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Our Team

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Frank Stewart

Associate Professor

Department of Microbiology and Immunology,

Montana State University

frank.stewart@montana.edu

Adjunct Professor, School of Biological Sciences,

Georgia Institute of Technology

frank.stewart@biology.gatech.edu

I am an environmental microbiologist interested in the dynamics of microbial systems.  My research is motivated by the beliefs that microbes are a frontier for natural history and scientific discovery, and that exploring this frontier is necessary and important for understanding biological diversity and its changing role in ecosystem processes. The first major research theme in my lab explores how aquatic microbes respond to environmental change, notably declines in ocean oxygen content.  The second major theme explores how life in symbiosis drives microbial evolution and ecology.  My research targets diverse systems, from the marine water column to the intestinal microbiomes of fishes.  This research aims to identify metabolic properties that underlie the ecology of microbes and microbe-host systems, the evolutionary context under which these functions arose, and the role of these functions in ecosystem-scale processes in a changing environment.  

 

I am an Associate Professor in the Department of Microbiology and Immunology at Montana State University and an Adjunct Professor in the School of Biological Sciences at Georgia Tech.  I received a B.A. in Biology from Middlebury College and a Ph.D. in Organismic and Evolutionary Biology from Harvard University.  I worked as a Postdoctoral Fellow at MIT for two years before moving to Georgia Tech in January 2011.  In February 2020, I moved my lab to the mountains of Montana.  My work has been recognized through an NSF CAREER award, a Sloan Research Fellowship, and a Simons Foundation Early Career investigator award.  

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Zoe Pratte

Senior Research Scientist 

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 am continuing 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.

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Anthony Bertagnolli

Senior Research Scientist 

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.

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Ana Gabriel Clavere Graciette

PhD Student 

Originally from France, I received an MS in Oceanography and Marine Environments from University Pierre and Marie Curie, characterizing the contribution of diazotroph derived nitrogen into the planktonic food web of the Southwest Pacific Ocean, in relation to diazotroph diversity. I am interested in how environmental change influences microbial communities in both host-associated and free living systems. In particular, I am exploring how spatial distribution and captivity affect microbial community assembly.

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Cameron Perry

PhD Student 

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 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.

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Graduate Students

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Andrew Maritan

PhD Student 

I am interested in how a host organism's biology is altered by its interactions with associated microbes. I am from Massachusetts and received my undergraduate degree in Biology from Middlebury College. 

 

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Undergraduate Students

Chloe Pryor

Georgia Institute of Technology

Dawson Hollingsworth

Oregon State University

Courtney Scott

Montana State University

Trisha Crowell

Montana State University

Cat Williams
Sweet Briar College

Collaborators 

Name/ Affiliation/ Project

Tom DiChristina

Georgia Tech

Biodiversity of Iron-Respiring Microorganisms (NSF Dimensions)

 

Al Dove

Georgia Aquarium

Marine microbiomes

 

Gustavia Evans

Georgia Tech

The Summer Workshop in Marine Science (SWiMS)

 

Jen Glass

Georgia Tech

Novel processes of anaerobic microbial methane oxidation (NSF BIO OCE, NASA)

 

Peter Girguis

Harvard University

OMZ methane cycling, deep-sea symbiont transcriptomics, in situ RNA sampler instrumentation

 

Mark Hay

Georgia Tech

Reef coral-microbiome-algae interactions

 

Kostas Konstantinidis

Georgia Tech

Single-cell genomics of OMZ bacteria (DOE CSP)

 

Nicole Lopanik

Georgia Tech

Computational analysis of metabolic pathway activity from RNA-seq data (NSF ABI)

 

Ion Mandoiu

University of Connecticut

Computational analysis of metabolic pathway activity from RNA-seq data (NSF ABI)

 

Koty Sharp

Roger Williams University

Microbiomes of facultatively symbiotic corals

 

Martial Taillefert

Georgia Tech

Biodiversity of Iron-Respiring Microorganisms (NSF Dimensions)

 

Bo Thamdrup

U. Southern Denmark

OMZ microbial biogeochemistry and novel processes of anaerobic methane oxidation (NSF BIO OCE, ERC)

 

Marion Usselman

Georgia Tech

The Summer Workshop in Marine Science (SWiMS)

Tanja Woyke

DOE Joint Genome Institute

Single-cell genomics of OMZ bacteria (DOE CSP)

 

Alex Zelikovsky

Georgia State

Computational analysis of metabolic pathway activity from RNA-seq data (NSF ABI)

Lab Alumni

Postdocs/Research Scientists

Nastassia Patin

Postdoc (2016-2019), Georgia Tech, project: “Metagenomics and bioinformatics of marine microbiomes”, Current: Postdoc, Atlantic Oceanic and Meteorological Laboratory, NOAA

Carlos Henríquez

Visiting scientist (2019), Universidad de Concepción, project: “Distribution, genomic potential and metatranscriptomic activity of bacteria from the genus Alteromonas in low oxygen waters”, Current: Principal researcher, Instituto Milenio de Oceangrafía, Chile

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, Georgia Institute of Technology - 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, Georgia Institute of Technology - School of Biological Sciences (in lab 2016-2019), thesis: “Microbiome Variation in wild vs. captive eagle rays (Aetobatus narinari)”

 

​Cory Padilla

Ph.D., 2017, Georgia Institute of Technology - 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, Georgia Institute of Technology - 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, Georgia Institute of Technology - 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

Undergraduate students

Jenn Crandall

Research Technician ETNP OMZ cruise (Dec 2020- Jan 2021), Middlebury College

Allie Caughman

Georgia Tech undergrad researcher (fall 2016-2020), project: “Determinants of microbiome diversity in reef fish” (supervised by Dr. Zoe Pratte)

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”