By: Connie Rojas, PhD Candidate at Michigan State University
It has been a year of traveling! Earlier this year, I traveled to the Masai Mara National Reserve, Kenya (MMNR) to conduct my field work, and currently, I am in Mexico City doing a visiting scholarship at the Universidad Nacional Autonoma de Mexico (UNAM)! In between, I visited UC Berkeley for the 2018 Science and Technology Centers (STC) Director’s Meeting and San Antonio, TX for the Society for the Advancement of Chicanos/Hispanics and Native Americans in Science (SACNAS) annual conference, where I shared recent research findings as part of a symposium with other BEACONITES. I am extremely grateful that my dissertation research on host-microbe interactions and the spotted hyena (Crocuta crocuta) microbiome has a strong field, laboratory, and computational component that allows me to travel and work with different collaborators!
I am a 4th year PhD Candidate in Dr. Kay Holekamp’s behavioral ecology laboratory at Michigan State University, in the Department of Integrative Biology and the Ecology, Evolutionary Biology, and Behavior program (EEBB). For my dissertation research, I am using next-generation sequencing technologies to assess how microbes and host-associated microbial communities (‘microbiome’) affect their host’s physiology, fitness, and behavior, and how host themselves, are influencing their microbiomes. I study these questions in a wild population of spotted hyenas. Hyenas are highly social carnivores and apex predators inhabiting much of Sub-Saharan Africa. Their societies are structured by linear dominance hierarchies, wherein an individual’s position in the hierarchy determines its priority of access to resources. Their social groups are also characterized by female dominance and male-biased dispersal.
For my field work, I traveled to my laboratory’s field camp at the MMNR and lived there for 4 months! I conducted 3 projects, all which investigated the role of microbes and microbiomes in shaping their host’s phenotype. One project involved me swabbing decomposing beef daily in order to survey microbial community succession across various stages of decomposition in the savanna environment. I wanted to emulate the environment and decomposition process of the carcasses hyenas eat and determine the types of beneficial and harmful microbes hyenas are acquiring this way. My second project was tons of fun; I conducted scent discrimination trials to ascertain if hyena scent gland secretions and their odors, which are hypothesized to be produced by microbes, contain information about the sender’s age, sex, and residency. I presented juvenile and adult female hyenas with the paste of two strangers (i.e. an immigrant male vs. adult female) and recorded the amount of time they spend sniffing each specimen. If my analyses show that hyenas spend a differential amount of time sniffing the paste samples, then this would indicate that the samples encode different information, and more importantly, that microbes are indeed contributing to their host’s chemical signaling! My last project was also very enjoyable and allowed me to interact with other animals in the reserve. I collected fecal samples from various species of antelope, elephants, and baboons to determine the role of host phylogeny in structuring the gut microbiomes of mammals in the savanna.
Right now, I am working with Dr. Valeria Souza (who gave an EEBB seminar in 2017; that is where I met her!) and Dr. Luis Eguiarte from the Institute of Ecology at the Universidad Nacional Autónoma de Mexico (UNAM) on the bioinformatics portion of my BEACON-funded gut microbiome project. This project investigates the socio-ecological drivers of gut microbiome structure and function in spotted hyenas, as well as its stability, its transmission across generations, and its potential to act as a reservoir for antibiotic resistance. We are using shotgun metagenomics (i.e. whole genome sequencing) to profile gut microbial community function and determine the metabolic pathways being provided by the community as a collective. Specifically, in their lab, I am being trained on the assembly, binning, annotation, and phylogenetic profiling of shotgun metagenomic data. From this data, we will be able to profile the taxonomic composition of the hyena’s gut bacterial communities, reconstruct the hyena’s diet, and survey the diversity of antibiotic resistance genes harbored by the community. We will also determine the relative importance of viruses in driving the evolution of these gut microbiomes and assay their heritability across generations and within an individual’s lifetime. The bioinformatic analyses are challenging and time-intensive, but I am making progress and it has all been very fun! Apart from work, I have been spending lots of time getting to know the city, eating as many tacos as I can, and making friends.
Although I am not looking forward to the bitter cold when I return to Michigan in January, I am looking forward to teaching my first class, taking a course on teaching college science, and co-organizing the 2019 EEBB Research Symposium, among other things. Until then, I am going to make the most of my time here in this great city!