Exploring the Microbiome of Yellow Rays

You are most likely a member of a community. This may include a city, your favorite sports team, your children’s school district, or maybe even a digital community like a Facebook group. But just as we are members of a community, we, as individuals, are communities ourselves. In fact, throughout your body, you are a home to several communities of microbes such as viruses, fungi, and bacteria.

Different parts of your body have their own unique mixture of microbes—but don’t worry, these little buggers work together to keep you healthy! They can be found in your gut to help digest your meals, on your skin to keep it clean, in your nose to fight off germs, and in many more places. It’s mostly a mutualistic agreement; the microbes get to have a home as long as they chip in and keep you healthy.

This collection of microscopic organisms, or microorganisms, living in a particular environment (the human body in this instance) is called a microbiome. And, studying how these microscopic organisms interact with each other and their communities is called microbial ecology. The rapidly-emerging field of microbial ecology is bringing these nearly invisible communities of millions of microorganisms living among humans, plants and animals into focus. Around the planet, unique blends of ecosystems, environments and conditions are all influencing the homes available for microbial communities.

Can you imagine all the mystery surrounding how and why this came to be and what this means for natural life? These questions are the broad basis for many scientific projects globally that investigate microbial communities.

The Microbiome of Wild Versus Aquarium Rays

Scientists have been fascinated by the human microbiome for decades, but a new study carried out by Shedd Aquarium researchers, veterinarians and animal caretakers sought answers about marine animals. The study, published in Marine and Freshwater Research, became the first investigation into the differences in microbial communities between wild and aquarium-raised yellow stingrays (Urobatis jamaicensis). It was the first step toward an important goal: to understand if differences in the microbial community creates differences in animal health.

The idea of looking closer at the microbial communities of yellow stingrays at Shedd originated from a member of Shedd’s animal care staff who has experience participating in research and rescue efforts in the wild—20-year animal care veteran, Michele Sattler.

Sattler and her team collected samples from aquarium-raised yellow rays, and then turned to the Bahamas to sample wild rays. This swabbing is like getting a COVID-19 test in your nose, but for rays, Shedd’s animal caretakers took swabs of their exterior skin surfaces. In the Bahamas, researchers opportunistically sampled rays using Shedd’s ocean-going research vessel, the R/V Coral Reef II. Once all samples were collected from both aquarium and wild rays, Shedd’s microbial ecology lab could begin DNA extraction and genetic sequencing of the microbes.

Again, in a similar fashion to COVID-19 testing, this lab utilizes the technique of PCR (polymerase chain reaction) to amplify the DNA samples for proper data analysis. (In fact, some of the Shedd’s lab equipment was lent for Covid-19 testing early in the pandemic in 2020!) Amplifying DNA is necessary to generate enough copies for the analysis. After the lab analysis was complete, scientists could begin to document the structures of the microbial communities between the two different populations of rays.

For the first time, researchers observed differences in the diversity and abundance of microbes in wild rays versus aquarium-housed rays. You might be able to attribute some of these differences to factors like pollution, which is not present in an aquarium setting. The scientists at Shedd also demonstrated that internal microbiomes are predominantly shaped by what the rays eat and complexities in their immune systems.

Why This Research is Useful

Now that we know what differences exist, future work can demonstrate the strengths and weaknesses that each community of microbes gives to its animal home. In the future, microbiomes could be tailored to improve wildlife reintroduction programs, aquaria habitat management and aquaculture. For example, if a particular microbe helps animals better digest certain foods, then staff could introduce animals to these bacteria to ensure a healthy diet. In another example, animal care organizations like Shedd contribute to “head-start” programs that are raising animals in an aquarium setting and later releasing them into the wild to help bolster wild populations; understanding the differences in their microbial communities can ensure or improve their chance of survival and, for some, broader population recovery.

While they may be microscopic, microbial communities are under-described and underappreciated components of larger ecosystems despite being critical to their function. Most often when we think of sharks and rays, we picture large or even monstrous creatures with sharp teeth, but if we think further and picture the microscopic communities they house, we can begin to understand the entire story for a group of truly magnificent animals.

This study is the first to look closely at the microbial communities of yellow rays and was conducted entirely through Shedd’s facilities and resources by researchers Dr. Lee J. Pinnel, Francis J. Oliaro, and Dr. William Van Bonn of Shedd Aquarium.

You can dive into aquatic science by visiting one of the many science centers in Chicago, including Shedd Aquarium, or through virtual programming. Visit www.sheddaquarium.org to learn more.