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.
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).
This image originally appeared in the Hartford Courant.
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. 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. 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
Add your name to this list by emailing DOMResearch@emory.edu.
Projects usually fall into three phases: 1. Planning, 2. Sampling & Sequencing and 3. Data analysis.
Each phase may include the following steps:
• 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
• 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
- Emory Integrated Genome Core: Has both microbiome DNA extraction and high-throughput sequencing technologies. See also: webinar highlighting resources available from this core.
- NIH Human Microbiome Website
- The Microbiome Project
- Human Microbiome sample preparation protocol (PDF)
- American Gut
- MOTHUR free analysis software
- QIIME (pronounced “chime”) Free analysis software
- MG-RAST: Free micro biome analysis web server
- Phyloseq R package for post-OTU assignment
Please send any questions or comments about this website to firstname.lastname@example.org.
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