Past Lab members

Post-doctoral fellows

Mike Doan
PhD Ecology, 2018
Post-doctoral fellow at the Sydney Institute of Marine Science (2018 – present)

My research focuses on the microbial communities that live on the skin of sharks. The shark species under investigation include common thresher sharks (Alopias vulpinus), whale sharks (Rhincodon typus), and leopard sharks (Triakis semifasciata). Sharks have a unique skin surface only found among the shark group that is covered by teeth-like structures call dermal denticles. The organized dermal denticle pattern of shark skin reduces fluid friction, a property that allows sharks to move with greater efficiency through the water; but this surface pattern also embodies characteristics that influence the settlement of small life forms, including bacteria. Some questions my work aims to address are 1) how is microbial community diversity distributed across shark species and 2) does microbial community diversity on the skin vary across gradients of spatial and temporal scales. My research interests center microbial community ecology, microbial biodiversity and ecosystem function.

Megan Morris
PhD Ecology

Megan is a Dinsdale Lab alum (2011-2018) and received her PhD in Ecology from the SDSU-UCDavis Joint Doctoral Program. While a student in the Dinsdale Lab, Megan was interested in using molecular tools to answer ecological questions on the diversity, structure, and function of microbial communities. Megan’s dissertation research focused on the microbial ecology of temperate kelp forest ecosystems, the temporal variability and the impact of environmental disturbance on microbiomes, and how microbial shifts may influence the kelp health. Last time we heard from Megan, she was a postdoc in the Fukami Lab at Stanford University.

Thiago Bruce
PhD Genetics

I am Post doc in the Dinsdale Lab. I was born in Brazil and have PhD in Genetics, Msc in Biotechnology and graduate in microbiology (2004). I have genuine interest in topics related to microbial molecular biology. I have been involved in research related to characterization and bioprospecting of microbial diversity. I had opportunity to handle with diverse approaches to characterize microbial communities from a variety of environments, searching for biocatalysts of industrial interest. Currently, I am involved with the Genotype to Phenotype Project. The lack of high-throughput phenotypic data is hindering our ability to describe the metabolic potential of microbes based on their genome annotation and our ability to predict gene complements from phenotypic analyses. The overall goal of this project is to improve our capability to reliably predict phenotype from genotype for microbial life across the bacterial kingdom. This project will result in genomic sequences, annotation and microbial metabolic models.

PhD students 

Matthew Haggerty
PhD Ecology, 2017
Microbiome consultant at USC

I am a PhD student in Ecology, I use metagenomics to identify differences in the composition of marine microbial communities in response to the environment. I have used sequence data to identify how microbial communities change with distance and environmental dissimilarity at a global scale. I have also applied these techniques to isolate potential super-heterotrophs implicated in coral reef decline and test the mechanisms regulating kelp decomposition.

 Archana Srinivas
PhD Ecology, 2016
Postdoctoral researcher at CSU Northridge

I am a doctoral candidate in the joint doctoral program in ecology hosted by San Diego State University and the University of California, Davis. My dissertation research is an investigation on the role played by siderophores (microbially synthesized iron chelating molecules) in dissimilatory iron reduction (DIR), which is a microbial anaerobic respiratory pathway, in Arctic tundra soils.

Graduate Students

Reema Maniyar
MS Bioinformatics and Medical Informatics, 2017

My research focuses on developing a pipeline to identify phycotidnaviruses from metagenomes.

Bhavya Nalagampalli Papudeshi
MS Bioinformatics and Medical Informatics, 2017
Bioinformatician at National Center for Genome Analysis Support

I am a Bioinformatics graduate student in Dinsdale lab. My research includes optimization of metagenome assembly and binning tools to reconstruct population genomes.

Kristen Aguinaldo
MS Ecology, 2017
Training team lead at Thermo Fisher Scientific

My research focused on Identification and genomic characterization of four novel Rhodobacteracae strains from the Point Loma kelp forest.

Jeremiah Minich
MS Cell and Molecular Biology, 2017
PhD student at UCSD

Research topic: Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption.

 Kevin Walsh
MS Ecology, 2017
Clinical Molecular Technologist at Tempus Inc.

 I have worked in the Dinsdale lab for 5 years working on a variety of metagenomic and sequencing projects. My research looks at benthic macro-organisms and how they interact with microbial communities in the water column on coral reefs, in particular reefs off the coast of North East Brazil.

Shashank Sathe
MS Bioinformatics and Medical Informatics, 2015
Staff bioinformatics analyst at UCSD

Research topic: The Minimalistic Approach of Plasmid Genomes and Identification of Plasmid Contigs From Within Bacterial Assemblies.

 Rohini Singh
MS Bioinformatics and Medical Informatics, 2015

My reseach focused on genome annotation of sea lion.

 Undergraduate Students

Felicia Miller
BS Biology, 2017
Graduate student at Moss landing marine laboratory

 I am currently working on a tide pool project where I am taking samples from two locations, Mission Beach and Ocean Beach. From each location I am taking samples from three different microhabitats, hermit crabs, algae, and the water column and I’ll plating each sample on three different carbon sources, erythritol, cellobiose, and aspartic acid.  My hypothesis is that the     microhabitats that I will sample from will determine the carbon usage rather    than the location, which will infer that the microbial community of each microhabitat is conserved.  I am working under a COAST grant that I was awarded in the fall of 2015.

Taylor Cram
BS Biology, 2017

I am currently working with microbial isolates that have been collected from La Jolla, Point Loma, Catalina, and San Diego Bay including both kelp and water samples. We will be plating the individual isolates on sodium alginate plate to see if the bacteria can use alginate as their carbon source.

Emma Bilings
BS Biology, 2017
Quality control Technician at Sekisui Diagnostics

Natalie Frixione
BS Biology, 2017

Alejandro Vega
BS Biology, 2016
Graduate student at UC Berkeley

 Since August 2015 I have been the lead researcher under the supervision of Dr. Rob Edwards and Dr. Elizabeth Dinsdale at San Diego State University (SDSU) on a global research project. We have been investigating a newly discovered bacteriophage known as crAssphage, which resides in roughly half the human population across the globe. In order to try to get a better understanding of crAssphage, I am studying the distribution and variance of crAssphage on a temporal and spatial scale. We are also attempting to look at the distribution of crAssphage on a global scale. So far we have contacted 22 potential collaborators to sequence crAssphage from around the globe. If you are interested in helping us out please email and

Mariah Foley
BS Biology, 2016
Graduate student at UC San Francisco

 Investigated the effect of ocean acidification on Rhodolith samples by decalcification techniques. Samples were previously collected, and exposed to varying pCO2 levels.

Ben Turner
BS Biology, 2015
PhD student at SDSU-UCSD

Taylor Dillon
BS Biology, 2018

I am an undergraduate studying Biology with an emphasis in Marine Biology and I have a minor in Sustainability at San Diego State University. I first peeked an interest in the marine sciences when I was hired on as a marine science instructor at the Mission Bay Aquatic Center. After a long summer of teaching children about marine life and conservation, I was hooked on the idea of becoming a marine biologist. After joining the Green Love club at SDSU, I have also found a love for sustainability and conservation. I’m really interested in how sustainable practices can better suit marine species, habitats, and ecosystems.  I am now a 5th year senior finishing up my undergraduate classes, volunteering, and getting ready for graduate school!

Dominic Cavalli
BS Biology, 2018

I am an undergraduate majoring in Biology with an emphasis in Cellular and Molecular Biology at San Diego State University. My interest in Marine Biology began in middle school when I competed in an ROV competition. From there I went to Monterey Academy of Oceanographic Science (MAOS) for high school. Currently I am working on project looking at the metabolic models of bacterial strains by testing bacterial usage of different carbon, nitrogen, phosphorus, and sulfur substrates.

 Visiting/Rotation students

 Amanda Alker

I am currently a first year PhD rotation student in the Cell and Molecular Biology (CMB) Joint Doctoral program (JDP) with San Diego State University (SDSU) and University of California San Diego (UCSD). Originally from Florida, most of my previous research incorporated the use of molecular techniques to address both coral and microbial ecology. I was recently awarded the Graduate Research Fellowship funded by the National Science Foundation (NSF), to investigate the underlying mechanisms associated with bacterially-induced metamorphosis in coral larvae. I plan to use metagenomics, comparative genomics, and transcriptomics to elucidate these bacterially-mediated cues.