College of Agriculture & Natural Resources

Lab website: 

• Shade Lab website

Biography:

Dr. Ashley Shade received her Ph.D. from the University of Wisconsin Microbiology Doctoral Training Program in 2010, and afterwards was a Gordon and Betty Moore Foundation postdoctoral fellow of the Life Sciences Research Foundation at Yale University. In 2014, she started her position in the Department of Microbiology and Molecular Genetics at Michigan State University. Her research interests concern the microbial ecology of environmental systems, including plants, soils, and their feedbacks. She applies an ecological approach to understand how microbial communities respond to stressors, and what determines their resilience as a system. Her lab employs ‘omics tools (metagenomics, metatranscriptomics, exometabolomics) with both field and laboratory studies. ShadeLab phytobiome research is focused on common dry bean, a legume important for human and livestock nutrition, and switchgrass, a biofuel feedstock.  Shade is an advocate of reproducible research and open science, and her lab’s analysis workflows are on GitHub. In addition, Shade has developed a popular workshop on microbial metagenome analysis. She is a member of the Earth Microbiome Project  and the International Society for Microbial Ecology, and serves as an editor at the American Society for Microbiology journal mSystems.

General areas of expertise:

Microbial ecology and evolution, environmental microbiology, macroecology applied to microbial systems, community dynamics, microbial diversity

Research:  We want to understand how microbiomes respond to stress so that we can manage them to be stable and resilient.  We apply methods in environmental microbiology, molecular biology, and quantitative meta 'omics (metagenomics, transcriptomics, metabolomics) to investigate the ecology of microbiomes and understand their functions.  We are interested in the consequences of diversity for microbiome stability, how the interactions among microbiome members and their host impact community functions.  We currently pursue research focused on plant-associated microbiomes (rhizosphere and phyllosphere), soils impacted by a severe long-term stressor (Centralia coal mine fire), and member interactions within synthetic microbial communities.  

Publications:

• Refer to Google Scholar
  
  

Web Sites of interest:

• ShadeLab GitHub site, for all statistical and bioinformatic analysis and code: https://github.com/ShadeLab
• EDAMAME course materials:  http://www.edamamecourse.org/

Courses Taught:

• Microbial Ecology MMG 425
• Statistical Analysis of Microbiomes MMG 991 Sec 003
• EDAMAME workshop in microbial metagenomics