Publications

2026

Ochsenkühn MA, Mohamed AR, Coe LSY, Fei C, Littman S, Tienken D, Seymour JR, Raina J-B, Amin SA. Vitamin B6 catabolites act as interkingdom signals within the marine microbiome. bioRxiv. 2026 Jan 20;2026.01.20.700305. doi: 10.64898/2026.01.20.700305.

Rahiman N, Ochsenkühn MA, Amin SA, Gunsalus KC. MIMI: Molecular Isotope Mass Identifier for stable isotope-labeled Fourier transform ultra-high mass resolution data analysis. BMC Bioinformatics. 2026 Jan 28;27(1):41. doi: 10.1186/s12859-025-06348-1.

2025

Roberts WR, Parks M, Ashner M, Ashworth MP, Denne N, Ruck EC, Spiliotopoulos E, Wang A, Amin SA, Schaack S, Wickett NJ, Alverson AJ. Reference genome for the benthic marine diatom Psammoneis japonica: Bacterial associations and repeat-driven genome size evolution in diatoms. J Phycol. 2025 Dec;61(6):1556-1565. doi: 10.1111/jpy.70101.

Abdelrazig S, McCabe Á, Yasin A, Chaudhary R, Ochsenkühn MA, Scicchitano D, Amin SA. LC-MS Orbitrap-based metabolomics using a novel hybrid zwitterionic hydrophilic interaction liquid chromatography and rigorous metabolite identification reveals doxorubicin-induced metabolic perturbations in breast cancer cells. RSC Adv. 2025 Jun 19;15(26):20745-20759. doi: 10.1039/d5ra01044f.

Mohamed, A.R., Amin, S.A., Voolstra, C.R., Cárdenas, A. (2025). Complexity of the Coral Microbiome Assembly. In: Peixoto, R.S., Voolstra, C.R. (eds) Coral Reef Microbiome. Coral Reefs of the World, vol 20. Springer, Cham. doi: 10.1007/978-3-031-76692-3_8

Brunet, M., Amin, S.A., Bodachivskyi, I. et al. An atlas of metabolites driving chemotaxis in prokaryotes. Nat Commun 16, 1242 (2025). doi: 10.1038/s41467-025-56410-y

Cong Fei, Anne Booker, Sarah Klass, Nayani K Vidyarathna, So Hyun Ahn, Amin R Mohamed, Muhammad Arshad, Patricia M Glibert, Cynthia A Heil, Joaquín Martínez Martínez, Shady A Amin, Friends and foes: symbiotic and algicidal bacterial influence on Karenia brevis blooms, ISME Communications, Volume 5, Issue 1, January 2025, ycae164, doi: 10.1093/ismeco/ycae164

Al Kaabi M, ElNaker NA, Jan N, Ochsenkühn MA, Amin SA, Yousef LF, et al. (2025) Extraction efficiency and bioactive evaluation of Tamarix nilotica and Arthrocnemum macrostachyum extracts for anti-cancer potential. PLoS ONE 20(1): e0311567. doi: 10.1371/journal.pone.0311567

2024

Peixoto, A. et al., Voolstra, C.R., Stein, L.Y. et al. Microbial solutions must be deployed against climate catastrophe. Nat Microbiol 9, 3084–3085 (2024).

https://doi.org/10.1038/s41467-024-53680-w

https://doi.org/10.1128/msystems.01416-24

https://doi.org/10.1093/ismejo/wrae219

https://doi.org/10.1093/femsec/fiae144

https://doi.org/10.1038/s44185-024-00066-2

https://doi.org/10.1038/s41579-024-01123-0

https://doi.org/10.1038/s43247-024-01817-6

https://doi.org/10.1038/s42003-024-07108-2

https://doi.org/10.1093/sumbio/qvae029

https://doi.org/10.1038/s44264-024-00033-1

Mystikou, A. et al. Rediscovery of the rare Cladochroa chnoosporiformis Skottsberg from the Falkland Islands and its merger with Utriculidium durvillei Skottsberg. Bot. Mar. 0, (2024). doi: 10.1515/bot-2023-0044

Isaac, A., Mohamed, A. R. & Amin, S. A. Rhodobacteraceae are key players in microbiome assembly of the diatom Asterionellopsis glacialis. Appl. Environ. Microbiol. 90, e00570-24 (2024). doi: 10.1128/aem.00570-24

C.R. Voolstra, J.B. Raina, M. Dörr, A. Cárdenas, C. Pogoreutz, C.B. Silveira, A.R. Mohamed, D.G. Bourne, H. Luo, S.A. Amin, R.S. Peixoto (2024). The coral microbiome in sickness, in health and in a changing world. Nature Rev. Microbiol., doi: 10.1038/s41579-024-01015-3

A.A. Shibl, M.A. Ochenkühn, A.R. Mohamed, L. Coe, Y. Yun, S.A. Amin (2024). Molecular mechanisms of microbiome modulation by the eukaryotic secondary metabolite azelaic acid. eLife, doi: 10.7554/eLife.88525

2023

Ochsenkühn, M. & Mohamed AR et al. 2023. Endozoicomonas provides corals with steroid hormones during thermal stress. doi: 10.1101/2023.09.19.558257

Coe, L. S. Y., Fei, C., Weston, J., & Amin, S. A. (2023). Phycobacter azelaicus gen. nov. sp. nov., a diatom symbiont isolated from the phycosphere of Asterionellopsis glacialis. International Journal of Systematic and Evolutionary Microbiology, 73, 006104. doi: 10.1099/ijsem.0.006104

T. Venit, O. Sapkota, W.S. Abdrabou, P. Loganathan, R. Parischa, S.R. Mahmood, N.H. El Said, S. Sherif, S. Thomas, S. Abdelrazig, S.A. Amin, D. Bedognetti, Y. Idaghdour, M. Magzoub, P. Percipalle (2023). Positive regulation of oxidative phosphorylation by nuclear myosin 1 protects cells from metabolic reprogramming and tumorigenesis in mice. Nature Commun., 14, 6328.

H. Mahmoud, W. Ismail, R.M.M. Abed, S.A. Amin (2023). Editorial: Microbial ecology of the Arabian/Persian Gulf. Front. Mar. Sci. 10, 1216257.

A.R. Amin, M.A. Ochsenkühn, A.M. Kazlak, A. Moustafa, S.A. Amin (2023). The coral microbiome: Towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol. Rev. 47, fuad005.

Chen, X. H., Yang, M. K., Li, Y. Y., Xie, Z. X., Zhang, S. F., Töpel, M., Amin, S. A., Lin, L., Ge, F., & Wang, D. Z. (2023). Improving the genome and proteome annotations of the marine model diatom Thalassiosira pseudonana. Marine Life Science & Technology, 5, 102–115.

2022

Allegue, T., Rafay, R., Chandran, S., Amin, S.A., Fowler, S.J., Rodriguez, J. (2022). Lactate addition boosts valerate yields in granular mixed culture carbohydrate fermentation. Journal of Environmental Chemical Engineering, 10, 108869.doi: 10.1016/j.jece.2022.108869

Helliwell, K.E., Shibl, A.A., Amin, S.A. (2022). The diatom microbiome: New perspectives for diatom-bacteria symbioses. In: Falciatore, A., Mock, T. (eds), The Molecular Life of Diatoms. Springer Nature Switzerland.doi: 10.1007/978-3-030-92499-7_10

Moran, M.A., Kujawinski, E.B., Schroer, W.F., Amin, S.A., et al. (2022). Microbial metabolites in the marine carbon cycle. Nature Microbiology, 7, 508–523. doi: 10.1038/s41564-022-01090-2

Daou, M., ElNaker, N.A., Ochsenkühn, M.A., Amin, S.A., Yousef, A.F., Yousef, L.F. (2022). In vitro α-glucosidase inhibitory activity of Tamarix nilotica shoot extracts and fractions. PLoS ONE, 17, e0264969.doi: 10.1371/journal.pone.0264969

2021

Isaac, A., Francis, B., Amann, R.I., Amin, S.A. (2021). Tight adherence (Tad) pilus genes indicate putative niche differentiation in phytoplankton bloom-associated Rhodobacterales. Frontiers in Microbiology, 12, 718297.doi: 10.3389/fmicb.2021.718297

Zhang, H., Xu, H., Zhang, S., Zhou, Y., He, Y., Amin, S.A., Chen, J., Yan, K., Lin, L., Liu, S., Wang, D. (2021). Metaproteomics reveals the molecular mechanism underlying bloom maintenance of a marine dinoflagellate under low ambient CO2 and inorganic nutrients. Science of the Total Environment, 768, 144515.doi: 10.1016/j.scitotenv.2020.144515

ElNaker, N.A., Daou, M., Ochsenkühn, M.A., Amin, S.A., Yousef, A.F., Yousef, L.F. (2021). A metabolomics approach to evaluate the effect of lyophilization versus oven drying on the chemical composition of plant extracts. Scientific Reports, 11, 1–11. doi: 10.1038/s41598-021-87806-5

Ochsenkühn, M.A., Fei, C., Bayaara, O., Romeo, E., Amosa, P., Idaghdour, Y., Goldstein, G., Bromage, T.G., Amin, S.A. (2021). Microbial contamination survey of environmental fresh and saltwater resources of Upolu Island, Samoa. Environments, 8, 112.doi: 10.3390/environments8110112

2020

Shibl, A.A., Isaac, A., Ochsenkühn, M.A., Cardenas, A., Fei, C., Behringer, G., Arnoux, M., Drou, N., Santos, M.P., Gunsalus, K.C., Voolstra, C.R., Amin, S.A. (2020). Diatom modulation of select bacteria through use of two unique secondary metabolites. Proceedings of the National Academy of Sciences USA, 117, 27445–27455. doi: 10.1073/pnas.2012088117

C. Fei, M.A. Ochsenkühn, A.A. Shibl, S.A. Amin (2020). Quorum sensing regulates ‘swim-or-stick’ lifestyle in the phycosphere. Environ. Microbiol. 22, 4761-4778.

W. Qin, Y. Zheng, F. Zhao, Y. Wang, H. Urakawa, W. Martens-Habbena, H. Liu, X. Huang, X. Zhang, T. Nakagawa, D.R. Mende, A. Bollmann, B. Wang, Y. Zhang, S.A. Amin, J.L. Nielsen, K. Mori, R. Takahashi, E.V. Armbrust, M. Winkler, E.F. DeLong, M. Li, P. Lee, J. Zhou, C. Zhang, T. Zhang, D.A. Stahl, A.E. Ingalls (2020). Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia oxidizing-archaea. ISME J. 14, 2595-2609.

Rabieh, S., Bayaraa, O., Romeo, E., Amosa, P., Calnek, K., Idaghdour, Y., Ochsenkühn, M.A., Amin, S.A., Goldstein, G., Bromage, T.G. (2020).MH-ICP-MS analysis of the freshwater and saltwater environmental resources of Upolu Island, Samoa.Molecules, 25, 4871. doi: 10.3390/molecules25204871

Fei, C., Zou, S., Wang, T., Wang, C., Kemuma, N.D., He, M., Amin, S.A., Wang, C. (2020).A quick method for obtaining high-quality DNA barcodes without DNA extraction in microalgae.Journal of Applied Phycology, 32, 1165–1175. doi: 10.1007/s10811-019-01931-2

2019

Solntsev, K.M., Schramm, S., Kremb, S., Gunsalus, K.C., Amin, S.A. (2019).Isolation of biologically active compounds from mangrove sediments. Analytical and Bioanalytical Chemistry, 411, 6521–6529. doi: 10.1007/s00216-019-02032-5

2018

Ochsenkühn, M.A., Harir, M., Schmitt-Kopplin, P., Amin, S.A. (2018).Coral metabolite gradients affect microbial community structures and act as a disease cue.Communications Biology, 1, 184. doi: 10.1038/s42003-018-0189-1

Qin, W., Amin, S.A., Lundeen, R.A., Heal, K.R., Martens-Habbena, W., Turkarslan, S., Urakawa, H., Costa, K.C., Hendrickson, E.L., Wang, T., Beck, D.A.C., Tequia-Arashiro, S.M., Taub, F., Holmes, A.D., Vajrala, N., Berube, P.M., Lowe, T.M., Moffett, J.W., Devol, A.H., Baliga, N.S., Arp, D.J., Sayavedra-Soto, L.A., Hackett, M., Armbrust, E.V., Ingalls, A.E., Stahl, D.A. (2018).Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations.The ISME Journal, 12, 508–519.doi: 10.1038/ismej.2017.173

Heal, K.R., Qin, W., Amin, S.A., Devol, A.H., Moffett, J.W., Armbrust, E.V., Stahl, D.A., Ingalls, A.E. (2018).Accumulation of NO2-cobalamin in nutrient-stressed ammonia-oxidizing archaea and in the oxygen deficient zone of the eastern tropical North Pacific. Environmental Microbiology Reports, 10, 453–457. doi: 10.1111/1758-2229.12660

Al Jitan, S., AlKhoori, S., Ochsenkühn, M.A., Amin, S.A., Yousef, L.F. (2018).Ethanol/water extracts from halophyte species Arthrocnemum macrostachyum and Tetraena qatarensis.Cogent Chemistry, 4, 1536311. doi: 10.1080/23312009.2018.1536311

2017

Seymour, J., Amin, S.A., Raina, J.B., Stocker, R. (2017).Zooming in on the phycosphere: The ecological interface for phytoplankton-bacteria relationships.Nature Microbiology, 2, 17065. doi: 10.1038/nmicrobiol.2017.65

Qin, W., Heal, K.R., Ramdasi, R., Kobelt, J.N., Martens-Habbena, W., Bertagnolli, A.D., Amin, S.A., Walker, C.B., Urakawa, H., Könneke, M., Devol, A.H., Moffett, J.W., Armbrust, E.V., Ingalls, A.E., Stahl, D.A. (2017).Nitrosopumilus maritimus nov. sp., Nitrosopumilus cobalaminogenes gen. nov., sp. nov., Nitrosopumilus oxyclinae gen. nov., sp. nov., and Nitrosopumilus ureaphilus gen. nov., sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota.International Journal of Systematic and Evolutionary Microbiology, 67, 5067–5079. doi: 10.1099/ijsem.0.002327

Durham, B.P., Dearth, S.P., Sharma, S., Amin, S.A., Smith, C.B., Campagna, S.R., Armbrust, E.V., Moran, M.A. (2017).Recognition cascade and metabolite transfer in a marine bacteria-phytoplankton model system.Environmental Microbiology, 19, 3500–3513. doi: 10.1111/1462-2920.13808

Van Tol, V.H.M., Amin, S.A., Armbrust, E.V. (2017).Ubiquitous marine bacterium inhibits diatom cell division. The ISME Journal, 11, 31–42. doi: 10.1038/ismej.2016.112

2015

Amin, S.A., Hmelo, L.R., Van Tol, H.M., Durham, B.P., Carlson, L.T., Heal, K.R., Morales, R.L., Berthiaume, C.T., Parker, M.S., Djunaedi, B., Ingalls, A.E., Parsek, M.R., Moran, M.A., Armbrust, E.V. (2015).Interactions and signaling between a cosmopolitan phytoplankton and associated bacteria.Nature, 522, 98–101. doi: 10.1038/nature14488

Durham, B.P., Sharma, S., Luo, H., Smith, C.B., Amin, S.A., Bender, S.J., Dearth, S.P., Van Mooy, B.A.S., Campagna, S.R., Kujawinski, E.B., Armbrust, E.V., Moran, M.A. (2015).Cryptic carbon and sulfur cycling between surface ocean plankton.Proceedings of the National Academy of Sciences USA, 112, 453–457. doi: 10.1073/pnas.1413137112

2014

Qin, W., Amin, S.A., Martens-Habbena, W., Walker, C.B., Urakawa, H., Devol, A.H., Ingalls, A.E., Moffett, J.W., Armbrust, E.V., Stahl, D.A. (2014).Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation.Proceedings of the National Academy of Sciences USA, 111, 12504–12509. doi: 10.1073/pnas.1324115111

Goodwin, J.T., Lynn, D.G., Burrows, C., Walker, S., Amin, S.A., Armbrust, E.V. (2014).Alternative chemistries of life: Empirical approaches. NSF and NASA Joint Workshop Report, 1–56.

Jacquot, J., Horak, R.E., Amin, S.A., Devol, A.H., Ingalls, A.E., Armbrust, E.V., Stahl, D.A., Moffett, J.W. (2014).Assessment of the potential for copper limitation of ammonia oxidation by Archaea in a dynamic estuary.Marine Chemistry, 162, 37–49. doi: 10.1016/j.marchem.2014.02.002

2013

Amin, S.A., Moffett, J.W., Martens-Habbena, W., Devol, A.H., Ingalls, A.E., Stahl, D.A., Armbrust, E.V. (2013).Copper requirements of the ammonia-oxidizing archaeon Nitrosopumilus maritimus SCM1 and implications to nitrification in the marine environment. Limnology and Oceanography, 58, 2037–2045. doi: 10.4319/lo.2013.58.6.2037

Weerasinghe, A.J., Amin, S.A., Baker, R.A., Othman, T., Romano, A.N., Siburt, C.P., Tisnado, J., Lambert, L.A., Huxford, T., Carrano, C.J., Crumbliss, A.L. (2013).Borate as a synergistic anion for Marinobacter algicola ferric binding protein, FbpA: A role for boron in iron transport in marine life. Journal of the American Chemical Society, 135, 14504–14507. doi: 10.1021/ja4074339

Romano, A.N., Trimble, L., Hobusch, A., Schroeder, K., Amin, S.A., Hartnett, A., Baker, R.A., Crumbliss, A.L., Carrano, C.J. (2013).Regulation of iron transport related genes by boron in the marine bacterium Marinobacter algicola.Metallomics, 5, 1025–1030. doi: 10.1039/c3mt00038a

Gärdes, A., Triana, C., Amin, S.A., Green, D.H., Trimble, L., Romano, A.N., Carrano, C.J. (2013).Detection of a photoactive siderophore biosynthetic gene cluster in the marine environment.BioMetals, 26, 507–516. doi: 10.1007/s10534-013-9629-6

2012

Amin, S.A., Parker, M.S., Armbrust, E.V. (2012).Interactions between diatoms and bacteria. Microbiology and Molecular Biology Reviews, 76, 667–684. doi: 10.1128/MMBR.00007-12

Amin, S.A., Green, D.H., Romano, A.N., Trimble, L., Carrano, C.J. (2012).Siderophore-mediated iron uptake in two clades of Marinobacter associated with phytoplankton: The role of light.BioMetals, 25, 181–192. doi: 10.1007/s10534-011-9501-5

Amin, S.A., Green, D.H., Hart, M.C., Küpper, F.C., Sunda, W.G., Carrano, C.J. (2009).Photolysis of iron–siderophore chelates promotes bacterial–algal mutualism. Proceedings of the National Academy of Sciences USA, 106, 17071–17076. doi: 10.1073/pnas.0905512106

2009

Amin, S.A., Green, D.H., Küpper, F.C., Carrano, C.J. (2009).Vibrioferrin, an unusual marine siderophore: Iron binding, photochemistry and biological implications.Inorganic Chemistry, 48, 11451–11458. doi: 10.1021/ic901950r

Zhang, G., Amin, S.A., Küpper, F.C., Holt, P.D., Carrano, C.J., Butler, A. (2009).Ferric stability constants of representative marine siderophores: Marinobactins, aquachelins, and petrobactin.Inorganic Chemistry, 48, 11466–11473. doi: 10.1021/ic901951d

Carrano, C.J., Schellenberg, S., Amin, S.A., Green, D.H., Küpper, F.C. (2009).Boron and marine life: A new look at an enigmatic bioelement. Marine Biotechnology, 11, 431–440. doi: 10.1007/s10126-008-9151-8

2007

Harris, W.R., Amin, S.A., Küpper, F.C., Green, D.H., Carrano, C.J. (2007).Borate binding to siderophores: Structure and stability. Journal of the American Chemical Society, 129, 12263–12271. doi: 10.1021/ja072381t

Amin, S.A., Küpper, F.C., Green, D.H., Harris, W.R., Carrano, C.J. (2007).Boron binding by a siderophore isolated from marine bacteria associated with the toxic dinoflagellate Gymnodinium catenatum. Journal of the American Chemical Society, 129, 478–479. doi: 10.1021/ja067546k