John Heidelberg

Summary Statement of Research Interests

Dr. John Heidelberg’s research interests are the field of microbial genomics. Specifically, he is studying the metabolic potential of the common and abundant marine bacteria by sequencing these organisms’ DNA. Because we are unable to bring the vast majority of bacteria into a pure culture, we are unable to use more common microbiological techniques to study these uncultured bacteria. Therefore, Dr. Heidelberg employs on of the newest DNA sequencers to look at the genomes of these bacteria without the need of first growing the bacteria in pure culture.

Journal Article

• Tully, B. J., Graham, E. D., Heidelberg, J. F. (2018). The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. SCIENTIFIC DATA. Vol. 5
• Tully, B. J., Sachdeva, R., Graham, E. D., Heidelberg, J. F. (2017). 290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology. PEERJ. Vol. 5
• Graham, E. D., Heidelberg, J. F., Tully, B. J. (2017). BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation. PEERJ. Vol. 5
• Tully, B. J., Heidelberg, J. F. (2016). Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. Vol. 82 (14), pp. 4232-4243.
• Tully, B. J., Heidelberg, J. F. (2013). Microbial communities associated with ferromanganese nodules and the surrounding sediments. FRONTIERS IN MICROBIOLOGY. Vol. 4
• Singer, E., Heidelberg, J. F., Dhillon, A., Edwards, K. J. (2013). Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lo’ihi, Hawai’l. FRONTIERS IN MICROBIOLOGY. Vol. 4
• Tully, B. J., Nelson, W. C., Heidelberg, J. F. (2012). Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine. Environmentl Microbiology. Vol. 14 (1), pp. 254-67. PubMed Web Address
• Biddle, J. F., Sylvan, J. B., Brazelton, W. J., Tully, B. J., Edwards, K. J., Moyer, C. L., Heidelberg, J. F., Nelson, W. C. (2012). Prospects for the study of evolution in the deep biosphere. Frontiers in Extreme Microbiology.
• Nelson, W. C., Bhaya, D., Heidelberg, J. F. (2012). Novel Miniature Transposable Elements in Thermophilic Synechococcus Strains and Their Impact on an Environmental Population. JOURNAL OF BACTERIOLOGY. Vol. 194 (14), pp. 3636-3642.
• Singer, E., Emerson, D., Webb, E. A., Barco, R. A., Kuenen, J. G., Nelson, W. C., Chan, C. S., Comolli, L. R., Ferriera, S., Johnson, J., Heidelberg, J. F., Edwards, K. J. (2011). Mariprofundus ferrooxydans PV-1 the first genome of a marine Fe(II) oxidizing Zetaproteobacterium. PLOS One. Vol. 6, pp. e25386. PubMed Web Address
• Campbell, B. J., Yu, L., Heidelberg, J. F., Kirchman, D. L. (2011). Activity of abundant and rare bacteria in a coastal ocean. Proc Natl Acad Sci U S A. Vol. 108, pp. 12776-81. PubMed Web Address
• Nelson, W. C., Wollerman, L., Bhaya, D., Heidelberg, J. F. (2011). Analysis of insertion sequences in thermophilic cyanobacteria: exploring the mechanisms of establishing, maintaining, and withstanding high insertion sequence abundance. Appl Environ Microbiol. Vol. 77, pp. 5458-66. PubMed Web Address
• Klatt, C. G., Wood, J. M., Rusch, D. B., Bateson, M. M., Hamamura, N., Heidelberg, J. F., Grossman, A. R., Bhaya, D., Cohan, F. M., Kühl, M., Bryant, D. A., Ward, D. M. (2011). Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. The ISME Journal. Vol. 5, pp. 1262–1278.
• Singer, E., Webb, E. A., Nelson, W. C., Heidelberg, J. F., Ivanova, N., Pati, A., Edwards, K. J. (2011). Genomic potential of Marinobacter aquaeolei, a biogeochemical “opportunitroph”. Appl Environ Microbio. Vol. 77, pp. 2763-71. PubMed Web Address
• Singer, E., Webb, A., Barco, A., Kuenen, J. G., Nelson, C., Comolli, R., Ferriera, S., Chan, S., Johnson, J., Heidelberg, F., Edwards, J., Emerson, D. (2011). Figure_S3.tif. Figshare.
• Singer, E., Webb, A., Barco, A., Kuenen, J. G., Nelson, C., Comolli, R., Ferriera, S., Chan, S., Johnson, J., Heidelberg, F., Edwards, J., Emerson, D. (2011). Figure_S2.tif. Figshare.
• Singer, E., Webb, A., Barco, A., Kuenen, J. G., Nelson, C., Comolli, R., Ferriera, S., Chan, S., Johnson, J., Heidelberg, F., Edwards, J., Emerson, D. (2011). Figure_S1.tif. Figshare.
• Tully, B. J., Nelson, W. C., Heidelberg, J. F.Metagenomic reconstruction of planktonic Archaea from Gulf of Maine surface waters. Vol. In Preparation
• Singer, E., Webb, E. A., Nelson, W. C., Heidelberg, J. F., Ivanova, N., Pati, A., Edwards, K. J.The genomic potential of Marinobacter aquaeolei – A biogeochemical opportunitroph. Applied and Environmental Microbiology. Vol. In Preparation
• Reysenbach, A., Hamamura, N., Podar, M., Griffiths, E., Ferreira, S., Hochstein, R., Heidelberg, J. F., Johnson, J., Mead, D., Pohorille, A., Sarmiento, M., Schweighofer, K., Seshadri, R., Voytek, M. A. (2009). Complete and Draft Genome Sequences of Six Members of the Aquificales. JOURNAL OF BACTERIOLOGY. Vol. 191, pp. 1992-1993.
• Heidelberg, J. F., Nelson, W., Schoenfeld, T., Bhaya, D. (2009). Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes. PLoSONE.
• Heidelberg, F., Schoenfeld, T., Nelson, C., Bhaya, D. (2009). Table_S5.doc. Figshare.
• Heidelberg, F., Schoenfeld, T., Nelson, C., Bhaya, D. (2009). Table_S4.xls. Figshare.
• Heidelberg, J. F., Schoenfeld, T., Nelson, C., Bhaya, D. (2009). CRISPR repeats in Synechococcus OS-A and OS-B’. Figshare.
• Heidelberg, J. F., Schoenfeld, T., Nelson, C., Bhaya, D. (2009). Virome sequences showing silent or conservative changes relative to the viritope Cluster_2_YMBCR81TF-SP-2 sequence. Figshare.
• Heidelberg, J. F., Schoenfeld, T., Nelson, C., Bhaya, D. (2009). CRISPR viritopes with similarity to virome sequences. Figshare.
• Kowalchuk, G. A., Heidelberg, J. F., Bailey, M. J. (2007). The ISME journal: Multidisciplinary journal of microbial ecology. ISME JOURNAL. Vol. 1 (1), pp. 1-3.
• Faruque, S. M., Tam, V. C., Chowdhury, N., Diraphat, P., Dziejman, M., Heidelberg, J. F., Clemens, J. D., Mekalanos, J. J., Nair, G. B. (2007). Genomic analysis of the Mozambique strain of Vibrio cholerae O1 reveals the oriqin of El Tor strains carrying classical CTX prophage. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. Vol. 104 (12), pp. 5151-5156.
• Seshadri, R., Joseph, S. W., Chopra, A. K., Sha, J., Shaw, J., Graf, J., Haft, D., Wu, M., Ren, Q., Rosovitz, M. J., Madupu, R., Tallon, L., Kim, M., Jin, S., Vuong, H., Stine, O. C., Ali, A., Horneman, A. J., Heidelberg, J. F. (2006). Genome sequence of Aeromonas hydrophila ATCC 7966(T): Jack of all trades. JOURNAL OF BACTERIOLOGY. Vol. 188 (23), pp. 8272-8282.
• Palenik, B., Ren, Q., Dupont, C. L., Myers, G. S., Heidelberg, J. F., Badger, J. H., Madupu, R., Nelson, W. C., Brinkac, L. M., Dodson, R. J., Durkin, A. S., Daugherty, S. C., Sullivan, S. A., Khouri, H., Mohamoud, Y., Halpin, R., Paulsen, I. T. (2006). Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. Vol. 103 (36), pp. 13555-13559.
• Pukatzki, S., Ma, A. T., Sturtevant, D., Krastins, B., Sarracino, D., Nelson, W. C., Heidelberg, J. F., Mekalanos, J. J. (2006). Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. Vol. 103 (5), pp. 1528-1533.
• Dziejman, M., Serruto, D., Tam, V. C., Sturtevant, D., Diraphat, P., Faruque, S. M., Rahman, M. H., Heidelberg, J. F., Decker, J., Li, L., Montgomery, K. T., Grills, G., Kucherlapati, R., Mekalanos, J. J. (2005). Genomic characterization of non-O1, non-O139 Vibrio cholerae reveals genes for a type III secretion system. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. Vol. 102 (9), pp. 3465-3470.
• Seshadri, R., Adrian, L., Fouts, D. E., Eisen, J. A., Phillippy, A. M., Methe, B. A., Ward, N. L., Nelson, W. C., Deboy, R. T., Khouri, H. M., Kolonay, J. F., Dodson, R. J., Daugherty, S. C., Brinkac, L. M., Sullivan, S. A., Madupu, R., Nelson, K. T., Kang, K. H., Impraim, M., Tran, K., Robinson, J. M., Forberger, H. A., Fraser, C. M., Zinder, S. H., Heidelberg, J. F. (2005). Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. SCIENCE. Vol. 307 (5706), pp. 105-108.
• Heidelberg, J. F., Seshadri, R., Haveman, S. A., Hemme, C. L., Paulsen, I. T., Kolonay, J. F., Eisen, J. A., Ward, N., Methe, B., Brinkac, L. M., Daugherty, S. C., Deboy, R. T., Dodson, R. J., Durkin, A. S., Madupu, R., Nelson, W. C., Sullivan, S. A., Fouts, D., Haft, D. H., Selengut, J., Peterson, J. D., Davidsen, T. M., Zafar, N., Zhou, L. W., Radune, D., Dimitrov, G., Hance, M., Tran, K., Khouri, H., Gill, J., Utterback, T. R., Feldblyum, T. V., Wall, J. D., Voordouw, G., Fraser, C. M. (2004). The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. NATURE BIOTECHNOLOGY. Vol. 22 (5), pp. 554-559.
• Moran, M. A., Buchan, A., Gonzalez, J. M., Heidelberg, J. F., Whitman, W. B., Kiene, R. P., Henriksen, J. R., King, G. M., Belas, R., Fuqua, C., Brinkac, L., Lewis, M., Johri, S., Weaver, B., Pai, G., Eisen, J. A., Rahe, E., Sheldon, W. M., Ye, W. Y., Miller, T. R., Carlton, J., Rasko, D. A., Paulsen, I. T., Ren, Q. H., Daugherty, S. C., Deboy, R. T., Dodson, R. J., Durkin, A. S., Madupu, R., Nelson, W. C., Sullivan, S. A., Rosovitz, M. J., Haft, D. H., Selengut, J., Ward, N. (2004). Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. NATURE. Vol. 432 (7019), pp. 910-913.
• Seshadri, R., Myers, G. S., Tettelin, H., Eisen, J. A., Heidelberg, J. F., Dodson, R. J., Davidsen, T. M., DeBoy, R. T., Fouts, D. E., Haft, D. H., Selengut, J., Ren, Q., Brinkac, L. M., Madupu, R., Kolonay, J., Durkin, S. A., Daugherty, S. C., Shetty, J., Shvartsbeyn, A., Gebregeorgis, E., Geer, K., Tsegaye, G., Malek, J., Ayodeji, B., Shatsman, S., McLeod, M. P., Smajs, D., Howell, J. K., Pal, S., Amin, A., Vashisth, P., McNeill, T. Z., Xiang, Q., Sodergren, E., Baca, E., Weinstock, G. M., Norris, S. J., Fraser, C. M., Paulsen, I. T. (2004). Comparison of the genome Treponema denticola with of the oral pathogen other spirochete genomes. Proceedings of the National Academy of Sciences of the United States of America. Vol. 101 (15), pp. 5646-5651.
• Leahy, J. G., Khalid, Z. M., Quintero, E. J., Jones-Meehan, J. M., Heidelberg, J. F., Batchelor, P. J., Colwell, R. R. (2003). The concentrations of hexadecane and inorganic nutrients modulate the production of extracellular membrane-bound vesicles, soluble protein, and bioemulsifier by Acinetobacter venetianus RAG-1 and Acinetobacter sp strain HO1-N. CANADIAN JOURNAL OF MICROBIOLOGY. Vol. 49 (9), pp. 569-575.
• Haveman, S. A., Brunelle, V., Voordouw, J. K., Voordouw, G., Heidelberg, J. F., Rabus, R. (2003). Gene expression analysis of energy metabolism mutants of Desulfovibrio vulgaris Hildenborough indicates an important role for alcohol dehydrogenase. JOURNAL OF BACTERIOLOGY. Vol. 185 (15), pp. 4345-4353.
• Miller, E. S., Heidelberg, J. F., Eisen, J. A., Nelson, W. C., Durkin, A. S., Ciecko, A., Feldblyum, T. V., White, O., Paulsen, I. T., Nierman, W. C., Lee, J., Szczypinski, B., Fraser, C. M. (2003). Complete genome sequence of the broad-host-range vibriophage KVP40: Comparative genomics of a T4-related bacteriophage. JOURNAL OF BACTERIOLOGY. Vol. 185 (17), pp. 5220-5233.
• Beja, O., Suzuki, M. T., Heidelberg, J. F., Nelson, W. C., Preston, C. M., Hamada, T., Eisen, J. A., Fraser, C. M., DeLong, E. F. (2002). Unsuspected diversity among marine aerobic anoxygenic phototrophs. NATURE. Vol. 415 (6872), pp. 630-633.
• Paulsen, I. T., Seshadri, R., Nelson, K. E., Eisen, J. A., Heidelberg, J. F., Read, T. D., Dodson, R. J., Umayam, L., Brinkac, L. M., Beanan, M. J., Daugherty, S. C., Deboy, R. T., Durkin, A. S., Kolonay, J. F., Madupu, R., Nelson, W. C., Ayodeji, B., Kraul, M., Shetty, J., Malek, J., Van Aken, S. E., Riedmuller, S., Tettelin, H., Gill, S. R., White, O., Salzberg, S. L., Hoover, D. L., Lindler, L. E., Halling, S. M., Boyle, S. M., Fraser, C. M. (2002). The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. Vol. 99 (20), pp. 13148-13153.
• Beliaev, A. S., Thompson, D. K., Khare, T., Lim, H., Brandt, C. C., Li, G., Murray, A. E., Heidelberg, J. F., Giometti, C. S., Yates, J. I., Nealson, K. H., Tiedje, J. M., Zhou, J. (2002). Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors. OMICS A Journal of Integrative Biology. Vol. 6 (1), pp. 39-60.
• Dziejman, M., Balon, E., Boyd, D., Fraser, C. M., Heidelberg, J. F., Mekalanos, J. J. (2002). Comparative genomic analysis of Vibrio cholerae: Genes that correlate with cholera endemic and pandemic disease. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. Vol. 99 (3), pp. 1556-1561.
• Heidelberg, J. F., Paulsen, I. T., Nelson, K. E., Gaidos, E. J., Nelson, W. C., Read, T. D., Eisen, J. A., Seshadri, R., Ward, N., Methe, B., Clayton, R. A., Meyer, T., Tsapin, A., Scott, J., Beanan, M., Brinkac, L., Daugherty, S., DeBoy, R. T., Dodson, R. J., Durkin, A. S., Haft, D. H., Kolonay, J. F., Madupu, R., Peterson, J. D., Umayam, L. A., White, O., Wolf, A. M., Vamathevan, J., Weidman, J., Impraim, M., Lee, K., Berry, K., Lee, C., Mueller, J., Khouri, H., Gill, J., Utterback, T. R., McDonald, L. A., Feldblyum, T. V., Smith, H. O., Venter, J. C., Nealson, K. H., Fraser, C. M. (2002). Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. NATURE BIOTECHNOLOGY. Vol. 20 (11), pp. 1118-1123.
• Eisen, J. A., Nelson, K. E., Paulsen, I. T., Heidelberg, J. F., Wu, M., Dodson, R. J., Deboy, R., Gwinn, M. L., Nelson, W. C., Haft, D. H., Hickey, E. K., Peterson, J. D., Durkin, A. S., Kolonay, J. L., Yang, F., Holt, I., Umayam, L. A., Mason, T., Brenner, M., Shea, T. P., Parksey, D., Nierman, W. C., Feldblyum, T. V., Hansen, C. L., Craven, M. B., Radune, D., Vamathevan, J., Khouri, H., White, O., Gruber, T. M., Ketchum, K. A., Venter, J. C., Tettelin, H., Bryant, D. A., Fraser, C. M. (2002). The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. Vol. 99 (14), pp. 9509-9514.
• Nierman, W. C., Feldblyum, T. V., Laub, M. T., Paulsen, I. T., Nelson, K. E., Eisen, J., Heidelberg, J. F., Alley, M., Ohta, N., Maddock, J. R., Potocka, I., Nelson, W. C., Newton, A., Stephens, C., Phadke, N. D., Ely, B., DeBoy, R. T., Dodson, R. J., Durkin, A. S., Gwinn, M. L., Haft, D. H., Kolonay, J. F., Smit, J., Craven, M. B., Khouri, H., Shetty, J., Berry, K., Utterback, T., Tran, K., Wolf, A., Vamathevan, J., Ermolaeva, M., White, O., Salzberg, S. L., Venter, J. C., Shapiro, L., Fraser, C. M. (2001). Complete genome sequence of Caulobacter crescentus. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. Vol. 98 (7), pp. 4136-4141.
• Nelson, K. E., Paulsen, I. T., Heidelberg, J. F., Fraser, C. M. (2000). Status of genome projects for nonpathogenic bacteria and archaea. NATURE BIOTECHNOLOGY. Vol. 18 (10), pp. 1049-1054.
• Eisen, J. A., Heidelberg, J. F., White, O., Salzberg, S. L. (2000). Evidence for symmetric chromosomal inversions around the replication origin in bacteria. GENOME BIOLOGY. Vol. 1 (6)
• Heidelberg, J. F., Wolf, A., Vamathevan, J., Qin, H., Weidman, J., Impraim, M., Kang, K., Lee, P., Mueller, J., Fraser, C. M. (2000). Shewanella oneidensis: A model organism for bioremediation. International Genome Sequencing and Analysis Conference. Vol. 12, pp. 65-66.
• Heidelberg, J. F., Eisen, J. A., Nelson, W. C., Clayton, R. A., Gwinn, M. L., Dodson, R. J., Haft, D. H., Hickey, E. K., Peterson, J. D., Umayam, L., Gill, S. R., Nelson, K. E., Read, T. D., Tettelin, H., Richardson, D., Ermolaeva, M. D., Vamathevan, J., Bass, S., Qin, H. Y., Dragoi, I., Sellers, P., McDonald, L., Utterback, T., Fleishmann, R. D., Nierman, W. C., White, O., Salzberg, S. L., Smith, H. O., Colwell, R. R., Mekalanos, J. J., Venter, J. C., Fraser, C. M. (2000). DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. NATURE. Vol. 406 (6795), pp. 477-483.
• White, O., Eisen, J. A., Heidelberg, J. F., Hickey, E. K., Peterson, J. D., Dodson, R. J., Haft, D. H., Gwinn, M. L., Nelson, W. C., Richardson, D. L., Moffat, K. S., Qin, H. Y., Jiang, L. X., Pamphile, W., Crosby, M., Shen, M., Vamathevan, J. J., Lam, P., McDonald, L., Utterback, T., Zalewski, C., Makarova, K. S., Aravind, L., Daly, M. J., Minton, K. W., Fleischmann, R. D., Ketchum, K. A., Nelson, K. E., Salzberg, S., Smith, H. O., Venter, J. C., Fraser, C. M. (1999). Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. SCIENCE. Vol. 286 (5444), pp. 1571-1577.
• HEIDELBERG, J. F., ONEILL, K. R., JACOBS, D., COLWELL, R. R. (1993). ENUMERATION OF VIBRIO-VULNIFICUS ON MEMBRANE FILTERS WITH A FLUORESCENTLY LABELED OLIGONUCLEOTIDE PROBE SPECIFIC FOR KINGDOM-LEVEL 16S RIBOSOMAL-RNA SEQUENCES. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. Vol. 59 (10), pp. 3474-3476.

Administative Appointment

• President of the Board, Southern California Marine Institute, 2018 –
• Associate Director, Wrigley Institute for Environmental Studies, 2016 – 2019
• Section Head, Marine and Environmental Biology, University of Southern California, 2015 – 2017