People

The Deutschbauer lab develops new approaches for the rapid functional characterization of diverse microorganisms and applies these approaches for targeted applications including microbiome-mediated agricultural, environmental, and human health solutions. Our current work is focused on addressing a number of outstanding microbiology questions using large-scale genetics data and the concurrent development of new high-throughput approaches to rapidly, inexpensively, and flexibly characterize microbial genomes. We are using large-scale genetics data to systematically fill in unknown gaps in amino acid biosynthesis pathways, to identify new carbon catabolism pathways, and to identify genes involved in host interactions. On the technology side, we are developing parts-based, pooled strategies to test thousands of genetic systems in parallel against diverse microorganisms. Lastly, we are developing a next-generation platform of chemical libraries, robotic automation, and miniaturized growth assays to enable the rapid phenotypic characterization of microorganisms and microbiomes.

Full publication list:

https://scholar.google.com/citations?user=FRU1LksAAAAJ&hl=en

Liu H, Shiver AL, Price MN, Carlson HK, Trotter VV, Chen Y, Escalante V, Ray J, Hern KE, Petzold CJ, Turnbaugh PJ, Huang KC, Arkin AP, Deutschbauer AM. Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments. Cell Rep. 2021 Mar 2;34(9):108789. doi: 10.1016/j.celrep.2021.108789.  PMID: 33657378

Carim S, Azadeh AL, Kazakov AE, Price MN, Walian PJ, Lui LM, Nielsen TN, Chakraborty R, Deutschbauer AM, Mutalik VK, Arkin AP. Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins. ISME J. 2021 Mar 1. doi: 10.1038/s41396-021-00921-1. PMID: 33649553

Price MN, Deutschbauer AM, Arkin AP. Four families of folate-independent methionine synthases. PLoS Genet. 2021 Feb 3;17(2):e1009342. doi:10.1371/journal.pgen.1009342. eCollection 2021 Feb. PMID: 33534785

Carlson HK, Lui LM, Price MN, Kazakov AE, Carr AV, Kuehl JV, Owens TK, Nielsen T, Arkin AP, Deutschbauer AM. Selective carbon sources influence the end products of microbial nitrate respiration. ISME J. 2020 Aug;14(8):2034-2045. doi:10.1038/s41396-020-0666-7. PMID: 32372050

Helmann TC, Deutschbauer AM, Lindow SE. Genome-wide identification of Pseudomonas syringae genes required for fitness during colonization of the leaf surface and apoplast. Proc Natl Acad Sci U S A. 2019 Sep 17;116(38):18900-18910. doi:10.1073/pnas.1908858116. PMID: 31484768

Thompson MG, Blake-Hedges JM, Cruz-Morales P, Barajas JF, Curran SC, Eiben CB, Harris NC, Benites VT, Gin JW, Sharpless WA, Twigg FF, Skyrud W, Krishna RN, Pereira JH, Baidoo EEK, Petzold CJ, Adams PD, Arkin AP, Deutschbauer AM, Keasling JD. Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism. mBio. 2019 May 7;10(3). pii: e02577-18. doi: 10.1128/mBio.02577-18. PMID: 31064836

Price MN, Ray J, Iavarone AT, Carlson HK, Ryan EM, Malmstrom RR, Arkin AP, Deutschbauer AM. Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism.  mSystems. 2019 Feb 5;4(1). pii: e00297-18. doi: 10.1128/mSystems.00297-18. PMID: 30746495

Mutalik VK, Novichkov PS, Price MN, Owens TK, Callaghan M, Carim S, Deutschbauer AM, Arkin AP. Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria. Nat Commun. 2019 Jan 18;10(1):308. doi: 10.1038/s41467-018-08177-8. PMID: 30659179

Carlson HK, Price MN, Callaghan M, Aaring A, Chakraborty R, Liu H, Kuehl JV, Arkin AP, Deutschbauer AM. The selective pressures on the microbial community in a metal-contaminated aquifer. ISME J. 2019 Apr;13(4):937-949. doi:10.1038/s41396-018-0328-1. PMID:30523276

Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM. Mutant phenotypes for thousands of bacterial genes of unknown function. Nature. 2018 May;557(7706):503-509. doi:10.1038/s41586-018-0124-0. PMID: 29769716

Liu H, Price MN, Waters RJ, Ray J, Carlson HK, Lamson JS, Chakraborty R, Arkin AP, Deutschbauer AM. Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria. mSystems. 2018 Jan 16;3(1). pii: e00143-17. doi:10.1128/mSystems.00143-17. PMID: 29359196

Price MN, Zane GM, Kuehl JV, Melnyk RA, Wall JD, Deutschbauer AM, Arkin AP. Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. PLoS Genet. 2018 Jan 11;14(1):e1007147. doi:10.1371/journal.pgen.1007147. PMID: 29324779