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Publications

2025

  • Pengfan Zhang, Breanna Roque, Pedro Romero, Nicole Shapiro, Emiley Eloe-Fadrosh, Ermias Kebreab, Spencer Diamond & Matthias Hess Diamond, S. (2025).Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteriaMicrobiome(https://link.springer.com/article/10.1186/s40168-025-02251-2)
  • Kust, A., Zorz, J., Cruañas Paniker, C., Bouma-Gregson, K., Krishnappa, N., Liu, W., Banfield, J. F., & Diamond, S. (2025).Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species.The ISME Journal, wraf142.(https://doi.org/10.1093/ismejo/wraf142)
  • Hessler, T., Chiniquy, D., Adler, B. A., Hoff, J., Tucker, E., Huddy, R., Sachdeva, R., Diamond, S., & Banfield, J. F. (2025).Phage-based microbiome manipulation elucidates interactions within community context.bioRxiv.(https://doi.org/10.1101/2025.06.20.660599)

2024

  • Zhang, P., Roque, B., Romero, P., Shapiro, N., Eloe-Fadrosh, E., Kebreab, E., Diamond, S., & Hess, M. (2024).Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria.bioRxiv.(https://doi.org/10.1101/2024.06.07.597961)
  • Kakouridis, A., Diamond, S., Eng, T., Mills, H. J., Gámez Holzhaus, O., Summers, M. L., Garcia-Pichel, F., & Mukhopadhyay, A. (2024).Desiccated Cyanobacteria Serve As Efficient Plasmid DNA Carriers in Space Flight.ACS synthetic biology, 13(9), 2733–2741.(https://doi.org/10.1021/acssynbio.3c00672)
  • Amano, Y., Sachdeva, R., Gittins, D., Anantharaman, K., Lei, S., Valentin-Alvarado, L. E., Diamond, S., Beppu, H., Iwatsuki, T., Mochizuki, A., Miyakawa, K., Ishii, E., Murakami, H., Jaffe, A. L., Castelle, C., Lavy, A., Suzuki, Y., & Banfield, J. F. (2024).Characterization of sediment and granite hosted deep underground research laboratories reveals diverse microbiome functions, limited temporal variation and substantial genomic conservation.bioRxiv.
    (https://doi.org/10.1101/2024.03.28.587102)

2023

  • Hessler, T., Huddy, R. J., Sachdeva, R., Lei, S., Harrison, S. T. L., Diamond, S., & Banfield, J. F. (2023).
    Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms.Nature communications, 14(1), 4768.
    (https://doi.org/10.1038/s41467-023-40360-4)
  • Acharya, S. M., Yee, M. O., Diamond, S., Andeer, P. F., Baig, N. F., Aladesanmi, O. T., Northen, T. R., Banfield, J. F., & Chakraborty, R. (2023).
    Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots.ISME communications, 3(1), 54.
    (https://doi.org/10.1038/s43705-023-00265-1)
  • Lou, Y. C., Hoff, J., Olm, M. R., West-Roberts, J., Diamond, S., Firek, B. A., Morowitz, M. J., & Banfield, J. F. (2023).
    Using strain-resolved analysis to identify contamination in metagenomics data.Microbiome, 11(1), 36.
    (https://doi.org/10.1186/s40168-023-01477-2)
  • Kust, A., Zorz, J., Cruañas Paniker, C., Bouma-Gregson, K., Krishnappa, N., Banfield, J. F., & Diamond, S. (2023).
    Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species.bioRxiv.
    (https://doi.org/10.1101/2023.12.09.570939)

2022

  • Crits-Christoph, A., Diamond, S., Al-Shayeb, B., Valentin-Alvarado, L., & Banfield, J. F. (2022).
    A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters.ISME communications, 2(1), 70.
    (https://doi.org/10.1038/s43705-022-00140-5)
  • Diamond, S., Lavy, A., Crits-Christoph, A., Matheus Carnevali, P. B., Sharrar, A., Williams, K. H., & Banfield, J. F. (2022).
    Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs).The ISME journal, 16(5), 1348–1362.
    (https://doi.org/10.1038/s41396-021-01177-5)

2021

  • Rubin, B. E., Diamond, S.(1), Cress, B. F., Crits-Christoph, A., Lou, Y. C., Borges, A. L., Shivram, H., He, C., Xu, M., Zhou, Z., Smith, S. J., Rovinsky, R., Smock, D. C. J., Tang, K., Owens, T. K., Krishnappa, N., Sachdeva, R., Barrangou, R., Deutschbauer, A. M., Banfield, J. F., … Doudna, J. A. (2022).
    Species- and site-specific genome editing in complex bacterial communities.Nature microbiology, 7(1), 34–47.
    (https://doi.org/10.1038/s41564-021-01014-7)
  • Matheus Carnevali, P. B., Lavy, A., Thomas, A. D., Crits-Christoph, A., Diamond, S., Méheust, R., Olm, M. R., Sharrar, A., Lei, S., Dong, W., Falco, N., Bouskill, N., Newcomer, M. E., Nico, P., Wainwright, H., Dwivedi, D., Williams, K. H., Hubbard, S., & Banfield, J. F. (2021).
    Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale.Microbiome, 9(1), 121.
    (https://doi.org/10.1186/s40168-020-00957-z)
  • Lou, Y. C., Olm, M. R., Diamond, S., Crits-Christoph, A., Firek, B. A., Baker, R., Morowitz, M. J., & Banfield, J. F. (2021).
    Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition.Medicine, 2(9), 100393.(https://doi.org/10.1016/j.xcrm.2021.100393)
  • Xu, L., Dong, Z., Chiniquy, D., Pierroz, G., Deng, S., Gao, C., Diamond, S., Simmons, T., Wipf, H. M., Caddell, D., Varoquaux, N., Madera, M. A., Hutmacher, R., Deutschbauer, A., Dahlberg, J. A., Guerinot, M. L., Purdom, E., Banfield, J. F., Taylor, J. W., Lemaux, P. G., … Coleman-Derr, D. (2021).
    Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics.Nature communications, 12(1), 3209.
    (https://doi.org/10.1038/s41467-021-23553-7)

2020

  • Xu, L., Dong, Z., Chiniquy, D., Pierroz, G., Deng, S., Gao, C., Diamond, S., Simmons, T., Wipf, H. M., Caddell, D., Varoquaux, N., Madera, M. A., Hutmacher, R., Deutschbauer, A., Dahlberg, J. A., Guerinot, M. L., Purdom, E., Banfield, J. F., Taylor, J. W., Lemaux, P. G., … Coleman-Derr, D. (2021).
    Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics.Nature communications, 12(1), 3209.
    (https://doi.org/10.1038/s41467-021-23553-7)
  • Sharrar, A. M., Crits-Christoph, A., Méheust, R., Diamond, S., Starr, E. P., & Banfield, J. F. (2020).
    Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type.mBio, 11(3), e00416-20.
    (https://doi.org/10.1128/mBio.00416-20)
  • Olm, M. R., Crits-Christoph, A., Diamond, S., Lavy, A., Matheus Carnevali, P. B., & Banfield, J. F. (2020).
    Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries.mSystems, 5(1), e00731-19.
    (https://doi.org/10.1128/mSystems.00731-19)

2019

  • Desmarais, J. J., Flamholz, A. I., Blikstad, C., Dugan, E. J., Laughlin, T. G., Oltrogge, L. M., Chen, A. W., Wetmore, K., Diamond, S., Wang, J. Y., & Savage, D. F. (2019).
    DABs are inorganic carbon pumps found throughout prokaryotic phyla.Nature microbiology, 4(12), 2204–2215.
    (https://doi.org/10.1038/s41564-019-0520-8)
  • Diamond, S., Andeer, P. F., Li, Z., Crits-Christoph, A., Burstein, D., Anantharaman, K., Lane, K. R., Thomas, B. C., Pan, C., Northen, T. R., & Banfield, J. F. (2019).
    Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms.Nature microbiology, 4(8), 1356–1367.
    (https://doi.org/10.1038/s41564-019-0449-y)
  • Welkie, D. G., Rubin, B. E., Diamond, S., Hood, R. D., Savage, D. F., & Golden, S. S. (2019).
    A Hard Day's Night: Cyanobacteria in Diel Cycles.Trends in microbiology, 27(3), 231–242.
    (https://doi.org/10.1016/j.tim.2018.11.002)

2018

  • Welkie, D. G., Rubin, B. E., Chang, Y. G., Diamond, S., Rifkin, S. A., LiWang, A., & Golden, S. S. (2018).
    Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA.Proceedings of the National Academy of Sciences of the United States of America, 115(30), E7174–E7183.
    (https://doi.org/10.1073/pnas.1802940115)
  • Crits-Christoph, A., Diamond, S., Butterfield, C. N., Thomas, B. C., & Banfield, J. F. (2018).
    Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis.Nature, 558(7710), 440–444.
    (https://doi.org/10.1038/s41586-018-0207-y)
  • Rubin, B. E., Huynh, T. N., Welkie, D. G., Diamond, S., Simkovsky, R., Pierce, E. C., Taton, A., Lowe, L. C., Lee, J. J., Rifkin, S. A., Woodward, J. J., & Golden, S. S. (2018).
    High-throughput interaction screens illuminate the role of c-di-AMP in cyanobacterial nighttime survival.PLoS genetics, 14(4), e1007301.
    (https://doi.org/10.1371/journal.pgen.1007301)
  • Kim, Y. S., Kim, J. J., Park, S. I., Diamond, S., Boyd, J. S., Taton, A., Kim, I. S., Golden, J. W., & Yoon, H. S. (2018).
    Expression of OsTPX Gene Improves Cellular Redox Homeostasis and Photosynthesis Efficiency in Synechococcus elongatus PCC 7942.Frontiers in plant science, 9, 1848.
    (https://doi.org/10.3389/fpls.2018.01848)