Monterey Bay Aquarium Blog Post

A blog post I wrote about the sea otter genome project has been featured on the Monterey Bay Aquarium Blog! I had a great time working on the post with Ken Peterson, the Aquarium’s Communications Director, and absolutely love the sweet infographic on the bottleneck designed by Tiffany Enriquez (courtesy of the Monterey Bay Aquarium).




SMM 2015 (continued)

It’s been an incredible few days here in San Francisco — meeting marine mammal researchers from around the globe and hearing talks on wide-ranging topics, some familiar and some very new.

I’ve learned there’s a “whale temple” in Thailand where fishermen bring the remains of stranded cetaceans for worship (Long Vu, Vietnam Marine Mammal Network).

We’ve heard experts discuss climate change’s effects on the Jet Stream (Jennifer Francis, Rutgers University) and the implications for marine mammal populations (Dr. Sue Moore, NOAA).

There was an entire session dedicated to sea otter research led by Dr. Tim Tinker (UCSC) and Dr. Jim Estes (UCSC), with presentations on a huge array of topics including diving behaviors (Joseph Tomoleoni, USGS), variance in reproductive success (Max Tarjan, UCSC), tactile sensing abilities (Sarah Macay Strobel, USGS/UCSC), and more!

I’ve learned about the genetics of scent in fur seals (Martin Stoffel, Bielefeld University) and the difficulties of SNP detection in the fur seal draft genome (Emily Humble, Bielefeld University).

I’ve had fantastic talks with otter researchers about the uses of isotopes from ancient otter bones for understanding changes in diet over time (Emma Elliott Smith, UNM) and gotten amazing advice about how to use ancient otter samples in my own genomic research (Dr. Shawn Larson, Seattle Aquarium).

My own talk on the whale gut microbiome was a blast — I got insightful questions and talked to interested researchers extensively afterward. Tomorrow, I’m looking forward to a last wander through the posters, more genetics talks, and a big Society for Marine Mammalogy “Birthday Bash” at SF City Hall!


Society for Marine Mammalogy Conference

This week I am attending the Society for Marine Mammalogy biennial conference in San Francisco. Around 3,000 marine mammal researchers have descended on the city for a week of workshops, talks, posters and get-togethers. I’ll be speaking on Thursday about our work on the whale gut microbiome.

Today I saw a variety of fascinating talks ranging from ancient whale dietary transitions (Robert Gooddall), to the use of DNA sequencing to determine prey biomass in pinniped feces (Austen Thomas), to the impacts of the Deepwater Horizon oil spill on bottlenose dolphin population dynamics and immune function (Lori Schwacke; Teri Rowles; Sylvain De Guise), to the use of gene expression data in understanding factors affecting population decline in sea otters (Elizabeth Bowen).

More updates to come during the week.

The Baleen Whale Gut Microbiome

Next-generation sequencing has allowed us to characterize cetacean gut microbial communities and discover surprising similarities to the microbiomes of terrestrial herbivores and carnivores.

I am thrilled to announce the publication of our paper on the whale gut microbiome in Nature Communications.

By sequencing the bacterial genomes contained in whale fecal samples, we explore the gut community of baleen whales and its functional potential. We find a remarkable ‘fusion’ microbiome that, while highly diverged overall from that of terrestrial mammals, contains functional elements characteristic of both terrestrial carnivore and terrestrial herbivore gut microbiomes. We find evidence to support the hypothesis that whales (which are descended from herbivorous terrestrial mammals, but are carnivores, eating small crustaceans and small fish) may use foregut fermentation to break down their food, much as ruminants do. In particular, the need to break down recalcitrant chitin in the exoskeletons of krill and copepods seems to have led the whale gut community to evolve the ability to bind and degrade chitin in the exoskeletons of krill and copepods.

This paper represents over four years of work carried out by Jon Sanders, myself, Joe Roman, Jarrod Scott, David Emerson, James McCarthy and Peter Girguis.

The study started as my senior thesis as an undergraduate at Harvard. In 2011, Dr. Roman and Dr. McCarthy were planning to collect right whale fecal samples in the Bay of Fundy to determine whales’ role as a ‘nutrient pump’ (bringing nitrogen up from the deep water where they feed, to the surface where they defecate), and I was eager to carry out marine fieldwork on a system that had always fascinated me. Given my interest in genetics, I wanted to add a molecular component to the research. Guided by Dr. McCarthy and Dr. Roman, we thought about exploring the whale gut microbiome. We teamed up with Dr. Girguis and Jon Sanders and worked together to conceive the microbiome study.

Dr. Roman, our colleague John Nevins and I traveled to Grand Manan in New Brunswick, Canada to carry out the fieldwork. We worked with Drs. Heather Koopman and Andrew Westgate at the Grand Manan Whale and Seabird Research Station to collect the fecal samples from right whales using fine mesh nets. We would stay on the water all day to search for “surface active groups” of right whales, then wait nearby until we smelled or saw the whale poop float to the surface in large brown clumps. We would then scoop it up and freeze a portion for genetic analysis.

I extracted DNA from the fecal samples and carried out an initial survey of the gut community using high throughput DNA sequencing. Jon Sanders and Peter Girguis advised me as I carried out initial analyses and found that the whale gut community is highly diverged from that of terrestrial mammals. We were excited by this result, and after I gradated from Harvard, Jon expanded the dataset to include metagenomic data and he and I worked with Dr. Emerson and Dr. Scott on the analyses to characterize the microbial community and its functionality.

Working with this amazing team of researchers to conceive such an exciting study was an unforgettable experience as an undergraduate and young researcher.