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Biodiversity Blog

 

Meet Stengl-Wyer Fellow: Alex Nishida

Nishida lab
Alex isolating bacterial strains from the gut microbiomes of captive great apes.

The Stengl-Wyer Endowment supports year-long fellowships for doctoral candidates pursuing dissertation research in the area of Diversity of life and organisms in their natural environments. Recipients will receive a 12-month stipend of $34,000, full tuition and fees, staff health insurance, and an allowance of $2,000 to cover research and travel expenses. 

The inaugural year of 2020-2021 supports four fellows. Alex Nishida is the fourth and last of our Q&As with the fellows. As a PhD student in the lab of Dr. Howard Ochman, she is interested in the specificity between animal hosts and their gut microbiomes. 

Tell us where you came from before UT, and what you studied then?

I got my undergraduate degree from Lewis & Clark College in Portland, OR. I started my research career in the lab of Dr. Greta Binford studying the evolutionary history and biodiversity of spiders in the Caribbean. I had the opportunity to do fieldwork collecting spiders and other arachnids in several countries including Puerto Rico, the Dominican Republic, Barbados, as well as St. Kitts and Nevis. One interesting discovery was the finding of an eyeless spider in a cave system in the Dominican Republic, which led to a research focus on the adaptations of organisms that dwell in caves.

After graduating from Lewis & Clark, I worked for Ecology Project International as a field instructor in the Galapagos Islands. In partnership with the Galapagos National Park, I led groups of high school students in monitoring the population sizes and migration patterns of the Giant Tortoises. Giant Tortoises play an important role in the ecosystem through the dispersal of plant seeds.

What got you interested in studying animals and their gut microbiomes?

The field of microbiome research exploded when I was an undergraduate. As someone who had spent a lot of time tracking biodiversity that I could see, I was fascinated by the notion that we are living in symbioses with trillions of diverse organisms we cannot see. Our gut microbiome contributes to nutrition, modulates the immune system, as well as many aspects of our physiology. I recommend I Contain Multitudes by Ed Yong for those interested in learning more about host-microbiome interactions across the tree of life.

Describe how your research interests have evolved during your graduate career?

When I first joined the Ochman Lab in 2015, I was interested in how hosts assemble specific gut microbiomes from the surrounding environment. Previous research had shown that animals experiencing a dietary change retain a microbiome composition that reflects their ancestral diet. I wondered how accurately genetic distance between hosts would predict similarity between their gut microbiomes, and at what divergence time this relationship would become saturated.

To investigate this question, I collated sequencing data from 114 species representing 12 mammalian orders. I investigated which specific host factors (e.g., dietary changes, body size, and gut physiology) were associated with changes in the rate of microbiome divergence over this evolutionary timescale. Some of the most dramatic changes in microbiomes are associated with the loss of bacterial taxa, such as those accompanying the transition from terrestrial to marine lifestyles and westernization of the human microbiome.

After observing the effect of host phylogeny on microbiome composition, I wanted to understand how resilient host regulation of microbiome composition is to changes in diet, lifestyle, and geography. In a review, I describe why great apes represent an ideal system to test the extent of host-microbiome specificity and how they have increased our understanding of the human microbiome. Great apes share many closely related bacterial taxa with humans, including some taxa that have been vertically transmitted among hominids for millions of years.  One way of probing the specificity of interaction between hosts and their associated microbial lineages is to determine whether these relationships are preserved in an artificial setting, where diet and environment are controlled and individuals are in close proximity. To investigate the resilience of host-microbiome specificity, I made contacts at several zoos and obtained fecal samples from great apes housed in multiple geographic locations. My research showed that captivity homogenizes the microbiome composition of great apes, such that the microbiomes of captive individuals become more similar to each other than their wild counterparts.

Where do you see your research agenda heading during your time as a Stengl-Wyer Fellow? And how about after?

As a Stengl-Wyer Fellow, I’m currently investigating genomic variation among bacterial strains that reside in humans and their closest relatives, the great apes. I’m interested in how the genomes of bacteria strains change after host-switching from humans into great apes residing in captivity. I’m at my computer these days looking at how bacterial strains isolated from captive apes have independently acquired genes to metabolize the mucin that lines your gut epithelial layer as well as additives present in preserved foods. This research is exciting because it demonstrates the extent of diversity within the strains of bacteria that belong to the same species. These strain-level differences impact how a bacteria interacts with the host and other members of the microbiome.

 

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