Microbiome

Welcome to Emory Microbiome Group page. This site aims to provide some basic information about resources available for microbiome projects at Emory, as well as information about seminars, courses and faculty interested in this area. The microbiome group also runs an informal research in progress seminar. 

What is the Microbiome?

The microbiome is the community of bacteria, viruses, fungi and protests associated with a particular ecological niche, such as soil or the human gut.  The microbiome is generally studied using high-throughput sequencing technologies, either through PCR amplification of conserved regions (commonly the bacterial 16S gene)  or random shotgun approaches.  

There is enormous interest in associating the composition of the microbiome with many aspects of human health (including diabetes, obesity, infectious disease, antibiotic overuse, cancer, to name a few).  

microbiome
This image originally appeared in the Hartford Courant.

Who is Running Microbiome Projects at Emory?

Dr. Timothy Read
Associate Professor, Emory Department of Medicine
My lab is interested in relating pathogen population genome diversity to niche within the microbiome. I collaborate on several ongoing micro biome sequencing projects at Emory. Lab Site | Contact
Click here to read one of Dr. Read's recent studies

Dr. Elizabeth Corwin and Dr. Anne Dunlop
Dual-PI’s of an NIH-funded R01 examining ‘Biobehavioral Determinants of the Microbiome and Preterm Birth in African American Women’ in which we are examining how stress, diet, and health behaviors influence the oral, vaginal, and gut microbiome during pregnancy and, in turn, how the microbiome impacts the risk of preterm birth. | Contact Dr. Corwin or Dr. Dunlop

Dr. Glen Satten
Senior Statistician at CDC
Adjunct Professor of Human Genetics and Biostatistics at Emory
Conducts research on statistical methods for analyzing data from microbiome studies. | Contact

Dr. Roberto Pacifici
Garland Herndon Professor of Medicine and Director, Division of Endocrinology, Metabolism and Lipids | Contact

Dr. Jennifer Mulle
Assistant Professor, Department of Epidemiology, Rollins School of Public Health Department of Human Genetics, School of Medicine
I work on analysis of human microbiome data as it relates to a range of health outcomes and disease measures. | Contact

Dr. Michael Zwick
Assistant Vice President for Research, Woodruff Health Sciences Center
Associate Professor of Human Genetics and Pediatrics; Assistant Dean of Research, Emory University School of Medicine
Scientific Director, Emory Integrated Genomics Core (EIGC)
The EIGC offers computational analysis services. | Contact

Dr. Colleen Kraft
Assistant Professor of Medicine (Infectious Diseases) and Pathology & Laboratory Medicine
Program Director, Medical Microbiology
Medical Director, Microbiology Laboratory
Known for her work on fecal transplant. | Contact

Dr. Andrew Neish
Professor of Pathology & Laboratory Medicine
His laboratory studies how interactions with bacteria contribute to intestinal epithelial integrity and healing. | Contact

Dr. Rheinallt Jones
Assistant Professor, Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine
Establishing a gnotobiotic mouse facility for his research into the influences of the microbiome on host physiology. | Contact

Dr. Karen Levy
Assistant Professor, Department of Enviornmental Health, Rollins School of Public Health
Engaging with international partners and contributing to large-scale microbiome studies. | Contact

Dr. Joanna Goldberg and Dr. Arlene Stecenko
They are studying the lung microbiome in connection with cystic fibrosis-related diabetes. | Contact Dr. Goldberg or Dr. Stecenko

Add your name to this list by emailing DOMResearch@emory.edu.

Checklist for a New Microbiome Sequencing Project

Projects usually fall into three phases: 1. Planning, 2. Sampling & Sequencing and 3. Data analysis.  

Each phase may include the following steps:

1. Planning

• Decide whether the project theme is discovery based or hypothesis driven
• Decide what sample metadata to collect (e.g clinical information ,location) and how it will be stored.
• Begin to obtain research compliances and approvals for human and animal use, biosafety, etc. (Visit this handy Hitchhiker's Guide.)
• Decide whether to use an amplicon based sequencing (e.g. 16S) or shotgun metagenomics approach
• How much sequence data per sample (this will depend on the sample type, sequence technology, aims of experiment, budget)
• Consider which sequencing technology is most appropriate and which software will likely be used for analysis
• Plan logistics of sample extraction and storage.
• Perform power calculations to estimate the number of samples necessary to achieve stated objectives
• Develop budget. Costs can  include  sampling & DNA extraction supplies, sequencing, sample and DNA storage, data storage and processing, labor for taking samples, DNA extraction and sequencing, data analysis

2. Sampling & Sequencing

• Collect samples
• Store before DNA extraction, if necessary
• DNA extraction
• Sequencing
• Long term storage of DNA and/or samples post-sequencing

3. Data analysis

• Sequence quality assessment
• Human sequence removal (if necessary)
• Data analysis pipeline (operational taxonomic unit assignment, metabolic reconstruction etc) OTU definition
• Exploratory data analysis
• Inferential analysis
• Hypothesis testing
• Public database submission
• Long term data storage
• Manuscript writing

Download this checklist as a PDF.

Additional Resources

Recent Publications by Microbiome faculty

Contact Us or Join Listserv

Please send any questions or comments about this website to domresearch@emory.edu.

This site is run by:

  • Timothy Read, PhD
    Associate Professor of Medicine (Infectious Diseases)
  • Colleen Kraft, MD
    Assistant Professor of Medicine (Infectious
    Diseases) and Pathology & Laboratory Medicine 
  • Andrew Neish, MD
    Professor of Pathology & Laboratory Medicine

Join the Microbiome E-mail Listserv

Microbiome Calendar