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).

Ph.D., Molecular and Cellular Biology, Oregon State University

B.S., Biological Sciences, Colorado State University

1. Kimbrel, J. et al. Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples. Viruses 14, 2775 (2022).
2. Hestrin, R. et al. Plant-associated fungi support bacterial resilience following water limitation. ISME J 16, 2752–2762 (2022).
3. Nuccio, E. E. et al. HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi. Microbiome 10, 199 (2022).
4. Foley, M. M. et al. Active populations and growth of soil microorganisms are framed by mean annual precipitation in three California annual grasslands. Soil Biology and Biochemistry 108886 (2022) doi:10.1016/j.soilbio.2022.108886.
5. Greenlon, A. et al. Quantitative Stable-Isotope Probing (qSIP) with Metagenomics Links Microbial Physiology and Activity to Soil Moisture in Mediterranean-Climate Grassland Ecosystems. mSystems e00417-22 (2022) doi:10.1128/msystems.00417-22.
6. McGowan, J. et al. SARS-CoV-2 Monitoring in Wastewater Reveals Novel Variants and Biomarkers of Infection. Viruses 14, 2032 (2022).
7. Morris, M. M. et al. Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina. mSphere 7, e0023122 (2022).
8. Sokol, N. W. et al. Life and death in the soil microbiome: how ecological processes influence biogeochemistry. Nat Rev Microbiol 20, 415–430 (2022).
9. Kimbrel, J. A., Jeffrey, B. M. & Ward, C. S. Prokaryotic Genome Annotation. Methods Mol. Biol. 2349, 193–214 (2022).
10. Kim, H. et al. Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate. ISME J. 1–10 (2021).
11. Trubl, G. et al. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome 9, 208 (2021).
12. Ecale Zhou, C. L. et al. MultiPhATE2: code for functional annotation and comparison of phage genomes. G3 11, jkab074- (2021).
13. Nayfach, S. et al. A genomic catalog of Earth’s microbiomes. Nat Biotechnol 39, 499–509 (2021).
14. Seaver, S. M. D. et al. 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 Res. 49, D575–D588 (2021).
15. Ecale Zhou, C. L. et al. multiPhATE: bioinformatics pipeline for functional annotation of phage isolates. Bioinformatics 35, 4402–4404 (2019).
16. Higgins, D. A. et al. Guanidine riboswitch-regulated efflux transporters protect bacteria against ionic liquid toxicity. J. Bacteriol. 201, (2019).
17. Kimbrel, J. A. et al. Host selection and stochastic effects influence bacterial community assembly on the microalgal phycosphere. Algal Research 40, 101489 (2019).
18. Fisher, C. L. et al. Bacterial communities protect the alga Microchloropsis salina from grazing by the rotifer Brachionus plicatilis. Algal Research 40, 101500 (2019).
19. Samo, T. J. et al. Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions. Environ. Microbiol. 20, 4385–4400 (2018).
20. Griesemer, M., Kimbrel, J. A., Zhou, C. E., Navid, A. & D’haeseleer, P. Combining multiple functional annotation tools increases coverage of metabolic annotation. BMC Genomics 19, 948 (2018).
21. Kimbrel, J. A. et al. Microbial Community Structure and Functional Potential Along a Hypersaline Gradient. Front. Microbiol. 9, 1492 (2018).
22. Kimbrel, E. H. et al. Experimental characterization of nonwetting phase trapping and implications for geologic CO2 sequestration. Int. J. Greenhouse Gas Control 42, 1–15 (2015).
23. Woo, H. L. et al. Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2. Stand. Genomic Sci. 9, 19 (2014).
24. Mason, O. U. et al. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J. 8, 1464–1475 (2014).
25. Kimbrel, J. A., Chang, J., Arp, D. J. & Sayavedra-Soto, L. A. The draft genome sequence of Nocardioides sp. Strain CF8 reveals the scope of its metabolic capabilities. Genome Announc. 1, (2013).
26. Fox, S. E. et al. Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae). Appl. Plant Sci. 1, 1200011 (2013).
27. Di, Y., Emerson, S. C., Schafer, D. W., Kimbrel, J. A. & Chang, J. H. Higher order asymptotics for negative binomial regression inferences from RNA-sequencing data. Stat. Appl. Genet. Mol. Biol. 12, 49–70 (2013).
28. Kimbrel, J. A. et al. Mutualistic co-evolution of type III effector genes in Sinorhizobium fredii and Bradyrhizobium japonicum. PLoS Pathog. 9, e1003204 (2013).
29. Kimbrel, J. A., Di, Y., Cumbie, J. S. & Chang, J. H. RNA-Seq for Plant Pathogenic Bacteria. Genes 2, 689–705 (2011).
30. Cumbie, J. S. et al. GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences. PLoS One 6, e25279 (2011).
31. Kimbrel, J. A., Givan, S. A., Temple, T. N., Johnson, K. B. & Chang, J. H. 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. Mol. Plant Pathol. 12, 580–594 (2011).
32. Sayavedra-Soto, L. A. et al. The membrane-associated monooxygenase in the butane-oxidizing Gram-positive bacterium Nocardioides sp. strain CF8 is a novel member of the AMO/PMO family. Environ. Microbiol. Rep. 3, 390–396 (2011).
33. Kimbrel, J. A. et al. An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6. BMC Genomics 11, 522 (2010).
34. Thomas, W. J., Thireault, C. A., Kimbrel, J. A. & Chang, J. H. Recombineering and stable integration of the Pseudomonas syringae pv. syringae hrp/hrc cluster into the genome of the soil bacterium Pseudomonas fluorescens Pf0-1. Plant J. 60, 919–928 (2009).
35. Cohu, C. M. et al. Copper delivery by the copper chaperone for chloroplast and cytosolic copper/zinc-superoxide dismutases: regulation and unexpected phenotypes in an Arabidopsis mutant. Mol. Plant 2, 1336–1350 (2009).