Plant Pathology Graduate Program

James Borneman

James Borneman
Office: 951-827-3584

Office Hours: , not specified - not specified
Email: borneman@ucr.edu

James Borneman


Microbial Ecology

Biography & Research Interests

Microorganisms play key roles in ecosystems and human civilization.  They are involved in soil formation, nutrient cycling, and detoxifying contaminated environments.  They contain a wealth of useful compounds and enzymes for biotechnology.  In addition, microbes can both cause and prevent infectious diseases.

In collaboration with other laboratories, we seek to understand the microbial roles in several pathogen or disease associated processes.  To address these topics, we employ ecological approaches utilizing a wide range of methods including high throughput sequencing, various “omics” methods, quantitative PCR, standard in vitro culture techniques as well as algorithmic and statistical analyses.

In the agricultural arena, our research goals include extending our understanding of microorganisms that suppress plant pathogens.  Previously, we identified a fungus (Dactylella oviparasitica)that suppresses a plant-parasitic nematode (Heterodera schachtii).  Current projects include adding the population levels of this fungus to cropping decision models, which we anticipate will lead to higher crop yields and profitability for the growers.  We are also developing new microbe-based strategies to control Huanglongbing, which is a bacterial disease that is dramatically impacting citrus production worldwide.

Other research projects include identifying microorganisms involved in various human health and disease processes.  Current projects include examining the role of intestinal bacteria in (i) inflammatory bowel disease (IBD), (ii) several types of cancer and, (iii) obesity and diabetes.

To facilitate the aforementioned studies, we have developed several new molecular and computational methods.  Recent efforts have produced PRISE2, a software program enabling the design of sequence-selective PCR primers and probes.  This program has several features not present in any other program, enabling us to design tools to track and quantify specific bacteria that co-exist with thousands of other bacteria, which is a capability that has been lacking in this type of experimentation.  We have also developed a new state-of-the-art DNA sequencing method for identifying bacteria at a much higher level of taxonomic resolution; all prior methods typically enable genus level assignments while our new method enables species and sometimes strain level assignments.




Ruegger PM, Clark RT, Weger JR, Braun J, Borneman J. 2014. Improved resolution of bacteria by high throughput sequence analysis of the rRNA internal transcribed spacer. J Microbiol Methods. 105:82-7.

Tong M, McHardy I, Ruegger P, Goudarzi M, Kashyap PC, Haritunians T, Li X, Graeber TG, Schwager E, Huttenhower C, Fornace AJ Jr, Sonnenburg JL, McGovern DP, Borneman J, Braun J. 2014. Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism. ISME J. doi: 10.1038/ismej.2014.64.

Treseder K, Bent E, Borneman J, McGuire KL. 2014. Shifts in fungal communities during decomposition of boreal forest litter. Fungal Ecology 10:58-69.

Tanaseichuk O, Borneman J, Jiang T. 2014. Phylogeny-based classification of microbial communities. Bioinformatics 30:449-56.

Huang YT, Jiue-in Yang, Marek Chrobak and James Borneman. 2014. PRISE2: Software for designing sequence-selective PCR primers and probes. BMC Bioinformatics 15:317.


Yamamoto ML, Maier I, Dang AT, Berry D, Liu J, Ruegger PM, Yang JI, Soto PA, Presley LL, Reliene R, Westbrook AM, Wei B, Loy A, Chang C, Braun J, Borneman J, Schiestl RH. 2013. Intestinal bacteria modify lymphoma incidence and latency by affecting systemic inflammatory state, oxidative stress, and leukocyte genotoxicity. Cancer Res. 73:4222-32.

Becker JS, Borneman J, Becker JO. 2013. Dactylella oviparasitica parasitism of the sugar beet cyst nematode observed in trixenic culture plates. Biological Control 64:51–56.

Benecke S, Jeske DR, Ruegger P, Borneman J. 2013. Bayes Neutral Zone Classifiers With Applications to Nonparametric Unsupervised Settings. Journal of Agricultural, Biological, and Environmental Statistics 18:39-52.

Tong M, Li X, Wegener Parfrey L, Roth B, Ippoliti A, Wei B, Borneman J, McGovern DP, Frank DN, Li E, Horvath S, Knight R, Braun J. 2013. A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease. PLoS One 8:e80702.

McHardy IH, Goudarzi M, Tong M, Ruegger PM, Schwager E, Weger JR, Graeber TG, Sonnenburg JL, Horvath S, Huttenhower C, McGovern DP, Fornace AJ Jr, Borneman J, Braun J. 2013. Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships. Microbiome 1:17.

McHardy IH, Li X, Tong M, Ruegger P, Jacobs J, Borneman J, Anton P, Braun J. 2013. HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota. Microbiome. 1:26.


Tanaseichuk O, Borneman J, Jiang T. 2012. Separating metagenomic short reads into genomes via clustering. Algorithms Mol Biol. 2012 Sep 26;7(1):27.

Yang JI, Ruegger PM, McKenry MV, Becker JO, Borneman J. 2012. Correlations between root-associated microorganisms and peach replant disease symptoms in a California soil. PLoS One. 2012;7(10):e46420

Presley LL, Ye J, Li X, Leblanc J, Zhang Z, Ruegger PM, Allard J, McGovern D, Ippoliti A, Roth B, Cui X, Jeske DR, Elashoff D, Goodglick L, Braun J, Borneman J. 2012. Host- microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosal-luminal interface. Inflammatory Bowel Diseases 18:409-17.

Ruegger PM, Bent E, Li W, Jeske DR, Cui X, Braun J, Jiang T, Borneman J. 2012. Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology. Journal of Microbiological Methods 90:235-240.

Yang, JI, Loffredo, A., Borneman, J, Becker, JO. 2012. Biocontrol Efficacy Among Strains of Pochonia chlamydosporia obtained from a Root-Knot Nematode Suppressive Soil. Journal of Nematology 44:67–71.

Godwin S, Bent E, Borneman J, Pereg L. 2012. The Role of Coral-Associated Bacterial Communities in Australian Subtropical White Syndrome of Turbinaria mesenterina. PLoS One 7:e44243.

Yang, Jiue-in, Scott Benecke, Daniel R. Jeske, Fernando Rocha, Jennifer Smith- Becker, Patricia Timper, J. Ole Becker, James Borneman. 2012. Population Dynamics of Dactylella oviparasitica and Heterodera schachtii: Toward a Decision Model for Sugar Beet Planting. Journal of Nematology 44:67-71.

Zhang Z, Cui X, Jeske DR, Borneman J. 2012. Biclustering Scatter Plots Using Data Depth Measures. Statistical Analysis and Data Mining 6:102-115.


Zhang, Z., Cui, X., Jeske, D. R., Li, X., Braun, J. and Borneman, J. 2011. Clustering Scatter Plots Using Data Depth Measures, Journal of Biometrics and Biostatistics. http://dx.doi.org/10.4172/2155-6180.S5-001.

Li X, LeBlanc J, Truong A, Vuthoori R, Chen SS, Lustgarten JL, Roth B, Allard J, Ippoliti A, Presley LL, Borneman J, Bigbee WL, Gopalakrishnan V, Graeber TG, Elashoff D, Braun J, Goodglick L. 2011. A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface. PLoS One 6:e26542.

Ruegger PM, Della Vedova G, Jiang T, Borneman J. 2011. Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences. BMC Bioinformatics 12:394.


Presley LL, Wei B, Braun J, Borneman J. 2010. Bacteria associated with immunoregulatory cells in mice. Applied and Environmental Microbiology 76:936-941.

Wei B, Wingender G, Fujiwara D, Chen DY, McPherson M, Brewer S, Borneman J, Kronenberg M, Braun J. 2010. Commensal microbiota and CD8+ T cells shape the formation of invariant NKT cells. Journal of Immunology 184:1218-26.

Li, Wei, Paul M. Ruegger, James Borneman and Tao Jiang. 2010. Polony Identification Using the EM Algorithm Based on a Gaussian Mixture Model. BIBE '10 Proceedings of the 2010 IEEE International Conference on Bioinformatics and Bioengineering, p. 220- 225.  

McGuire, K. L., E. Bent, J. Borneman, A. Majumder, S. D. Allison, and K. K. Treseder. 2010. Functional diversity in resource use by fungi. Ecology 91: 2324-2332.

Hua Y, Jeske DR, Ruegger P, and Borneman J. 2010. Neutral Zone Classifiers Using a Decision-Theoretic Approach With Application to DNA Array Analyses in the following paginated issue of Journal of Agricultural, Biological, and Environmental Statistics 15:474. 


Bent E, Loffredo A, Yang J, McKenry MV, Becker JO, and Borneman J. 2009. Investigations into peach seedling stunting caused by a replant soil. FEMS Microbiology Ecology 68:192-200. 


Bent E, Loffredo A, McKenry MV, Becker JO, and Borneman J. 2008. Detection and Investigation of a Soil with Biological Activity Against Meloidogyne incognita. Journal of Nematology 40:109-118. 

Gao X, Yin B, Borneman J, and Becker JO. 2008. Assessment of parasitic activity of Fusarium strains obtained from a Heterodera schachtii-suppressive soil. Journal of Nematology 40:1-6. 

Fujiwara D, Wei B, Presley LL, Brewer S, McPherson M, Lewinski MA, Borneman J, and Braun J. 2008. Systemic control of plasmacytoid dendritic cells by CD8+ T Cells and commensal microbiota. Journal of Immunology 180:5843-5852. 

Ye J, Lee JW, Presley LL, Bent E, Wei B, Braun J, Schiller NL, Straus DS, and Borneman J. 2008. Bacteria and bacterial rRNA genes associated with the development of colitis in IL-10-/- Mice. Inflammatory Bowel Diseases 14:1041-1050. 

Fu, Q, Ruegger, P, Bent, E, Chrobak, M, Borneman, J. 2008. PRISE (PRImer SElector): software for designing sequence-selective PCR primers. Journal of Microbiological Methods 72:263-267. 

Wei B, Su TT, Dalwadi H, Stephan RP, Fujiwara D, Huang TT, Brewer S, Chen L, Arditi M, Borneman J, Rawlings DJ, Braun J. 2008. Resident enteric microbiota and CD8(+) T cells shape the abundance of marginal zone B cells. Eur J Immunol. 38:3411-3425. 


Borneman J, Becker J. 2007. Identifying microorganisms involved in specific pathogen suppression in soil. Annual Review of Phytopathology 45:153-172.

Borneman J, Becker JO, Bent E, Lanoil B, Gardener BM, Olatinwo R, Presley L, Scupham AJ, Valinsky L, Yin B. 2007. Identifying microorganisms involved in specific in situ functions: experimental design considerations for rRNA gene-based population studies and sequence-selective PCR assays, In Christon Hurst (ed.) Manual for Environmental Microbiology (3rd ed) ASM Press (p 748-757).

Jeske DR, Liu Z, Bent E, Borneman J. 2007. Classification Rules that Include Neutral Zones and their Application to Microbial Community Profiling. Communications in Statistics - Theory and Methods 36:1965-1980.

Fu Q, Bent E, Borneman J, Chrobak M, Young N. 2007. Algorithmic Approaches to Selecting Control Clones in DNA Array Hybridization Experiments. Journal of Bioinformatics and Computational Biology 5:937-961.


Olatinwo, R., B. Yin, J. O. Becker, and J. Borneman. 2006. Suppression of the plant-parasitic nematode Heterodera schachtii by the fungus Dactylella oviparasitica. Phytopathology 96:111-114.

Olatinwo, R., J. Borneman, and J. O. Becker. 2006. Field trial induction of beet-cyst nematode suppressiveness by Dactylella oviparasitica and Fusarium oxysporum in field microplot trials. Phytopathology 96:855-859.

Olatinwo, R., J. O. Becker, J. Borneman. 2006. Suppression of Heterodera schachtii populations by Dactylella oviparasitica in Four Soils. Journal of Nematology 38:345-348.

Scupham, A. J, L. L. Presley, B. Wei, E. Bent, N. Griffith, M. McPherson, F. Zhu, O. Oluwadara, N. Rao, J. Braun, and J. Borneman. 2006. Abundant and diverse fungal microbiota in the murine intestine. Applied and Environmental Microbiology 72:793-801.

Bent, E., B. Yin, A. Figueroa, J. Ye, Q. Fu, Z. Liu, V. McDonald, D. Jeske, T. Jiang, and J. Borneman. 2006. Development of a 9,600-clone procedure for oligonucleotide fingerprinting of rRNA genes: utilization to identify soil bacterial rRNA genes that correlate in abundance with the development of avocado root rot. Journal of Microbiological Methods 67:171-180.

Liu, Z., J. Borneman, T. Jiang. 2006. A software system for gene sequence database construction based on fast approximate string matching. International Journal of Bioinformatics Research and Applications 1:273-291.


Jampachaisri, K., L. Valinsky, J. Borneman, and S. J. Press. 2005. Classification of Oligonucleotide Fingerprints: Application for Microbial Community and Gene Expression Analyses. Bioinformatics 21:3122-3130.

Huang, T., B. Wei, P. Velazquez, J. Borneman and J. Braun. 2005. Commensal microbiota alter the abundance and TCR responsiveness of splenic naïve CD4+ T lymphocytes. Clinical Immunology 117:221-230.

  Liu, Z., X. Chen, J. Borneman, T. Jiang. 2005. A fast algorithm for approximate string matching on gene sequences. Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM 2005), LNCS 3537, p. 79-90.

Fu, Q. J. Borneman; J. Ye, and M. Chrobak. 2005. Improved probe selection for DNA arrays using nonparametric kernel density estimation. Proceedings of the 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference, page: 902-905.


Yin, B., A.J. Scupham, J.A. Menge, J. Borneman. 2004. Identifying microorganisms which fill a niche similar to that of the pathogen: a new investigative model for biological control research. Plant and Soil 259:19-27.

Borneman, J., R. Olatinwo, B. Yin and J. O. Becker. 2004. An experimental approach for identifying microorganisms involved in specified functions: utilisation for understanding a nematode suppressive soil. Australasian Plant Pathology 33:151-155.

Valinsky, L., A. J. Scupham, G. Della Vedova, Z. Liu, A. Figueroa, K. Jampachaisri, B. Yin, E. Bent, R. Mancini-Jones, J. Press, T. Jiang and J. Borneman. 2004. Oligonucleotide fingerprinting of ribosomal RNA genes (OFRG). In Molecular Microbial Ecology Manual, Kowalchuk, G.A.; de Bruijn, F.J.; Head, I.M.; Akkermans, A.D.; van Elsas, J.D. (Eds.), 2nd Edition.

Yin, B. A. J Scupham, E. Bent, and J. Borneman. 2004. BrdU substrate utilization assay. In Molecular Microbial Ecology Manual, Kowalchuk, G.A.; de Bruijn, F.J.; Head, I.M.; Akkermans, A.D.; van Elsas, J.D. (Eds.), 2nd Edition.

Figueroa A, Borneman J, Jiang T. 2004. Clustering binary fingerprint vectors with missing values for DNA array data analysis. Journal of Computational Biology 11:887-901.

Figueroa, A., Z. Liu, R. Mancini-Jones, J. Borneman, and T. Jiang. 2004. Building phylogenetic trees from binary oligonucleotide fingerprint vectors. Proceedings of the 26th Annual International Conferences of the IEEE EMBC, p. 2844-2847.

Liu, Z., J. Borneman, T. Jiang. 2004. A software system for gene sequence database construction. Proceedings of the 26th Annual International Conferences of the IEEE EMBS, p. 2797-2800.


Yin, B., L. Valinsky, X. Gao, J.O. Becker, and J. Borneman. 2003. Identification of fungal rDNA associated with soil suppressiveness against Heterodera schachtii using oligonucleotide fingerprinting of ribosomal RNA genes. Phytopathology 93:1006-1013.

Yin, B., L. Valinsky, X. Gao, J.O. Becker, and J. Borneman. 2003. Bacterial rDNA associated with soil suppressiveness against the plant-parasitic nematode Heterodera schachtii. Applied and Environmental Microbiology 69:1573-1580.

Figueroa, A. J. Borneman, and T. Jiang. Clustering binary fingerprint vectors with missing values for DNA array data analysis. Proc. of 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference (CSB), Stanford, CA., August 11-14, 2003, pp. 38-47.


Valinsky, L., G. Della Vedova, T. Jiang, and J. Borneman. 2002. Oligonucleotide fingerprinting of rRNA genes for analysis of fungal community composition. Applied and Environmental Microbiology 68:5999-6004.

Valinsky, L., G. Della Vedova, A. J Scupham, S. Alvey, A. Figueroa, B. Yin, R. J. Hartin, M. Chrobak, D. E. Crowley, T. Jiang, and J. Borneman. 2002. Analysis of bacterial community composition using oligonucleotide fingerprinting of ribosomal RNA genes. Applied and Environmental Microbiology 68:3243-3250.

Steddom, K, J.A. Menge, D. Crowley, and J. Borneman. 2002. Effect of repetitive applications of the biocontrol bacterium Pseudomonas putida 06909-rif/nal on citrus soil microbial communities. Phytopathology 92:857-862.


Borneman, J., M. Chrobak, G. Della Vedova, A. Figueroa, and T. Jiang. 2001. Probe selection algorithms with applications in the analysis of microbial communities. Bioinformatics 17(Suppl. 1):S39-S48.

Bekal, S., J. Borneman, M.S. Springer, R.M. Giblin-Davis, and J.O. Becker. 2001. Phenotypic and molecular analysis of a Pasteuria strain parasitic to the sting nematode. Journal of Nematology 33:110-115.


Yin, B., D. E. Crowley, G. Sparovek, J. Wanderley, and J. Borneman. 2000. Bacterial functional redundancy along a soil reclamation gradient. Applied and Environmental Microbiology 66:4361-4365.

Borneman, J. and R. J. Hartin. 2000. PCR Primers that amplify fungal ribosomal RNA genes from environmental samples. Applied and Environmental Microbiology 66:4356-4360.


Borneman, J. 1999. Culture-independent identification of microorganisms that respond to specified stimuli. Applied and Environmental Microbiology 65:3398-3400.

More Information

General Campus Information

University of California, Riverside
900 University Ave.
Riverside, CA 92521
Tel: (951) 827-1012

Career OpportunitiesUCR Libraries
Campus StatusDirections to UCR

Contact Information

Graduate Program in Plant Pathology
1140 Batchelor Hall

Tel: (800) 735-0717 or (951) 827-5688
Fax: (951) 827-5517
E-mail: laura.mcgeehan@ucr.edu

Department of Plant Pathology and Microbiology
Boyce Hall 1463

Tel: (951) 827-3598
Fax: (951) 827-4294
E-mail: margarita.flores@ucr.edu