Jeff Kimbrel

Contact information

Lawrence Livermore National Laboratory
7000 East Avenue, L-452
Livermore, CA 94550

email: kimbrel1@llnl.gov
phone: 925 409 6015
 

Education

Ph.D., Molecular and Cellular Biology, Oregon State University
B.S., Biological Sciences, Colorado State University

Research

My research interests focus primarily on the interactions of microbes (bacteria, archaea and bacteriophage) with other organisms and their environment. I utilize a broad range of computational biology and molecular techniques, largely focusing on improving functional annotation of prokaryotic and phage genomes, either isolated or binned from metagenomes (MAGs).

Publications​

  1. Robert Riley, Robert M Bowers, Antonio Pedro Camargo, Ashley Campbell, Rob Egan, Emiley A Eloe-Fadrosh, Brian Foster, Steven Hofmeyr, Marcel Huntemann, Matthew Kellom, Jeffrey A Kimbrel, Leonid Oliker, Katherine Yelick, Jennifer Pett-Ridge, Asaf Salamov, Neha J Varghese, Alicia Clum. Terabase-Scale Coassembly of a Tropical Soil Microbiome. Microbiology Spectrum (2023). doi:10.1128/spectrum.00200-23
  2. François Maillard, Talia J. Michaud, Craig R. See, Lang C. DeLancey, Steven J. Blazewicz, Jeffrey A. Kimbrel, Jennifer Pett-Ridge, Peter G. Kennedy. Melanization slows the rapid movement of fungal necromass carbon and nitrogen into both bacterial and fungal decomposer communities and soils. mSystems (2023). 
  3. Vanessa Brisson, Courtney Swink, Jeffrey Kimbrel, Xavier Mayali, Ty Samo, Suzanne M. Kosina, Michael Thelen, Trent R. Northen, Rhona K. Stuart. Dynamic Phaeodactylum tricornutum exometabolites shape surrounding bacterial communities. New Phytologist (2023). doi:10.1111/nph.19051
  4. Colleen E Yancey, E Anders Kiledal, Subba Rao Chaganti, Vincent J Denef, Reagan M Errera, Jacob T Evans, Lauren N Hart, Dragan Isailovic, William S James, Jenan K Kharbush, Jeffrey A Kimbrel, Wei Li, Xavier Mayali, Helena Nitschky, Catherine A Polik, McKenzie A Powers, Sanduni H Premathilaka, Nicole A Rappuhn, Laura A Reitz, Sara R Rivera, Claire C Zwiers, Gregory J Dick. The Western Lake Erie Culture Collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome. Harmful Algae (2023). doi:10.1016/j.hal.2023.102440
  5. Megan M Foley, Steven J Blazewicz, Karis J McFarlane, Alex Greenlon, Michaela Hayer, Jeffrey A Kimbrel, Benjamin J Koch, Victoria L Monsaint-Queeney, Keith Morrison, Ember Morrissey, Bruce A Hungate, Jennifer Pett-Ridge. Active populations and growth of soil microorganisms are framed by mean annual precipitation in three California annual grasslands. Soil Biology and Biochemistry (2023). doi:10.1016/j.soilbio.2022.108886
  6. Alex Greenlon, Ella Sieradzki, Olivier Zablocki, Benjamin J Koch, Megan M Foley, Jeffrey A Kimbrel, Bruce A Hungate, Steven J Blazewicz, Erin E Nuccio, Christine L Sun, Aaron Chew, Cynthia-Jeanette Mancilla, Matthew B Sullivan, Mary Firestone, Jennifer Pett-Ridge, Jillian F Banfield. Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems. mSystems (2022). doi:10.1128/msystems.00417-22
  7. Jeffrey Kimbrel, Joseph Moon, Aram Avila-Herrera, Jose Manuel Martí, James Thissen, Nisha Mulakken, Sarah H Sandholtz, Tyshawn Ferrell, Chris Daum, Sara Hall, Brent Segelke, Kathryn T Arrildt, Sharon Messenger, Debra A Wadford, Crystal Jaing, Jonathan E Allen, Monica K Borucki. Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples. Viruses (2022). doi:10.3390/v14122775
  8. Hestrin R, Kan M, Lafler M, Wollard J, Kimbrel JA, Ray P, Blazewicz SJ, Stuart R, Craven K, Firestone M, Nuccio EE, Pett-Ridge J. Plant-associated fungi support bacterial resilience following water limitation. ISME J (2022). doi:10.1038/s41396-022-01308-6
  9. Nuccio EE, Blazewicz SJ, Lafler M, Campbell AN, Kakouridis A, Kimbrel JA, Wollard J, Vyshenska D, Riley R, Tomatsu A, Hestrin R, Malmstrom RR, Firestone M, Pett-Ridge J. HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi. Microbiome (2022). doi:10.1186/s40168-022-01391-z
  10. McGowan J, Borucki M, Omairi H, Varghese M, Vellani S, Chakravarty S, Fan S, Chattopadhyay S, Siddiquee M, Thissen JB, Mulakken N, Moon J, Kimbrel JA, Tiwari AK, Taylor RT, Kang D, Jaing C, Chakravarti R, Chattopadhyay S. SARS-CoV-2 Monitoring in Wastewater Reveals Novel Variants and Biomarkers of Infection. Viruses (2022). doi:10.3390/v14092032
  11. Morris MM, Kimbrel JA, Geng H, Tran-Gyamfi MB, Yu ET, Sale KL, Lane, TW, Mayali X. Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina. mSphere (2022). doi:10.1128/msphere.00231-22
  12. Sokol, et al, LLNL Soil Consortium. Life and Death in the Soil Microbiome: How Ecological Processes Influence Biogeochemistry. Nature Reviews Microbiology (2022). doi:10.1038/s41579-022-00695-z
  13. Kimbrel JA, Jeffrey BM, Ward, CS. Prokaryotic Genome Annotation. Microbial Systems Biology: Methods and Protocols 2nd Edition. Springer (2022). doi:10.1007/978-1-0716-1585-0_10
  14. Nayfach, et al, IMG/M Data Consortium. A Genomic Catalog of Earthy’s Microbiomes. Nature Biotechnology (2021). doi:10.1038/s41587-020-0718-6
  15. Trubl G, Kimbrel JA, Liquet-Gonzalez J, Nuccio EE, Weber PK, Pett-Ridge J, Jansson JK, Waldrop MP, Blazewicz SJ. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome (2021). doi:10.1186/s40168-021-01154-2
  16. Kim H, Kimbrel JA, Vaiana CA, Wollard JR, Mayali X, Buie CR. Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate. ISME J (2021). doi:10.1038/s41396-021-01147-x
  17. Zhou CE, Kimbrel JA, Edwards R, McNair K, Souza BA, Malfatti S. MultiPhATE2: code for functional annotation and comparison of phage genomes. G3|Genes|Genomes|Genetics (2021). doi: 10.1093/g3journal/jkab074
  18. Samuel MD Seaver, Filipe Liu, Qizhi Zhang, James Jeffryes, José P Faria, Janaka N Edirisinghe, Michael Mundy, Nicholas Chia, Elad Noor, Moritz E Beber, Aaron A Best, Matthew DeJongh, Jeffrey A Kimbrel, Patrik D’haeseleer, Sean R McCorkle, Jay R Bolton, Erik Pearson, Shane Canon, Elisha M Wood-Charlson, Robert W Cottingham, Adam P Arkin, Christopher S Henry. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Research (2021). doi.org/10.1093/nar/gkaa746
  19. Higgins DA, Gladden J, Kimbrel JA, Simmons BA, Singer SW, Thelen MP. Bacterial guanidine riboswitch regulated SMR-type efflux transporters protect against ionic liquid toxicity. Journal of Bacteriology (2019). doi:10.1128/JB.00069-19
  20. Zhou CE, Malfatti S, Kimbrel JA, Philipson C, McNair K, Hamilton T, Edwards R, Souza B. multiPhATE: Bioinformatics Pipeline for Functional Annotation of Phage Isolates. Bioinformatics (2019). doi:10.1093/bioinformatics/btz258
  21. Fisher CL, Ward CS, Lane PD, Kimbrel JA, Stuart RK, Mayali X, Lane TW. Bacterial communities protect the alga Microchloropsis salinafrom grazing by the rotifer Brachionus plicatilis. Algal Research (2019). doi:10.1016/j.algal.2019.101500
  22. Kimbrel JA, Samo TJ, Nilson D, Thelen MP, Siccardi A, Zimba P, Lane TW, Mayali X. Host Selection and Stochastic Effects Influencing Bacterial Community Assembly on the Microalgal Phycosphere. Algal Research (2019). doi:10.1016/j.algal.2019.101489
  23. Griesemer M*, Kimbrel JA*, Zhou CE, Navid A, D'haeseleer P. Combining multiple functional annotation tools increases completeness of metabolic annotation. BMC Genomics (2018). doi:10.1186/s12864-018-5221-9
  24. Samo TJ, Kimbrel JA, Nilson D, Pett-Ridge J, Weber P, Mayali X. Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions. Environmental Microbiology (2018). doi:10.1111/1462-2920.14357
  25. Kimbrel JA, Ballor N, Wu Y, David M, Hazen TC, Simmons BA, Singer SW, Jansson JK. Microbial Community Structure and Functional Potential Along a Hypersaline Gradient. Frontiers in Microbiology (2018). doi:10.3389/fmicb.2018.01492
  26. Woo HL, Ballor NR, Hazen TC, Fortney JL, Simmons BA, Davenport KW, Goodwin L, Ivanova NN, Kyrpides NC, Mavromatis K, Woyke T, Jansson J, Kimbrel JA, DeAngelis KM. Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2. Standards in Genomic Sciences (2014). doi:10.1186/1944-3277-9-19
  27. Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Bælum J, Kimbrel JA, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J (2014). doi:10.1038/ismej.2013.254
  28. Kimbrel JA, Chang JH, Arp DJ, Sayavedra-Soto LA. The draft genome sequence of Nocardioides sp. strain CF8 reveals the scope of its metabolic capabilities. Genome Announcements. August 2013. Volume 1, Issue 4. http://genomea.asm.org/content/1/4/e00439-13.short
  29. Fox SE, Preece J, Kimbrel JA, Marchini GL, Sage A, Youens-Clark K, Cruzan MB, Jaiswal P. Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae). Applications in Plant Sciences. March 2013. Volume 1, Issue 3. http://www.bioone.org/doi/abs/10.3732/apps.1200011
  30. Kimbrel JA*, Thomas WJ*, Jiang Y, Creason AL, Thireault CA, Sachs JL, Chang JH. Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum. PLoS Pathogens. February 2013, Volume 9, Issue 2. http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat...(*co-first authors)
  31. Di Y, Emerson SC, Shafer DW, Kimbrel JA, Chang JH. Higher Order Asymptotics for Negative Binomial Regression Inferences from RNA-Sequencing Data. Statistical Applications in Genetics and Molecular Biology. January 2013. Volume 12, Issue 1, pages 49-70. 
  32. Kimbrel JA, Di Y, Cumbie JS, Chang JC. RNA-Seq for Plant Pathogenic Bacteria. Genes. October 2011. http://www.mdpi.com/2073-4425/2/4/689
  33. Cumbie JS*, Kimbrel JA*, Di Y, Schafer DW, Wilhelm LJ, Fox SE, Sullivan CM, Curzon AD, Carrington JC, Mockler TC, Chang JH. GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences, PLoS ONE. October 2011. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.00252...(*co-first authors)
  34. Sayavedra-Soto L, Hamamura N, Liu C, Kimbrel JA, Chang JH, Arp D. The membrane-associated monooxygenase in the butane-oxidizing Gram-positive bacterium Nocardioides sp. strain CF8 is a novel member of the AMO/PMO family. Environmental Microbiology Reports. 2011. http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2010.00239.x/full
  35. Kimbrel JA, Givan SA, Temple TN, Johnson KB, Chang JH. Genome sequencing and comparative analysis of the carrot bacterial blight pathogen, Xanthomonas hortorum pv. carotae M081, for insights into pathogenicity and applications in molecular diagnostics. Molecular Plant Pathology. January, 2011. http://onlinelibrary.wiley.com/doi/10.1111/j.1364-3703.2010.00694.x/full
  36. Kimbrel JA, Givan SA, Halgren AB, Creason AL, Mills DI, Banowetz GM, Armstrong DJ, Chang JH. An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6. BMC Genomics 2010, 11:522. September 28, 2010. http://www.biomedcentral.com/1471-2164/11/522/abstract
  37. International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. February 11, 2010. Kimbrel JA and Chang JH contributing authors. http://www.nature.com/nature/journal/v463/n7282/full/nature08747.html
  38. Cohu CM, Abdel-Ghany SE, Gogolin Reynolds KA, Onofrio AM, Bodecker JR, Kimbrel JA, Niyogi KK, Pilon M. Copper delivery by the copper chaperone for chloroplast and cytosolic copper/zinc-superoxide dismutases: regulation and unexpected phenotypes in an Arabidopsis mutant. Molecular Plant. October 21, 2009. http://mplant.oxfordjournals.org/content/2/6/1336.abstract
  39. Thomas WJ, Thireault CA, Kimbrel JA, Chang JH. Recombineering and stable integration of the Pseudomonas syringae pv. syringae 61 hrp/hrc cluster into the genome of the soil bacterium Pseudomonas fluorescens Pf0-1. The Plant Journal. August 6, 2009. http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2009.03998.x/abst...