Murray, E. R., Minich, J. J., Saxton, J., De Gracia, M., Eck, N., Allsing, N., Kitony, J., Patel-Jhawar, K., Allen, E. E., Michael, T. P., & Shakoor, N. (2025). Soil depth determines the microbial communities in Sorghum bicolor fields within a uniform regional environment. Microbiology Spectrum, e02928-24. https://doi.org/10.1128/spectrum.02928-24

Neu, A. T., Torchin, M. E., Allen, E. E., & Roy, K. (2024). Microbiome divergence of marine gastropod species separated by the Isthmus of Panama. Applied and Environmental Microbiology, 90(11), e01003-24. https://doi.org/10.1128/aem.01003-24

Suárez-Moo, P., García-Martínez, N. C., Márquez-Velázquez, N. A., Figueroa, M., Allen, E., & Prieto-Davó, A. (2024). Exploring the microbial community and biotechnological potential of the sponge Xestospongia sp. from an anchialine cave in the Yucatán Peninsula. Ciencias Marinas, 50. https://doi.org/10.7773/cm.y2024.3442

Oliver, A., Podell, S., Wegley Kelly, L., Sparagon, W. J., Plominsky, A. M., Nelson, R. S., Laurens, L. M. L., Augyte, S., Sims, N. A., Nelson, C. E., & Allen, E. E. (2024). Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish. MBio, e00496-24. https://doi.org/10.1128/mbio.00496-24

Podell, S., Oliver, A., Kelly, L. W., Sparagon, W. J., Plominsky, A. M., Nelson, R. S., Laurens, L. M. L., Augyte, S., Sims, N. A., Nelson, C. E., & Allen, E. E. (2023). Herbivorous Fish Microbiome Adaptations to Sulfated Dietary Polysaccharides. Applied and Environmental Microbiology, 89(5), e02154-22. https://doi.org/10.1128/aem.02154-22

Wilson, K., De Rond, T., Burkhardt, I., Steele, T. S., Schäfer, R. J. B., Podell, S., Allen, E. E., & Moore, B. S. (2023). Terpene biosynthesis in marine sponge animals. Proceedings of the National Academy of Sciences, 120(9), e2220934120. https://doi.org/10.1073/pnas.2220934120

Minich, J. J., Härer, A., Vechinski, J., Frable, B. W., Skelton, Z. R., Kunselman, E., Shane, M. A., Perry, D. S., Gonzalez, A., McDonald, D., Knight, R., Michael, T. P., & Allen, E. E. (2022). Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species. Nature Communications, 13(1), 6978. https://doi.org/10.1038/s41467-022-34557-2

Oliver, A., Cavalheri, H. B., Lima, T. G., Jones, N. T., Podell, S., Zarate, D., Allen, E., Burton, R. S., & Shurin, J. B. (2022). Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation. PLOS ONE, 17(7), e0265103. https://doi.org/10.1371/journal.pone.0265103

Kunselman, E., Minich, J. J., Horwith, M., Gilbert, J. A., & Allen, E. E. (2022). Variation in Survival and Gut Microbiome Composition of Hatchery-Grown Native Oysters at Various Locations within the Puget Sound. Microbiology Spectrum, e01982-21. https://doi.org/10.1128/spectrum.01982-21

Blanton, J. M., Peoples, L. M., Gerringer, M. E., Iacuaniello, C. M., Gallo, N. D., Linley, T. D., Jamieson, A. J., Drazen, J. C., Bartlett, D. H., & Allen, E. E. (2022). Microbiomes of Hadal Fishes across Trench Habitats Contain Similar Taxa and Known Piezophiles. MSphere, 7(2), e00032-22. https://doi.org/10.1128/msphere.00032-22

Sparagon, W. J., Gentry, E. C., Minich, J. J., Vollbrecht, L., Laurens, L. M. L., Allen, E. E., Sims, N. A., Dorrestein, P. C., Kelly, L. W., & Nelson, C. E. (2022). Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes. Animal Microbiome, 4(1), 33. https://doi.org/10.1186/s42523-022-00182-z

Klau, L. J., Podell, S., Creamer, K. E., Demko, A. M., Singh, H. W., Allen, E. E., Moore, B. S., Ziemert, N., Letzel, A. C., & Jensen, P. R. (2022). The Natural Product Domain Seeker version 2 (NaPDoS2) webtool relates ketosynthase phylogeny to biosynthetic function. Journal of Biological Chemistry, 298(10), 102480. https://doi.org/10.1016/j.jbc.2022.102480

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

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

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

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

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

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

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

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

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

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

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.

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

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

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