Summer 2018
Frank Stewart
Associate Professor
Associate Director, Center for Microbial Dynamics and Infection
School of Biological Sciences, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1242
frank.stewart@biology.gatech.edu
Curriculum Vitae
Post-Docs
Anthony Bertagnolli
School of Biological Sciences, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1120
My primary research interests surround the impact of lithotrophic microbes on oceanic and atmospheric chemistry. I’m specifically interested in the diversity, activity, and abundance of microorganisms involved in methane and ammonia oxidation and how these organisms are impacted by dissolved oxygen. To understand these populations, a combination of culture independent molecular approaches, culture dependent enrichment approaches, and process based rate estimates will be applied to water-column and sediment samples from differing oxygen minimum zone regimes.
Nastassia Patin
School of Biological Sciences, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1124
www.nastassiavpatin.com
nastassia.patin@biosci.gatech.edu
I received my Ph.D. from Scripps Institution of Oceanography at UC San Diego, where I studied the chemical ecology of marine actinomycete bacteria. As a postdoc in the Stewart Lab I am using metagenomics and metatranscriptomics to understand how marine microbiomes affect ecosystem function and respond to perturbations. My study systems include the Georgia Aquarium’s Ocean Voyager exhibit, the bryozoan Bugula neritina, the red tide dinoflagellate Karenia brevis, and blue hole formations in the Gulf of Mexico.
Zoe Pratte
School of Biological Sciences, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1124
zoe.pratte@biology.gatech.edu
I received my Ph.D. from Florida International University, examining bleaching and disease susceptibilities of two closely related brain corals. For my Ph.D. investigations, I used a combination of microscopy, coral transcriptomics, and bacterial 16S rRNA metagenomics. In this lab, I plan to continue my work with bacterial metagenomics, exploring how gut microbiome communities differ in diversity and function among species and families of marine fish. Future investigations will elucidate how differences in fish microbiome communities affect the ecological behavior and health of fishes.
Graduate Students
Cameron Perry
School of Biological Sciences, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1124
cperry60@gatech.edu
I received a joint MS in Marine Biology and Coastal Zone Management from Nova Southeastern University, examining age and growth from non-invasive measurements of free-swimming whale sharks in the South Ari Atoll, Maldives. Currently, I am a PhD candidate in the Stewart lab working on a collaborative project with Dr. Al Dove from Georgia Aquarium investigating an aggregation of whale sharks at St. Helena in the South Central Atlantic. This project aims to investigate the habitat usage of whale sharks around the island as well as to categorize the microbiome of the large mature individuals in these waters. I am broadly interested in life history, population demographics, and movement ecology as well as understanding how the microbiome plays a role in ecology, health and behavior.
Ana Gabriel Clavere Graciette
School of Biological Sciences, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1124
aclavere@gatech.edu
Coming from a background in biogeochemistry, I am broadly interested in how microbes are influenced and contribute to nutrient cycling in the ocean. Currently, I am trying to better characterize the archaeal diversity in sediments from the Gulf of Mexico, where differences in chemistry affect the diversity of microbes associated with nitrogen and manganese cycling. In the future, I would like to further explore marine microbial diversity and function, including microbe-host interactions.
Undergraduate Students
Allie Caughman
Georgia Tech undergrad researcher (fall 2016-present), project: “Determinants of microbiome diversity in reef fish” (supervised by Dr. Zoe Pratte)
Collaborators
Name
Affiliation
Project
Harvard University
OMZ methane cycling, deep-sea symbiont transcriptomics, in situ RNA sampler instrumentation
Georgia Tech
Computational analysis of metabolic pathway activity from RNA-seq data (NSF ABI)
University of Connecticut
Computational analysis of metabolic pathway activity from RNA-seq data (NSF ABI)
U. Southern Denmark
OMZ microbial biogeochemistry and novel processes of anaerobic methane oxidation (NSF BIO OCE, ERC)
Georgia State
Computational analysis of metabolic pathway activity from RNA-seq data (NSF ABI)
Lab Alumni
Postdocs/Research Scientists
Andrew Burns
Postdoc (2015-2018), Georgia Tech, project: “Microbial ecology of thiol-driven iron reduction”, Current: research scientist, Hay lab (Georgia Tech)
Neha Sarode
Postdoc (2012-2016), Georgia Tech, project: “Microbial ecology of oxygen minimum zones”, Current: research associate at Harvard
Jieying Wu
Postdoc (2014-2016), Georgia Tech, project: “Metagenomic and genomic analysis of novel anaerobic bacteria from marine environments”
Sherry Seston
Visiting Professor (2013), Alverno College, project: “Comparative metatranscriptomic analysis of Ifremeria nautilei endosymbionts in multiple individuals under different electron donating conditions”
Alejandro Caro-Quintero
Postdoc (2013), Georgia Tech, project: “Metagenomics of the Gulf of Mexico hypoxic zone”
Graduate students
Sangita Ganesh
Ph.D., 2016, School of Biological Sciences (in lab 2011-2016), thesis: “Environmental niche partitioning of microbial community genomic diversity, gene expression, and metabolism in a marine oxygen minimum zone”, current: genomics researcher at Radiant Genomics
Mary Beth McWhirt
M.S., 2019, School of Biological Sciences (in lab 2016-2019), thesis: “Microbiome Variation in wild vs. captive eagle rays (Aetobatus narinari)”
Cory Padilla
Ph.D., 2017, School of Biological Sciences (in lab 2012-2017), thesis: “Unrecognized diversity of microbes linking methanotrophy to nitrogen loss in marine oxygen minimum zones”, current: genomics scientist at Dovetail Genomics
Piyush Ranjan
M.S., 2018, School of Biological Sciences (in lab 2014-2018), thesis: “Applied bioinformatics for exploring diversity patterns in meta-omic data”, current: Bioinformaticist, Michigan Medicine
Darren Joshua Parris
Ph.D., 2018, School of Biological Sciences (in lab 2012-2018, first as a research scientist, then as a student), thesis: “Microbiome community change in the guts of marine fish: Feeding and life stage transition as significant organizing factors”, current: postdoc, USDA; Athens, Georgia
Undergraduates
Zoe Dietrich
ACE REU undergrad (2019), Bowdoin College, project: “Water column and sediment microbial ecology of a West Florida Shelf blue hole”
Nigel Blackwood
U. Penn undergrad (summer intern, 2018), U. Pennsylvania, project: “Metagenomic analysis: evidence for the use of alternative nitrogen substrates by anammox bacteria”
Micayla Cochran
High school intern/rising Vanderbilt undergrad (summer intern, 2018), project: “Marine fish microbiomes”
Claire Garfield
ACE REU undergrad (2018), Stony Brook University, project: “Drivers of microbial community composition and metabolite profiles during a Karenia brevis bloom”
Amelia Barber
ACE REU undergrad (2017), University of North Carolina, project: “The effect of host genetics on the gut microbiome of African Cichlid fish”
Alex Price
Georgia Tech undergrad (in lab 2016-2017), independent research: “Microbial community diversity linked to chemical gradients in marine sediments”
Casey Smith
Georgia Tech undergrad (in lab 2016-2017), independent research: “Clownfish microbiome diversity in response to astaxanthin enrichment in diet”
Rebecca Hollman
Georgia Tech undergrad (in lab 2016), independent research: “Phylogenetic and diet determinants of microbiome diversity in diverse reef fish of Moorea”
Max Beecroft
Georgia Tech undergrad (in lab 2016), independent research: “Cichlid gut microbiome not dependent on diet”
Michael Morgan
Georgia Tech undergrad (in lab 2014-2016), independent research: “Determinants of gut microbiome diversity in reef fish”
Shelby Gantt
Georgia Tech undergrad (in lab 2014-2016), BIOL 4690 manuscript (2016): “Effects on the Pocillopora verrucosa microbiome when in contact with macroalgae under ocean acidification”
Natalie Moise
Georgia Tech undergrad – Sustainable Aquatics internship program, BIOL 4690 manuscript (2015): “Gut microbiome diversity shifts during development in the clownfish Amphiprion ocellaris”
Alex Huhman
Georgia Tech undergrad (in lab 2014-2015), BIOL 4690 manuscript (2015): “Variation in the gut microbiota diversity across subregions of the lionfish gastrointestinal tract”
Ben Stone
ACE REU undergrad (2015), Bowdoin College, project: “Quantitative gene analysis indicates dominance of SAR11 narG in a marine oxygen minimum zone”
Catherine Benson
ACE REU undergrad (2014), Middlebury College, project: “Methane cycling microorganisms in the Eastern Tropical North Pacific oxygen minimum zone”
Jack Cartee
Georgia Tech undergrad, senior thesis (2014): “Significant changes in microbial community composition in the Gulf of Mexico ‘dead zone’ over a diel cycle”
Abigail Shockey
Georgia Tech undergrad, senior thesis (2014): “The effects of variation in electron donor concentration and species on deep-sea endosymbiont community composition and gene expression”
Niko Alexandre
ACE REU undergrad (2012), Vassar College, project: “Effects of salinity changes on coastal water column microbial communities”
Sarah York
ACE REU undergrad (2011), U. Miami, project: “Development of new water contamination assessment tests for Escherichia coli”