Modern life messes with the microbiome -– the trillions of bacteria and other microbes that live inside the body. Could reconnecting with nature bring this internal ecosystem back into balance?
A new study suggests it can, at least in lemurs. Led by Duke Ph.D. alumnus Sally Bornbusch and her graduate advisor Christine Drea, the research team collected fecal samples from more than 170 ring-tailed lemurs living in various conditions in Madagascar: some were living in the wild, some were kept as pets, and some were rescued from the pet and tourism industries and then relocated to a rescue center in southwestern Madagascar where they ate a more natural diet and had less exposure to people.
Then the researchers sequenced DNA from the fecal samples to identify their microbial makeup. They found that the longer lemurs lived at the rescue center, the more similar their gut microbes were to those of their wild counterparts. Former pet lemurs with more time at the rescue center also showed fewer signs of antibiotic resistance.
By “rewilding” the guts of captive animals, researchers say we may be able to better prime them for success, whether after rescue or before translocation or reintroduction into the wild.
This research was supported by grants from the National Science Foundation (1945776, 1749465), the Triangle Center for Evolutionary Medicine, Duke’s Kenan Institute for Ethics, the Margot Marsh Biodiversity Fund and Lemur Love.
CITATION: “Microbial Rewilding in the Gut Microbiomes of Captive Ring-Tailed Lemurs (Lemur catta) in Madagascar,” Sally L. Bornbusch, Tara A. Clarke, Sylvia Hobilalaina, Honore Soatata Reseva, Marni LaFleur & Christine M. Drea. Scientific Reports, Dec. 27, 2022. DOI: 10.1038/s41598-022-26861-0.
Jason Dinh’s research career began unintentionally with a semester at Duke’s Marine Lab. A current fourth-year PhD candidate in Duke’s Biology Department, Dinh ventured to the Marine Lab for a mental reset in the spring of his sophomore year as a Duke undergraduate. “While I was there, I realized that people can just get paid to ask questions about how the world works,” Dinh told me, “And I really didn’t know that was a thing that you could do.” Maybe this is what I want to do, he thought.
Dinh spent his remaining undergraduate summers investigating the impacts of soundscapes on oyster and fish larvae development. Now, he studies snapping shrimp – a small oceanic species that is “one of the biggest sound producers in the ocean,” bested only by toothed whales.
Dinh first became aware of snapping shrimp during his undergraduate research. He told me that you can find snapping shrimp “basically anywhere, from the equator up to Virginia or maybe North Carolina.” While conducting research on ocean sounds and oyster and fish larvae, Dinh noticed the frequent snapping sounds of the snapping shrimp when he placed underwater microphones. “We didn’t really know what they were doing,” Dinh said.
The male snapping shrimp is asymmetrical with one very large claw and one that is regular-sized. The large claw has a tiny hook on the end and when the shrimp clamps down or “snaps” the claw, the top half latches into the bottom, shooting out an air bubble at sixty miles per hour that “essentially boils the water behind it,” producing the loud snapping noise in its wake. When many shrimp are snapping at once, it sounds almost like the frying grease when cooking bacon, Dinh tells me. (Click here to watch a video of the snapping shrimp in action.)
At first, researchers suspected the bubble from the snap was a means of stunning prey, but “It turns out that snapping shrimp also fight each other,” Dinh said. And when fighting, male snapping shrimp shoot the air bubbles at one another. The bigger the shrimp’s body size, the larger the snapping claw and the louder the snapping sound.
Going into his PhD, Dinh wanted to continue his undergraduate work in acoustics and figure out novel ways animals were producing sounds. His investigation of the snapping shrimp took him in new directions, however. Through his projects, Dinh has conducted work on the costs and benefits that keep the claw size as an honest indicator of shrimp size in competitions and approached a plethora of questions from the physiological and physical mechanisms of sending and assessing snaps, up to the evolutionary implications of the sexual selection for claw size.
“I don’t think I really knew I wanted to do research until right before I applied for grad school,” Dinh said at the beginning of our conversation. He remembers being a child curious about nature and bringing in “hundreds of cicadas” and “random critters into the house.” A few decades later and his research is centered on living creatures, which is both a rewarding and tricky process.
“Live animals are going to do what live animals want to do,” Dinh stated simply. “One thing my advisor always tells us is that you don’t get to tell the animal what to do, it tells you what you are going to do.” This has certainly held true for Dinh. While he has had many detailed and well-planned experimental ideas, he says he’s ultimately ended up doing what the “animals told him they were willing and happy to do in the lab.” However, along the way Dinh basks in the “joys in tiny discoveries in the process of research.”
I asked Dinh how he ended up at Duke in the first place and why he chose to stick around for his PhD. “So I ended up at Duke for undergrad because I really liked basketball, which is a really bad reason to choose a school.” But ultimately, this choice “paid off really well because my first year was the last year we won the National Championship,” Dinh said. He traveled to Indianapolis for the event which he says was the “best basketball game of [his] life.”
Dinh decided to do his PhD at Duke because of how deeply he admires his advisor, Sheila Patek (PhD), as a scientist. “I think she’s just a wonderful, passionate, passionate defender of basic science and just doing science because more knowledge is good for society,” Dinh elaborated, “Sheila’s also a staunch and fearless advocate for her students.” Though Dinh considers himself an “outlier” in the lab – primarily a behavioral ecologist in a lab of researchers investigating biomechanics – the way that Patek approaches science is the way that he wants to approach science as well.
“I feel like science is being a professional rabbit holer,” Dinh stated. While Dinh is on the pursuit of the weapon size and fighting strategies of snapping shrimp, he doesn’t know exactly where he wants to head next, following the completion of his PhD. Like the snapping shrimp that collect information about their opponents to make an informed decision about engaging in fights, Dinh says he is conducting a sort of Bayesian method of his own. He’s assessing his experiences as he goes and sorting out the right next step for him.
A fan of the meditative art of writing, long morning walks with his dog, and reality TV, Dinh appreciates being “on the frontier of what we know” and is sure to let his deep-rooted curiosity about the natural world continue to guide him.
Look at the palm of your hand and spread your fingers wide. Now imagine squeezing your body through a gap narrower than the distance between the tip of your thumb and the tip your pinkie finger. Let’s make this a bit worse: the gap is in complete darkness, its walls are rough stone, and all you have is a tiny headlamp. Ok, now that you are there, all you have to do is carefully find and recover dime-sized fragments of an invaluable treasure.
That’s how researchers recovered the first Homo naledi child’s skull ever to be found.
The finding was revealed this week in two papers published in the journal PaleoAnthropology by an international team of 21 researchers.
Homo naledi are possibly our most mysterious long-lost cousins. They are an ancient human relative that lived in what is now South Africa, approximately 350 to 250 thousand years ago. They were first discovered in the Rising Star Cave system in 2013, in a research expedition led by Lee Berger, Professor and chair of Palaeo-Anthropology and Director of the Centre for Exploration of the Deep Human Journey at the University of Witwatersand.
The research team, which includes Steven Churchill, professor of evolutionary anthropology at Duke, named the child Leti (pronounced Let-e), after the Setswana word “letimela” meaning “the lost one”.
Leti was found in one of the previously unexplored narrow fissures that radiate from Rising Star’s known chambers. His resting site was a 15 cm wide and 80 cm long gap where only the smallest (and bravest) of explorers could fit.
Marina Elliot, lead author of the first paper and one of the explorers to first discover Homo naledi, said in a press conference that excavating Leti’s remains required explorers to wedge themselves practically upside down between two rock walls.
Finding yet another fossil in a prolific site may not seem groundbreaking, but finding a child’s skull is a major achievement. First of all, children’s bones are thin and fragile, and rarely withstand the test of time.
Second, finding a child’s skull gives researchers a precious glimpse into the development of Homo naledi.
“A child’s skull allows us to study how Homo naledi grew and developed, and how their growth rate and schedule compares to other hominid species, and to our own,” Churchill said.
In addition to skull fragments, researchers also recovered two worn baby teeth and four unworn adult teeth that were yet to erupt. These findings show that Leti would have been between four and six years old at the time of her or his death.
Based on similarities between the soil of the fissure where Leti was found and the better-known areas of the cave, Tebogo Makhubela, senior lecturer of Geology at the University of Johannesburg and author of the papers, estimated that Leti has been hidden in Rising Star for over 250,000years.
The discovery of Leti’s skull also deepens the mystery of how Homo naledi’s remains ended up in such a deep, dark, and treacherous cave.
Berger’s team had previously hypothesized that the first 15 Homo naledi individuals found in Rising Star had been disposed there by their own species, as a burial. This hypothesis created an uproar: could a small-brained hominin from over 300,000years ago bury their dead, just like we do?
Leti’s skull was found on a small shelf at the back of the cave’s fissure. No other bones were found, suggesting that Leti’s head may have been deliberately placed there. Leti, as well as all other Homo naledi fossils ever found, showed no evidence of being dragged by predators, carried by water, or tumbled around in any other way.
“Those were social individuals. Seeing one of their own being picked apart by animals could have been very distressing,” Churchill said. “Purposeful disposal of their bodies still seems like the most likely explanation.”
Berger is undeterred by nay-sayers. “This is science,” Berger said at a press conference. “We will continue testing and challenging our hypotheses with every piece of data that we get.”
The researchers hope that other teams around the world will study Leti and other Homo naledi fossils. To that end, Leti’s skull was CT-scanned, and its scans can be downloaded from Morphosource, an open access repository of museum specimens’ 3D scans hosted at Duke University.
Leti will probably not be the last treasure to come out of Rising Star’s spider web of narrow passages.
“I can’t wait to go back to South Africa and see what else is waiting for us in that cave,” said Juliet Brophy, Professor of Geography and Anthropology at Louisiana State University and lead author of the paper describing Leti’s skull.
“This finding makes us remember that exploration is always worth doing,” said Elliot, who is a researcher at Simon Fraser University and Witwatersand University. “There is a lot still out there to be found”.
Elliot et al. was funded by the National Geographic Society, the Lyda Hill Foundation, the South African National Research Foundation, and the Gauteng Provincial Government, for funding the discovery, recovery and ongoing analyses of the material. Additional support was provided by ARC (DP140104282).
Brophy et al. was funded by the National Geographic Society, the Lyda Hill Foundation, the South African National Research Foundation, the South African Centre for Excellence in Palaeosciences, The University of the Witwatersrand, the Vilas Trust, the Fulbright Scholar Program, Louisiana State University, North Carolina State University, the Texas A&M University College of Liberal Arts Seed Grant program and the Texas A&M College of Liberal Arts Cornerstone Faculty Fellowship.
“Expanded Explorations of the Dinaledi Subsystem, Rising Star Cave System, South Africa.” Marina C. Elliot,Tebogo V. Makhubela, Juliet K. Brophy, Steven E. Churchill, Becca Peixoto, Elen M. Feuerriegel, Hannah Morris, Rick Hunter, Steven Tucker, Dirk Van Rooyen, Maropeng Ramalepa, Mathabela Tsikoane,Ashley Kruger, Carl Spander, Jan Kramers, Eric Roberts, Paul H.G.M. Dirks,John Hawks,Lee R. Berger. PaleoAnthropology, November 2021. DOI: https://doi.org/10.48738/2021.iss1.68.
“Immature Hominin Craniodental Remains From a New Localityin the Rising Star Cave System, South Africa.” Juliet K. Brophy, Marina C. Elliot, Darryl J. De Ruiter, Debra R. Bolter, Steven E. Churchill, Christopher S. Walker, John Hawks, Lee Berger. PaleoAnthropology, November 2021, DOI: https://doi.org/10.48738/2021.iss1.64.