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 DNA arrays, quantitative PCR, standard in vitro culture techniques as well as algorithmic and statistic analyses.

In the agricultural arena, our research goals include extending our understanding of soils naturally suppressive to plant pathogens.  Previously, we identified a fungus (Dactylella oviparasitica) that suppresses a plant-parasitic nematode (Heterodera schachtii).  Current projects include elucidating the interactions among the nematode, fungus and host crops that lead to the development of this beneficial phenomenon.  We are also investigating soils that suppress root knot nematodes and that cause peach replant disease. 

Other areas of interest include identifying microorganisms involved in various human health and disease processes.  Current projects include examining (i) the role of bacteria in inflammatory bowel disease (IBD), (ii) a mouse model that possesses immunologic features similar to those occurring in human atopy, colitis, immune regulation and immune-disease susceptibility, and (iii) a mouse model of cancer. 

To facilitate the aforementioned studies, we have developed several molecular and computational methods.  Recent efforts have produced PRISE, a software program enabling the design of sequence-selective PCR primers.  Current projects include adapting the polymerase colony (polony) method for analyzing rRNA genes and developing new statistical approaches for identifying associations in complex data sets. 

2009

Bent E, Loffredo A, McKenry MV, Becker JO, and Borneman J. 2009. Fungal rRNA genes associated with biological suppression of Meloidogyne incognita in a California soil. Journal of Nematology (in press).

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 (in press). 

2008

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. 

2007

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. 

2006

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. Induction of beet-cyst nematode suppressiveness by Dactylella oviparasitica and Fusarium oxysporum in field microplots. 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.

2005

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.

2004

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 specific 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.

2003

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.

2002

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.

2001

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.

2000

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.

1999

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