Publications


Neu, A. T., Allen, E. E., & Roy, K. (2021). Defining and quantifying the core microbiome: Challenges and prospects. Proceedings of the National Academy of Sciences of the United States of America, 118(51), 10. https://doi.org/10.1073/pnas.2104429118
Neu, A. T., Allen, E. E., & Roy, K. (2021). Do host-associated microbes show a contrarian latitudinal diversity gradient? Insights from Mytilus californianus, an intertidal foundation host. Journal of Biogeography, 14. https://doi.org/10.1111/jbi.14243
Oliver, A., Podell, S., Pinowska, A., Traller, J. C., Smith, S. R., McClure, R., Beliaev, A., Bohutskyi, P., Hill, E. A., Rabines, A., Zheng, H., Allen, L. Z., Kuo, A., Grigoriev, I. V., Allen, A. E., Hazlebeck, D., & Allen, E. E. (2021). Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom. Scientific Reports, 11(1), 14. https://doi.org/10.1038/s41598-021-95106-3
Minich, J. J., Poore, G. D., Jantawongsri, K., Johnston, C., Bowie, K., Bowman, J., Knight, R., Nowak, B., Allen, E. E., & Liu, S.-J. (2021). Microbial ecology of Atlantic salmon (Salmo salar) hatcheries: Impacts of the built environment on fish mucosal microbiota. Applied and Environmental Microbiology, 86(12), e00411-20. https://doi.org/10.1128/AEM.00411-20
Petras, D., Minich, J. J., Cancelada, L. B., Torres, R. R., Kunselman, E., Wang, M. X., White, M. E., Allen, E. E., Prather, K. A., Aluwihare, L. I., & Dorrestein, P. C. (2021). Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater. Chemosphere, 271. https://doi.org/10.1016/j.chemosphere.2020.129450
Minich, J. J., Nowak, B., Elizur, A., Knight, R., Fielder, S., & Allen, E. E. (2021). Impacts of the marine hatchery built environment, water and feed on across ontogeny in yellowtail kingfish, Seriola lalandi. Frontiers in Marine Science, 8, 14. https://doi.org/10.3389/fmars.2021.676731
Allemann, M. N., Allen, E. E., & Atomi, H. (2021). Genetic suppression of lethal mutations in fatty acid biosynthesis mediated by a secondary lipid synthase. Applied and Environmental Microbiology, 87(12), e00035-21. https://doi.org/10.1128/AEM.00035-21
Minich, J., Nowak, B., Elizur, A., Knight, R., Fielder, S., & Allen, E. (2021). Impacts of the marine hatchery built environment on mucosal microbiome colonization across ontogeny in yellowtail kingfish, Seriola Lalandi. Research Square. https://doi.org/10.21203/rs.3.rs-75521/v1
Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu, D., Paez-Espino, D., Chen, I. M., Huntemann, M., Palaniappan, K., Ladau, J., Mukherjee, S., Reddy, T. B. K., Nielsen, T., Kirton, E., Faria, J. P., Edirisinghe, J. N., Henry, C. S., … Img M. Data Consortium. (2021). A genomic catalog of Earth’s microbiomes. Nature Biotechnology, 39(4), 499–509. https://doi.org/10.1038/s41587-020-0718-6
Allemann, M. N., & Allen, E. E. (2021). Genetic suppression of lethal mutations in fatty acid synthesis mediated by a secondary lipid synthase. Applied and Environmental Microbiology, 87(12). https://doi.org/10.1128/AEM.00035-21
Minich, J. J., Ali, F., Marotz, C., Belda-Ferre, P., Chiang, L., Shaffer, J. P., Carpenter, C. S., McDonald, D., Gilbert, J., Allard, S. M., Allen, E. E., Knight, R., Sweeney, D. A., & Swafford, A. D. (2021). Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Microbiome, 9(1). https://doi.org/10.1186/s40168-020-00960-4
Neu, A. T., Hughes, I. V., Allen, E. E., & Roy, K. (2021). Decade-scale stability and change in a marine bivalve microbiome. Molecular Ecology. https://doi.org/10.1111/mec.15796
Minich, J. J., Power, C., Melanson, M., Knight, R., Webber, C., Rough, K., Bott, N. J., Nowak, B., & 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. https://doi.org/10.1101/2020.05.19.105270
Podell, S., Blanton, J. M., Oliver, A., Schorn, M. A., Agarwal, V., Biggs, J. S., Moore, B. S., & Allen, E. E. (2020). A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. Microbiome, 8. https://doi.org/10.21203/rs.2.17204/v1
Allemann, M. N., & Allen, E. E. (2020). Genetic regulation of the bacterial omega-3 polyunsaturated fatty acid biosynthesis pathway. Journal of Bacteriology. https://doi.org/10.1128/JB.00050-20
Fedarko, M. W., Martino, C., Morton, J. T., González, A., Rahman, G., Marotz, C. A., Minich, J. J., Allen, E. E., & Knight, R. (2020). Visualizing ’omic feature rankings and log-ratios using Qurro. NAR Genomics and Bioinformatics, 2(2). https://doi.org/10.1093/nargab/lqaa023
Schulhof, M. A., Allen, A. E., Allen, E. E., Mladenov, N., McCrow, J. P., Jones, N. T., Blanton, J., Cavalheri, H. B., Kaul, D., Symons, C. C., & Shurin, J. B. (2020). Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location. Molecular Ecology. https://doi.org/10.1111/mec.15469
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. https://doi.org/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. https://doi.org/10.3390/md18020124
Kolody, B. C., McCrow, J. P., Allen, L. Z., Aylward, F. O., Fontanez, K. M., Moustafa, A., Moniruzzaman, M., Chavez, F. P., Scholin, C. A., Allen, E. E., Worden, A. Z., Delong, E. F., & Allen, A. E. (2019). Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. The ISME Journal. https://doi.org/10.1038/s41396-019-0472-2
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. https://doi.org/10.1111/1758-2229.12743
Schorn, M. A., Jordan, P. A., Podell, S., Blanton, J. M., Agarwal, V., Biggs, J. S., Allen, E. E., & Moore, B. S. (2019). Comparative genomics of cyanobacterial symbionts reveals distinct, specialized metabolism in tropical Dysideidae sponges. Mbio, 10. https://doi.org/10.1128/mBio.00821-19
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. https://doi.org/10.3389/fmicb.2019.00702
Peoples, L. M., Grammatopoulou, E., Pombrol, M., Xu, X. X., Osuntokun, O., Blanton, J., Allen, E. E., Nunnally, C. C., Drazen, J. C., Mayor, D. J., & Bartlett, D. H. (2019). Microbial community diversity within sediments from two geographically separated hadal trenches. Frontiers in Microbiology, 10. https://doi.org/10.3389/fmicb.2019.00347
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). https://doi.org/10.1128/mSystems.00166-18
Podell, S., Blanton, J. M., Neu, A., Agarwal, V., Biggs, J. S., Moore, B. S., & Allen, E. E. (2018). Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles. The ISME Journal. https://doi.org/10.1038/s41396-018-0292-9
Minich, J. J., Zhu, Q., Xu, Z. Z., Amir, A., Ngochera, M., Simwaka, M., Allen, E. E., Zidana, H., & Knight, R. (2018). Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). MicrobiologyOpen, 0(0), e00716. https://doi.org/10.1002/mbo3.716
Plominsky, A. M., Henriquez-Castillo, C., Delherbe, N., Podell, S., Ramirez-Flandes, S., Ugalde, J. A., Santibanez, J. F., van den Engh, G., Hanselmann, K., Ulloa, O., De la Iglesia, R., Allen, E. E., & Trefault, N. (2018). Distinctive archaeal composition of an artisanal crystallizer pond and functional insights into salt-saturated hypersaline environment adaptation. Frontiers in Microbiology, 9. https://doi.org/10.3389/fmicb.2018.01800
Guillemette, R., Kaneko, R., Blanton, J., Tan, J., Witt, M., Hamilton, S., Allen, E. E., Medina, M., Hamasaki, K., Koch, B. P., & Azam, F. (2018). Bacterioplankton drawdown of coral mass-spawned organic matter. The ISME Journal. https://doi.org/10.1038/s41396-018-0197-7
Minich, J. J., Zhu, Q. Y., Janssen, S., Hendrickson, R., Amir, A., Vetter, R., Hyde, J., Doty, M. M., Stillwell, K., Benardini, J., Kim, J. H., Allen, E. E., Venkateswaran, K., & Knight, R. (2018). KatharoSeq enables high-throughput microbiome analysis from low-biomass samples. MSystems, 3(3). https://doi.org/10.1128/mSystems.00218-17
Peoples, L. M., Donaldson, S., Osuntokun, O., Xia, Q., Nelson, A., Blanton, J., Allen, E. E., Church, M. J., & Bartlett, D. H. (2018). Vertically distinct microbial communities in the Mariana and Kermadec trenches. PLOS ONE, 13(4). https://doi.org/10.1371/journal.pone.0195102
Plominsky, A. M., Trefault, N., Podell, S., Blanton, J. M., De la Iglesia, R., Allen, E. E., von Dassow, P., & 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. https://doi.org/10.1111/1462-2920.14109
Allemann, M. N., & Allen, E. E. (2018). Characterization and Application of Marine Microbial Omega-3 Polyunsaturated Fatty Acid Synthesis. In B. S. Moore (Ed.), Methods in Enzymology (Vol. 605, pp. 3–32). Academic Press.
Agarwal, V., Blanton, J. M., Podell, S., Taton, A., Schorn, M. A., Busch, J., Lin, Z., Schmidt, E. W., Jensen, P. R., Paul, V. J., Biggs, J. S., Golden, J. W., Allen, E. E., & Moore, B. S. (2017). Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges. Nat Chem Biol, advance online publication. https://doi.org/10.1038/nchembio.2330
Leao, T., Castelao, G., Korobeynikov, A., Monroe, E. A., Podell, S., Glukhov, E., Allen, E. E., Gerwick, W. H., & 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. https://doi.org/10.1073/pnas.1618556114
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. https://doi.org/10.3389/fmicb.2016.02167
Paerl, R. W., Bouget, F.-Y., Lozano, J.-C., Verge, V., Schatt, P., Allen, E. E., Palenik, B., & Azam, F. (2016). Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton. Isme Journal. https://doi.org/10.1038/ismej.2016.145
Traller, J. C., Cokus, S. J., Lopez, D. A., Gaidarenko, O., Smith, S. R., McCrow, J. P., Gallaher, S. D., Podell, S., Thompson, M., Cook, O., Morselli, M., Jaroszewicz, A., Allen, E. E., Allen, A. E., Merchant, S. S., Pellegrini, M., & 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. https://doi.org/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. https://doi.org/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). https://doi.org/10.1128/genomeA.00823-16
Andrade, K., Logemann, J., Heidelberg, K. B., Emerson, J. B., Comolli, L. R., Hug, L. A., Probst, A. J., Keillar, A., Thomas, B. C., Miller, C. S., Allen, E. E., Moreau, J. W., Brocks, J. J., & Banfield, J. F. (2015). Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. Isme Journal, 9(12), 2697–2711. https://doi.org/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. https://doi.org/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. https://doi.org/10.3389/fmicb.2014.00749
Plominsky, A. M., Delherbe, N., Ugalde, J. A., Allen, E. E., Blanchet, M., Ikeda, P., Santibañez, F., Hanselmann, K., Ulloa, O., De la Iglesia, R., von Dassow, P., Astorga, M., Gálvez, M. J., González, M. L., Henríquez-Castillo, C., Vaulot, D., Lopes do Santos, A., van den Engh, G., Gimpel, C., … Trefault, N. (2014). Metagenome sequencing of the microbial community of a solar saltern crystallizer pond at Cáhuil Lagoon, Chile. Genome Announcements, 2(6). https://doi.org/10.1128/genomeA.01172-14
Keeling, P. J., Burki, F., Wilcox, H. M., Allam, B., Allen, E. E., Amaral-Zettler, L. A., Armbrust, E. V., Archibald, J. M., Bharti, A. K., Bell, C. J., Beszteri, B., Bidle, K. D., Cameron, C. T., Campbell, L., Caron, D. A., Cattolico, R. A., Collier, J. L., Coyne, K., Davy, S. K., … 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. https://doi.org/10.1371/journal.pbio.1001889
Agarwal, V., El Gamal, A. A., Yamanaka, K., Poth, D., Kersten, R. D., Schorn, M., Allen, E. E., & Moore, B. S. (2014). Biosynthesis of polybrominated aromatic organic compounds by marine bacteria. Nat Chem Biol, 10(8), 640–647. https://doi.org/10.1038/nchembio.1564
Coates, R. C., Podell, S., Korobeynikov, A., Lapidus, A., Pevzner, P., Sherman, D. H., Allen, E. E., Gerwick, L., & Gerwick, W. H. (2014). Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways. PLOS ONE, 9(1), e85140. https://doi.org/10.1371/journal.pone.0085140
Podell, S., Emerson, J. B., Jones, C. M., Ugalde, J. A., Welch, S., Heidelberg, K. B., Banfield, J. F., & Allen, E. E. (2013). Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. Isme Journal. https://doi.org/10.1038/ismej.2013.221
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). https://doi.org/10.1128/genomeA.01001-13
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. https://doi.org/10.1128/aem.02367-13