Assistant Professor

Dr. Scarborough's research focuses on the application of microbiomes (aka, microbial communities) to protect the natural environment and public health. He currently focuses on management of wastes from agricultural processes with the goal of harnessing microbiomes to convert renewable feedstocks to valuable products. This work aims to provide additional revenue for farmers while reducing water and air pollution. Dr. Scarborough's work encapsulates many scales, from studying the function of individual enzymes to implementing full-scale microbiome-based conversion platforms.

Dr. Scarborough earned his Ph.D. from the University of Wisconsin - Madison where he worked as part of the Great Lakes Bioenergy Research Center. He previously worked for a large environmental consulting company as a wastewater engineer and is a licensed professional engineer in Vermont. In addition to conducting environmental engineering research, Dr. Scarborough uses a teaching-as-research framework to assess teaching practices and develop learner-centered courses.


Scarborough, MJ., Myers, KS., Fortney, NW., Ingle, AT., Donohue, TJ., Noguera, DR. 2022. Metagenome-assembled genomes from a microbiome converting xylose to medium-chain carboxylic acids. Microbiology Resource Announcements 11(4): e0115121.
Neher, D., Harris, J., Horner, C., Scarborough, M. Badireddy, R., Faulkner, J., White, A., Darby, H., Farley, J., Von-Wettberg, E. 2022. Resilient Soils for Resilient Farms: An Integrative Approach to Assess, Promote and Value Soil Health for Small- and Medium-Size Farms. Phytobiomes.

Scarborough, MJ., Lawson, CE., DeCola, AC., Gois, IM. 2022. Microbiomes for sustainable biomanufacturing. Current Opionin in Micorbiology (65) 8.

Stamatopoulou, P., Malkowski, J.*, Conrado, L., Brown, K.*, Scarborough, M. 2020. Fermentation of Organic Residues to Beneficial Chemicals: A Review of Medium-Chain Fatty Acid Production. Processes 8(12), 1571.

Scarborough, MJ., Hamilton, JJ., Erb, EE., Donohue, TJ., Noguera, DR. 2020. Diagnosing and predicting mixed culture fermentations with unicellular and guild-based metabolic models. mSystems 5:e00755- 20.

Scarborough, MJ., Meyers, KM., Donohue, TJ., Noguera, DR. 2020. Multi-omic analysis of medium-chain fatty acid synthesis by Candidatus Pseudoramibacter fermentans, sp. nov., and Candidatus Weimeria bifida, gen. nov., sp. nov.. Applied and Environmental Microbiology 10.1128/AEM.02242-19.

Scarborough MJ, Lawson CE, Hamilton JJ, Donohue TJ, Noguera DR. 2018. Metatranscriptomic and thermodynamic insights into medium-chain fatty acid
production using an anaerobic microbiome. mSystems 3:e00221-18.

Scarborough, M. J., Lynch, G., Dickson, M., McGee, M., Donohue, T. J., &
Noguera, D. R. 2018. Increasing the economic value of lignocellulosic
stillage through medium-chain fatty acid production. Biotechnology for
Biofuels, 11(1), 200. doi:10.1186/s13068-018-1193-x

Y Hu, M Scarborough, H Aguirre-Villegas, RA Larson, DR Noguera. 2018. A
Supply Chain Framework for the Analysis of the Recovery of Biogas and Fatty
Acids from Organic Waste. ACS Sustainable Chemistry & Engineering 6 (5),

Keene, N. A., Reusser, S. R., Scarborough, M. J., Grooms, A. L., Seib, M.,
Santo Domingo, J., & Noguera, D. R. 2017. Pilot plant demonstration of stable
and efficient high rate biological nutrient removal with low dissolved oxygen
conditions. Water Res, 121, 72-85. doi:10.1016/j.watres.2017.05.029

Burger, B. T., Imam, S., Scarborough, M. J., Noguera, D. R., & Donohue, T. J.
2017. Combining Genome-Scale Experimental and Computational Methods To
Identify Essential Genes in Rhodobacter sphaeroides. mSystems, 2(3).

Areas of Expertise and/or Research

Biological Wastewater Treatment, Anaerobic Bioprocessing of Wastes, Microbiome Engineering, Modeling of Microbiomes


  • Ph.D., University of Wisconsin - Madison
  • B.S., University of Wyoming


  • 802-656-2463
Office Location:

Votey 213D

  1. Lab Website

Courses Taught

  • CE 151 Water and Wastewater Engineering
  • CE 256 Biological Processes for Water and Wastewater Treatment
  • CE 247 Sustainable Resource Recovery Design
  • CE 395 Special Topics: Multi-scale Modeling of Biological Processes