| Department of Microbiology

Work in the Ottesen lab seeks to understand the structure and function of complex microbial communities, and the ways in which microbes interact with and perceive complex environments. A major focus is the use of molecular ecological tools to observe microbial behavior in the environment. This includes not only observing and tracking changes in which microbes are present in an environment, but also using community transcriptomics to observe changes in microbial gene expression over time. By studying microbial behavior “in the wild”, we hope to gain a better understanding of the roles and significance of diverse members of the uncultured microbial majority.

Host and microbial contributions to microbiome stability and dynamics

We (and most other higher organisms) are hosts to complex gut microbial communities that aid in digestion and help shape our overall health. We are using the American cockroach (Periplaneta americana) and its gut microbiome as a model system to understand gut microbiome stability and dynamics, particularly responses to dietary perturbation. We use the cockroach as a model host organism because they are robust, low-maintenance insects that reproduce quickly, eat a diverse, omnivorous diet, and their digestive tract hosts a highly diverse gut microbiome dominated by bacterial families found in the guts of many other animals, including mammals and humans.

Interestingly, we have found that despite its diversity, the cockroach gut microbiome is highly robust to diet shifts. This makes them an ideal system for understanding host and microbial factors driving gut microbiome stability and resilience. We are now working to understand how the host and microbes work together to maintain this stability. We have established methods for metatranscriptomic and metagenomic investigation of cockroach gut microbiome composition and activity. We have also established a robust system for producing and maintaining gnotobiotic cockroaches in the lab, enabling us to conduct experiments featuring gnoto- and xeno-biotic insects to continue investigating gut community dynamics in the cockroach host.

Understanding the assembly and ecological roles of stream and river microbial communities.

Streams and rivers play key roles in global biogeochemical cycles and act as the major conduits for the movement of carbon and nutrients between land and sea. We are exploring how streamwater microbial communities form and how this process is influenced by human impacts on the stream and the surrounding landscape.

Read more about Ottesen

Jonathan Frye

Adjunct Research Microbiologist

Our laboratory investigates antibiotic resistance, pathogenicity, genomics, and the evolution of Salmonella enterica. Salmonella is one of the most prevalent foodborne pathogens globally and is estimated to cause over one million infections in the U.S. each year. Antimicrobial resistance is also common in Salmonella and has been increasing over the past few decades. We have pioneered the application of microarrays, next-generation sequencing, and other innovative methods for investigating Salmonella. These studies identified IncA/C and other plasmids that are responsible for much of the multi drug resistance (MDR) in Salmonella isolated from food animals. These plasmids are large (100-250kb), can encode resistance to twelve or more antimicrobials, and are self-transmissible. Our current studies have determined that the resistance genes found in Salmonella isolated from food animals, retail meats, and human infections are genetically similar indicating that some MDR Salmonella likely developed in animals and were transmitted to humans via food. New studies will test this hypothesis and identify points in food production where antimicrobial resistance develops that can be targeted to improve food safety.

Our laboratory’s genomic analysis projects identified genes found in different Salmonella serovars that are responsible for their variability in host range and pathogenicity. We developed assays based on these genetic differences to detect dangerous Salmonella serovars such as Heidelberg and Typhimurium in food. We have also used this data to develop an automated, high-throughput PCR and capillary analysis technique to identify the top 100 clinical Salmonella serotypes (SMART: Salmonella multiplex assay for rapid typing). Testing has shown that SMART is more accurate, easier, quicker, and cheaper than traditional serotyping. Our ongoing investigation of Salmonella genomics has completed the sequencing of 200 Salmonella genomes that represent the genetic diversity found in the most prevalent clinical Salmonella serovars. Our laboratory’s new studies use this database to improve our understanding of Salmonella evolution and enable us to identify genetic markers for pathogenicity, host range, and host specificity. These markers will be used to develop rapid methods for Salmonella outbreak investigations and improve our ability to protect human health. Recently we have expanded our work to address a major data gap by determining what role surface water plays in the development of antimicrobial resistance in bacteria and its spread to humans and animals. This work is a collaboration with Dr. Elizabeth Ottesen, Dr. Erin Lipp., and Dr. Charlene Jackson. Together we are working with the Upper Oconee River Watershed Network (UWON), a group of volunteers that do a quarterly evaluation of the surface waters that feed the Oconee River. We have been sampling the water with their help since Winter of 2015. While Dr. Ottesen focuses on the metagenome of the watershed and Dr. Lipp looks at the ecology of the watershed, Dr. Jackson and I are isolating bacteria, investigating their prevalence, antimicrobial resistance, and genotypes. Our current work is looking at Salmonella, Escherichia coli, and Enterococcus spp. Together we hope to get a comprehensive picture of what is in the watershed and how it changes over time.

Education:

Ph.D. in Microbiology, University of Georgia (2000)
B.S. in Biology, East Carolina University (1993)

Research

Research Areas:

Bioinformatics and -omics/Computational Biology

Microbe-Host Interactions

Microbial Ecology

Labs (via personnel):

Jonathan Frye

Labs:

Frye

Read more about Jonathan Frye

Mark A. Eiteman

Adjunct Professor

Education:

Undergrad: B.S., Chemical Engineering, Summa cum laude, Virginia Tech, 1986

Graduate work: M.S., Chemical Engineering, University of Virginia, 1988

Ph.D., Chemical Engineering, University of Virginia, 1991

Research

Research Areas:

Applied Microbiology and Biotechnology

Microbial Physiology

Research Interests:

The research interests of Mark A. Eiteman are in fermentation and biotechnology with emphasis on microbial processes to generate fuels and chemicals. He has special interests in nutrient-limited processes, which can be used very effectively to drive a metabolic network toward a particular biochemical product. Dr. Eiteman focuses on central metabolism and the effect of redox constraints: genetic perturbations and operational conditions have a significant impact on the balance of NAD(P)H/NAD(P) available to direct central metabolites to the biochemical product of interest. While much current research elsewhere typically focuses on synthetic biology at the small scale, Dr. Eiteman’s work additionally transitions small scale results into bioprocess operations, involving scale-up to a controlled bioreactor. By working at the interface of synthetic biology and fermentation process design, Dr. Eiteman’s work uniquely allows process conditions to inform the desirable metabolic engineering strategy needed, and vice versa. Recent work has included a variety of products from central metabolism such as citramalic acid, succinic acid, lactic acid, pyruvic acid and 5-aminolevulinic acid, as well as glycosylated small molecules and rare sugars. Dr. Eiteman also has a continued interest in biological approaches to other problems, such as methods to convert effectively into products the sugar mixtures found in lignocellulosic hydrolysates, and the process of adaptive evolution.

Dr. Eiteman regularly teaches senior-level and graduate-level courses in biochemical engineering (ENGR4510/6510) and bioseparations (ENGR4520/6520). Dr. Eiteman also serves as an instructor for Fermentation Engineering Laboratory (BCHE8210) presenting advanced fermentation principles coupled with design of experiments and interpretation of results.

Selected Publications

Selected Publications:

https://scholar.google.com/citations?user=VeldEEEAAAAJ&hl=en&oi=sra

Of note:

Editorial Board, Applied and Environmental Microbiology (2016-)

President, Institute of Biological Engineering (2019-2020)