Enzymology (pp. 3-32). : Academic Press. doi: 10.1016/bs.mie.2018.02.018

2017

Leao, T., Castelao, G., Korobeynikov, A., Monroe, E. A., Podell, S., Glukhov, E., ... Gerwick, L. (2017). Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea. Proceedings of the National Academy of Sciences of the United States of America, 114(12), 3198-3203. doi: 10.1073/pnas.1618556114
Agarwal, V., Blanton, J. M., Podell, S., Taton, A., Schorn, M. A., Busch, J., ... Moore, B. S. (2017). Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges. Nat Chem Biol, advance online publication. doi: 10.1038/nchembio.2330
Demidenko, A., Akberdinl, I. R., Allemann, M., Allen, E. E., & Kalyuzhnaya, M. G. (2017). Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G(B1). Frontiers in Microbiology, 7(2167). doi: 10.3389/fmicb.2016.02167

2016

Paerl, R. W., Bouget, F., Lozano, J., Verge, V., Schatt, P., Allen, E. E., ... Azam, F. (2016). Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton. ISME J. doi: 10.1038/ismej.2016.145
Traller, J. C., Cokus, S. J., Lopez, D. A., Gaidarenko, O., Smith, S. R., McCrow, J. P., ... Hildebrand, M. (2016). Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. Biotechnology for Biofuels, 9(1), 258. doi: 10.1186/s13068-016-0670-3
Hogle, S. L., Bundy, R. M., Blanton, J. M., Allen, E. E., & Barbeau, K. A. (2016). Copiotrophic marine bacteria are associated with strong iron-binding ligand production during phytoplankton blooms. Limnology and Oceanography Letters. doi: 10.1002/lol2.10026
Fuentes-Valdés, J. J., Plominsky, A. M., Allen, E. E., Tamames, J., & Vásquez, M. (2016). Complete genome sequence of a cylindrospermopsin-producing cyanobacterium, Cylindrospermopsis raciborskii cs505, containing a circular chromosome and a single extrachromosomal element. Genome Announcements, 4(4). doi: 10.1128/genomeA.00823-16

2015

Andrade, K., Logemann, J., Heidelberg, K. B., Emerson, J. B., Comolli, L. R., Hug, L. A., ... Banfield, J. F. (2015). Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. Isme Journal, 9(12), 2697-2711. doi: 10.1038/ismej.2015.66
Tully, B. J., Emerson, J. B., Andrade, K., Brocks, J. J., Allen, E. E., Banfield, J. F., & Heidelberg, K. B. (2015). De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape. Archaea.(875784). doi: 10.1155/2015/875784
Marietou, A., Nguyen, A. T. T., Allen, E. E., & Bartlett, D. H. (2015). Adaptive laboratory evolution of Escherichia coil K-12 MG1655 for growth at high hydrostatic pressure. Frontiers in Microbiology, 5(749). doi: 10.3389/fmicb.2014.00749

2014

Plominsky, A. M., Delherbe, N., Ugalde, J. A., Allen, E. E., Blanchet, M., Ikeda, P., ... Trefault, N. (2014). Metagenome sequencing of the microbial community of a solar saltern crystallizer pond at Cáhuil Lagoon, Chile. Genome Announcements, 2(6). doi: 10.1128/genomeA.01172-14
Agarwal, V., El Gamal, A. A., Yamanaka, K., Poth, D., Kersten, R. D., Schorn, M., ... Moore, B. S. (2014). Biosynthesis of polybrominated aromatic organic compounds by marine bacteria. Nat Chem Biol, 10(8), 640-647. doi: 10.1038/nchembio.1564
Keeling, P. J., Burki, F., Wilcox, H. M., Allam, B., Allen, E. E., Amaral-Zettler, L. A., ... Worden, A. Z. (2014). The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol, 12(6), e1001889. doi: 10.1371/journal.pbio.1001889
Coates, R. C., Podell, S., Korobeynikov, A., Lapidus, A., Pevzner, P., Sherman, D. H., ... Gerwick, W. H. (2014). Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways. PLoS ONE, 9(1), e85140. doi: 10.1371/journal.pone.0085140

2013

Ugalde, J. A., Narasingarao, P., Kuo, S., Podell, S., & Allen, E. E. (2013). Draft genome sequence of “Candidatus halobonum tyrrellensis” strain g22, isolated from the hypersaline waters of Lake Tyrrell, Australia. Genome Announcements, 1(6). doi: 10.1128/genomeA.01001-13
Podell, S., Emerson, J. B., Jones, C. M., Ugalde, J. A., Welch, S., Heidelberg, K. B., ... Allen, E. E. (2013). Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J. doi: 10.1038/ismej.2013.221
Kharbush, J. J., Ugalde, J. A., Hogle, S. L., Allen, E. E., & Aluwihare, L. I. (2013). Composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current. Applied and Environmental Microbiology. doi: 10.1128/aem.02367-13
Ugalde, J. A., Gallardo, M. J., Belmar, C., Munoz, P., Ruiz-Tagle, N., Ferrada-Fuentes, S., ... Gallardo, V. A. (2013). Microbial life in a fjord: Metagenomic analysis of a microbial mat in Chilean Patagonia. Plos One, 8(8). doi: 10.1371/journal.pone.0071952
Summers, M. M., Katz, S., Allen, E. E., & Rouse, G. W. (2013). Association of rhizobia with a marine polychaete. Environmental Microbiology Reports, 5(4), 492-498. doi: 10.1111/1758-2229.12043
Emerson, J. B., Andrade, K., Thomas, B. C., Norman, A., Allen, E. E., Heidelberg, K. B., & Banfield, J. F. (2013). Virus-host and CRISPR dynamics in archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia. Archaea-an International Microbiological Journal. doi: 10.1155/2013/370871
Podell, S., Ugalde, J. A., Narasingarao, P., Banfield, J. F., Heidelberg, K. B., & Allen, E. E. (2013). Assembly-driven community genomics of a hypersaline microbial ecosystem. Plos One, 8(4). doi: 10.1371/journal.pone.0061692

2012

Emerson, J. B., Thomas, B. C., Andrade, K., Allen, E. E., Heidelberg, K. B., & Banfield, J. F. (2012). Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Applied and Environmental Microbiology, 78(17), 6309-6320. doi: 10.1128/aem.01212-12
Allen, L. Z., Allen, E. E., Badger, J. H., McCrow, J. P., Paulsen, I. T., Elbourne, L. D. H., ... Allen, A. E. (2012). Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. ISME Journal, 6(7), 1403-1414. doi: 10.1038/ismej.2011.201
Mosier, A. C., Allen, E. E., Kim, M., Ferriera, S., & Francis, C. A. (2012). Genome Sequence of "Candidatus Nitrosopumilus salaria" BD31, an Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary. Journal of Bacteriology, 194(8), 2121-2122. doi: 10.1128/jb.00013-12
Mosier, A. C., Allen, E. E., Kim, M., Ferriera, S., & Francis, C. A. (2012). Genome Sequence of “Candidatus Nitrosoarchaeum limnia” BG20, a Low-Salinity Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary. Journal of Bacteriology, 194(8), 2119-2120. doi: 10.1128/jb.00007-12
Ziemert, N., Podell, S., Penn, K., Badger, J. H., Allen, E., & Jensen, P. R. (2012). The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity. Plos One, 7(3). doi: 10.1371/journal.pone.0034064
Narasingarao, P., Podell, S., Ugalde, J. A., Brochier-Armanet, C., Emerson, J. B., Brocks, J. J., ... Allen, E. E. (2012). De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME Journal, 6(1), 81-93. doi: 10.1038/ismej.2011.78

2011

Ugalde, J. A., Podell, S., Narasingarao, P., & Allen, E. E. (2011). Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria. Biology Direct, 6(52). doi: 10.1186/1745-6150-6-52
Eloe, E. A., Shulse, C. N., Fadrosh, D. W., Williamson, S. J., Allen, E. E., & Bartlett, D. H. (2011). Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environment. Environmental Microbiology Reports, 3(4), 449-458. doi: 10.1111/j.1758-2229.2010.00223.x
Shulse, C. N., & Allen, E. E. (2011). Widespread Occurrence of Secondary Lipid Biosynthesis Potential in Microbial Lineages. Plos One, 6(5). doi: 10.1371/journal.pone.0020146
Eloe, E. A., Fadrosh, D. W., Novotny, M., Allen, L. Z., Kim, M., Lombardo, M. J., ... Bartlett, D. H. (2011). Going Deeper: Metagenome of a Hadopelagic Microbial Community. Plos One, 6(5). doi: 10.1371/journal.pone.0020388
Jones, A. C., Monroe, E. A., Podell, S., Hess, W. R., Klages, S., Esquenazi, E., ... Gerwick, L. (2011). Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula. Proceedings of the National Academy of Sciences of the United States of America, 108(21), 8815-8820. doi: 10.1073/pnas.1101137108
Shulse, C. N., & Allen, E. E. (2011). Diversity and distribution of microbial long-chain fatty acid biosynthetic genes in the marine environment. Environmental Microbiology, 13(3), 684-695. doi: 10.1111/j.1462-2920.2010.02373.x
Sun, S. L., Chen, J., Li, W. Z., Altintas, I., Lin, A., Peltier, S., ... Wooley, J. (2011). Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Research, 39, D546-D551. doi: 10.1093/nar/gkq1102

2010

Morin, P. A., Archer, F. I., Foote, A. D., Vilstrup, J., Allen, E. E., Wade, P., ... Harkins, T. (2010). Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Research, 20(7), 908-916. doi: 10.1101/gr.102954.109
Han, S., Narasingarao, P., Obraztsova, A., Gieskes, J., Hartmann, A. C., Tebo, B. M., ... Deheyn, D. D. (2010). Mercury Speciation in Marine Sediments under Sulfate-Limited Conditions. Environmental Science & Technology, 44(10), 3752-3757. doi: 10.1021/es903112m

2009

Penn, K., Jenkins, C., Nett, M., Udwary, D. W., Gontang, E. A., McGlinchey, R. P., ... Jensen, P. R. (2009). Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. Isme Journal, 3(10), 1193-1203. doi: 10.1038/ismej.2009.58

2008

Podell, S., Gaasterland, T., & Allen, E. E. (2008). A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm. BMC Bioinformatics, 9(419). doi: 10.1186/1471-2105-9-419
Robidart, J. C., Bench, S. R., Feldman, R. A., Novoradovsky, A., Podell, S. B., Gaasterland, T., ... Felbeck, H. (2008). Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. Environmental Microbiology, 10(3), 727-737. doi: 10.1111/j.1462-2920.2007.01496.x

2007

Lo, I., Denef, V. J., VerBerkmoes, N. C., Shah, M. B., Goltsman, D., DiBartolo, G., ... Banfield, J. F. (2007). Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature, 446(7135), 537-541. doi: 10.1038/nature05624
Allen, E. E., Tyson, G. W., Whitaker, R. J., Detter, J. C., Richardson, P. M., & Banfield, J. F. (2007). Genome dynamics in a natural archaeal population. Proceedings of the National Academy of Sciences of the United States of America, 104(6), 1883-1888. doi: 10.1073/pnas.0604851104

2006

Baker, B. J., Tyson, G. W., Webb, R. I., Flanagan, J., Hugenholtz, P., Allen, E. E., & Banfield, J. F. (2006). Lineages of acidophilic archaea revealed by community genomic analysis. Science, 314(5807), 1933-1935. doi: 10.1126/science.1132690

2005

Tyson, G. W., Lo, I., Baker, B. J., Allen, E. E., Hugenholtz, P., & Banfield, J. F. (2005). Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp nov from an acidophilic microbial community. Applied and Environmental Microbiology, 71(10), 6319-6324. doi: 10.1128/aem.71.10.6319-6324.2005
Allen, E. E., & Banfield, J. F. (2005). Community genomics in microbial ecology and evolution. Nature Reviews Microbiology, 3(6), 489-498. doi: 10.1038/nrmicro1157
Banfield, J. R., Tyson, G. W., Allen, E. E., & Whitaker, R. J. (2005). The search for a molecular-level understanding of the processes that underpin the earth's biogeochemical cycles. Molecular Geomicrobiology, 59, 1-7. doi: 10.2138/rmg.2005.59.1

2004

Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., ... Banfield, J. F. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428(6978), 37-43. doi: 10.1038/nature02340

2003

Palenik, B., Brahamsha, B., Larimer, F. W., Land, M., Hauser, L., Chain, P., ... Waterbury, J. (2003). The genome of a motile marine Synechococcus. Nature, 424, 1037. doi: 10.1038/nature01943

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

2003

2002

2000

1999