Gund Fellow, Assistant Professor, College of Engineering and Mathematical Sciences

Matthew J. Scarborough directs the Environmental Microbiome Engineering Research Group whose members study and develop microbial community based platforms to protect the environment and public health. Scarborough’s group aims to develop technologies for recovering valuable products from agricultural and municipal organic wastes. This work aims to provide additional revenue for farmers while reducing water and air pollution. Matthew's work encapsulates many scales, from studying the function of individual enzymes to implementing full-scale microbiome-based conversion platforms.

Scarborough previously worked for a large environmental consulting company as a water and wastewater engineer for 7 years and is a licensed professional engineer in Vermont.



  • Porterfield, K., Scarborough, M. Roy, E. 2023. Organics recycling tradeoffs: Biogas potential and microplastic content of mechanically depackaged food waste. ACS Sustainable Chemistry and Engineering. ttps:// [IF = 9.22]
  • Myers, K., Ingle, A., Walters, K., Fortney, N., Scarborough, M., Donohue, T., Noguera, D. 2023. Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization. Frontiers in Bioengineering and Biotechnology. 11. [IF = 5.66]
  • 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. [IF = 3.24]
  • Scarborough, MJ., Lawson, CE., DeCola, AC., Gois, IM. 2022. Microbiomes for sustainable biomanufacturing. Current Opionin in Micorbiology (65) 8. [IF = 7.93]
  • 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. [IF = 3.04]
  • 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.  [IF = 6.63]
  • 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. (Spotlight Selection) [IF = 4.02]
  • Scarborough, MJ., Lawson, CE., Hamilton, JJ., Donohue, TJ., Noguera, DR. 2018. Metatranscriptomic and thermodynamic insights into medium-chain fatty acid production. mSystems 3 (6) 00221-18. [Editor’s Pick] [IF = 6.60]
  • Scarborough, MJ., Lynch, G., Dickson, M., McGee, M., Donohue, T., Noguera, DR. 2018. Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production. Biotechnology for Biofuels 11 (1), 200. [IF = 5.45]
  • Hu, Y., Scarborough, M., Aquirre-Villega, H., Larson, R., Noguera, D., Zavala, V. 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), 6211 – 6222. [IF: 6.97]

Areas of Expertise and/or Research

Anaerobic digestion, bioprocessing, waste valorization, wastewater treatment, microbiomes, microbial ecology


  • PhD, Civil & Environmental Engineering, University of Wisconsin-Madison
  • BS, Civil Engineering, University of Wyoming


  • 802-656-2463
Office Location:

213E Votey