What does it mean to be specialized for a certain diet? The relationship between diet, genetics, and animal health
I defended my PhD dissertation in August 2023. The goals of my dissertation research were the following:
1) To determine how dietary shifts can affect the gene expression of prickleback fishes with different natural diets: can specialists broaden their resource base in response to changing environmental conditions and different diets? (Herrera, M.J., J. Heras, D.P. German 2022)
2) By integrating transcriptomics and the gut microbiome, I am examining how dietary changes impact Cebidichthys violaceus, an herbivorous fish with an active microbial community in its hindgut.
3) By utilizing the unique prickleback fish system, I am investigating the gut microbiome within the context of environment, diet, and genetics by first, comparing wild prickleback fish with fishes fed different diets in the lab, and second, comparing closely-related, sympatric species across different geographical locations along the California coast.
4) In a collaborative internship project with San Diego Zoo Wildlife Alliance that applies the skills I have gained in my graduate research to wildlife conservation efforts, we are evaluating the use of fecal microbiota transplantations to ameliorate chronic gastrointestinal imbalance in greater one-horned rhinoceros (Rhinoceros unicornis) by examining shifts in the microbiota and metabolome.
1) To determine how dietary shifts can affect the gene expression of prickleback fishes with different natural diets: can specialists broaden their resource base in response to changing environmental conditions and different diets? (Herrera, M.J., J. Heras, D.P. German 2022)
2) By integrating transcriptomics and the gut microbiome, I am examining how dietary changes impact Cebidichthys violaceus, an herbivorous fish with an active microbial community in its hindgut.
3) By utilizing the unique prickleback fish system, I am investigating the gut microbiome within the context of environment, diet, and genetics by first, comparing wild prickleback fish with fishes fed different diets in the lab, and second, comparing closely-related, sympatric species across different geographical locations along the California coast.
4) In a collaborative internship project with San Diego Zoo Wildlife Alliance that applies the skills I have gained in my graduate research to wildlife conservation efforts, we are evaluating the use of fecal microbiota transplantations to ameliorate chronic gastrointestinal imbalance in greater one-horned rhinoceros (Rhinoceros unicornis) by examining shifts in the microbiota and metabolome.
Additional Research as an Undergraduate Researcher
Digestive Specialization in Prickleback Fishes: Molecular Underpinnings
and Potential for Plasticity
As an REU fellow (Blinks-NSF REU-BEACON Internship Program) at University of Washington’s Friday Harbor Laboratory, I investigated the digestive specialization of prickleback fishes, with Dr. German as my mentor. My REU transitioned me into a larger undergraduate research project in Dr. German's lab. I investigated the digestive specialization of prickleback fishes (Family Stichaeidae) to provide insight into how vertebrates specialize to use specific resources, and how plastic the digestive system can be by conducting tests spanning from the molecular to whole organism level. My REU with Dr. German was a life-changing experience. Dr. German’s dedication to help me grow as a scientist encouraged me to apply for graduate school in the Department of Ecology and Evolutionary Biology at UCI, with Dr. German as my advisor.
Phylogenetics of Prickleback Fishes in the Family Stichaeidae
During my first year as an undergraduate researcher in the German lab, I focused on building a robust phylogeny for prickleback fishes (Family Stichaeidae), which are a model system for understanding the evolution of dietary specialization in vertebrates. I sequenced fragments of the genes for bone morphogenetic protein 4 (bmp4) and cytochrome c oxidase subunit 1 (Co-1) in prickleback fishes. The resultant tree, especially when combined with previously sequenced genes for 16S, cytb, and tmo4c4, was useful in calling out species and identifying the structure of the family Stichaeidae. A robust phylogeny is needed for prickleback fishes because they are a model for understanding the evolution of dietary specialization in vertebrates.
Aeromonas spp. from Environmental Waters are Resistant to Beta-Lactam Antibiotics
As an undergraduate in Dr. Luis Mota-Bravo's lab, I studied antibiotic resistance in aquatic environments. Specifically, I studied the gram-negative Aeromonas species from the family Aeromonadaceae, which occurs ubiquitously in aquatic environments. Of critical concern is when the Aeromonas spp. becomes resistant to extended-spectrum beta-lactam antibiotics. The aim of this study was to assess the presence of beta-lactam resistance in Aeromonas spp. from aquatic environments as well as to detect the occurrence of extended-spectrum beta-lactamases (ESBLs) and extended-spectrum cephalosporin AmpC beta-lactamases in Aeromonas spp..