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.
DURHAM, N.C. — Some of us live and die by our phone’s GPS. But if we can’t get a signal or lose battery power, we get lost on our way to the grocery store.
Yet animals can find their way across vast distances with amazing accuracy.
Take monarch butterflies, for example. Millions of them fly up to 2,500 miles across the eastern half of North America to the same overwintering grounds each year, using the Earth’s magnetic field to help them reach a small region in central Mexico that’s about the size of Disney World.
Or sockeye salmon: starting out in the open ocean they head home each year to spawn. Using geomagnetic cues they manage to identify their home stream from among thousands of possibilities, often returning to within feet of their birthplace.
Now, new research offers clues to how migrating animals get to where they need to go, even when they lose the signal or their inner compass leads them astray. The key, said Duke Ph.D. student Jesse Granger: “they can get there faster and more efficiently if they travel with a friend.”
Many animals can sense the Earth’s magnetic field and use it as a compass. What has puzzled scientists, Granger said, is the magnetic sense is not fail-safe. These signals coming from the planet’s molten core are subtle at the surface. Phenomena such as solar storms and man-made electromagnetic noise can disrupt them or drown them out.
It’s as if the ‘needle’ of their inner compass sometimes gets thrown off or points in random directions, making it hard to get a reliable reading. How do some animals manage to chart a course with such a noisy sensory system and still get it right?
“This is the question that keeps me up at night,” said Granger, who did the work with her adviser, Duke Biology Professor Sönke Johnsen.
Multiple hypotheses have been put forward to explain how they do it. Perhaps, some scientists say, migrating animals average multiple measurements taken over time to get more accurate information.
Or maybe they switch from consulting their magnetic compass to using other ways of navigating as they near the end of their journey — such as smell, or landmarks — to narrow in on their goal.
In a paper published Nov. 16 in the journal Proceedings of the Royal Society B, the Duke team wanted to pit these ideas against a third possibility: That some animals still manage to find their way, even when their compass readings are unreliable, simply by sticking together.
To test the idea, they created a computer model to simulate virtual groups of migrating animals, and analyzed how different navigation tactics affected their performance.
The animals in the model begin their journey spread out over a wide area, encountering others along the route. The direction an animal takes at each step along the way is a balance between two competing impulses: to band together and stay with the group, or to head towards a specific destination, but with some degree of error in finding their bearings.
The scientists found that, even when the simulated animals started to make more mistakes in reading their magnetic map, the ones that stuck with their neighbors still reached their destination, whereas those that didn’t care about staying together didn’t make it.
“We showed that animals are better at navigating in a group than they are at navigating alone,” Granger said.
Even when their magnetic compass veered them off course, more than 70% of animals in the model still made it home, simply by joining with others and following their lead. Other ways of compensating didn’t measure up, or would need to guide them perfectly for most of the journey to accomplish the same feat.
But the strategy breaks down when species decline in number, the researchers found. The team showed that animals who need friends to find their way are more likely to get lost when their population shrinks below a certain density.
“If the population density starts dropping, it takes them longer and longer along their migratory route before they find anyone else,” Granger said.
Previous studies have made similar predictions, but the Duke team’s model could help future researchers quantify the effect for different species. In some runs of the model, for example, they found that if a hypothetical population dropped by 50% — akin to what monarchs have experienced in the last decade, and some salmon in the last century — 37% fewer of the remaining individuals would make it to their destination.
“This may be an underappreciated aspect of concern when studying population loss,” Granger said.
This research was supported in part by the Air Force Office of Scientific Research (FA9550-20-1-0399) and by a National Defense Science & Engineering Graduate Fellowship to Jesse Granger.
CITATION: “Collective Movement as a Solution to Noisy Navigation and its Vulnerability to Population Loss,” Jesse Granger and Sönke Johnsen. Proceedings of the Royal Society B, Nov. 16, 2022. DOI: 10.1098/rspb.2022.1910
Some dogs have to eat in a high chair—or, more specifically, a Bailey Chair. The chair keeps them in a vertical position while they eat so that gravity can do the work their bodies can’t: moving food from the mouth to the stomach.
These dogs have megaesophagus, an esophagus disorder that can prevent dogs from properly digesting food and absorbing nutrients. When you swallow a bite of food, it travels down a muscular tube, the esophagus, to the stomach. In humans, the esophagus is vertical, so our esophageal muscles don’t have to fight against gravity. But because dogs are quadrupeds, a dog’s esophagus is more horizontal, so “there is a greater burden on peristaltic contractions to transport the food into the stomach.” In dogs with megaesophagus, the esophagus is dilated, and those contractions are less effective. Instead of moving properly into the stomach, food can remain in the esophagus, exacerbating the problem and preventing proper digestion and nutrient absorption.
Leigh Anne Clark, Ph.D., an associate professor at Clemson University, recently spoke at Duke about megaesophagus in dogs and its genetic underpinnings. She has authored dozens of publications on dog genetics, including five cover features. Her research primarily involves “[mapping] alleles and genes that underlie disease in dogs.” In complex diseases like megaesophagus, that’s easier said than done. “This disease has a spectrum,” Clark says, and “Spoiler: that makes it more complicated to map.”
Clinical signs of megaesophagus, or mega for short, include regurgitation, coughing, loss of appetite, and weight loss. (We might use the word “symptom” to talk about human conditions, but “a symptom is something someone describes—e.g., I feel nauseous. But dogs can’t talk, so we can only see ‘clinical signs.’”) Complications of mega can include aspiration pneumonia and, in severe cases, gastroesophageal intussusception, an emergency situation in which dogs “suck their stomach up into their esophagus.”
Sometimes megaesophagus resolves on its own with age, but when it doesn’t it requires lifelong management. Mega has no cure, but management can involve vertical feeding, smaller and more frequent meals, soft foods, and sometimes medication. Even liquid water can cause problems, so some dogs with mega receive “cubed water,” made by adding a “gelatinous material” to water, instead of a normal water bowl.
In dogs, mega can be either congenital, meaning present at birth, or acquired. In cases of acquired megaesophagus, the condition is “usually secondary to something else,” and the root cause is often never determined. (Humans can get mega, too, but as with acquired mega in dogs, mega in humans is usually caused by a preexisting condition. The best human comparison, according to Clark, might be achalasia, a rare disorder that causes difficulty swallowing.) Clark’s current research focuses on the congenital form of the disease in dogs.
Her laboratory recently published a paper investigating the genetic foundation of mega. Unlike some diseases, mega isn’t caused by just one genetic mutation, so determining what genes might be at play required some genetic detective work. “You see mega across breeds,” Clark says, which suggests an environmental component, but the disease is more prevalent in some breeds than others. For instance, 28 percent of all diagnoses are in German shepherds. That was a “red flag” indicating that genes were at least partly responsible.
Clark and her collaborators chose to limit their research study to German shepherds. Despite including a wide range of dogs in the study, they noticed that males were significantly overrepresented. Clark thinks that estrogen, a hormone more abundant in females, may have a protective effect against mega.
Clark and her team performed a genome-wide association study (GWAS) to look for alleles that are more common in dogs with mega. One allele that turned out to be a major risk factor was a variant of the MCHR2 gene, which plays a role in feeding behaviors. In breeds where mega is overrepresented, like German shepherds, “we have a situation where the predominant allele in the population is also the risk allele,” says Clark.
Using the results of the study, they developed a test that can identify which version of the gene a given dog has. The test, available at veterinary testing companies, is designed “to help breeders reduce the frequency of the risk allele and to plan matings that are less likely to produce affected puppies.”
“Krithi Karanth is…” begins a long sentence if not pruned, so I will settle on the following: Dr. Karanth is the Chief Conservation Scientist and Director at the Centre for Wildlife Studies in India, an adjunct professor in the Nicholas School at Duke, and a Vogue Woman of the Year.
On Oct. 13, she visited her alma mater to catch us up on her work.
Karanth grew up in close contact with an abundance of wildlife as the daughter of tiger biologist Dr. Ullas K. Karanth in India. Her first experience in the jungle was at the ripe age of one, and she credits this “sheer joy of watching nonhumans uninterrupted” as the basis for her deep concern and care for wildlife.
She received her Ph.D from the Nicholas School after scouring historic hunting journals and interviewing Indian wildlife scientists to build a database that documents the havoc wreaked on wildlife populations in India, beginning in the mid-nineteenth century. The results are gut-wrenching, among them: an estimated 96% plunge in the lion population, 67% drop in tigers, and a 62% decline in wolves.
After thirteen years studying and researching in the U.S., Karanth returned home to India, where she felt her impact could be greater.
Today, large British hunting parties are no longer the main cause of species decline in India. Instead, man and beast find themselves stepping on each other’s toes and tails more and more as towns expand and animals like elephants and leopards lose their habitats.
At the Centre for Wildlife Studies, Karanth’s work focuses on mitigating the most prevalent problems in human-wildlife interaction: crop and property damage, livestock predation, and human injury and death.
Her tactics for doing so are expansive. At CWS, she leads several initiatives targeting different sides of the problem.
WildSeve deploys timely assistance to people, most often farmers, dealing with destructive wildlife encounters. Farmers can call a toll free number, and a member of the team will ride out to their farm to help document the incident and file a claim for government compensation, allowing farmers to complete what would otherwise be an arduous and expensive legal process. In “peak season,” between October and November when many farmers are growing a cover crop known to attract elephants, WildSeve deploys as many as thirty conflict responders per day.
The goal of these interactions is not simply response, but mitigation. WildSeve helps farmers understand what factors increase the likelihood of human-wildlife conflict (HWC) and how to avoid these encounters in the future.
Another project in the works, WildCarbon, will assist farmers in transitioning their land from agriculture to carbon-sequestering agro-forests in places where the benefits can outweigh the costs.
Karanth says that trust is key to ensuring that the advice from the team is well-received. It is often difficult to convince a farmer to change their practices. Farming technique is both a careful science and the basis of a farmer’s livelihood. The project is in its seventh year, and Karanth says it has taken time for farmers to see that their assistance works. One factor that helps build this trust is that many members of the WildSeve team are locals in the communities.
Another program, WildShaale, is designed to foster understanding and appreciation for local wildlife in schoolchildren. Karanth pointed out that many school-age children easily recognize a kangaroo despite their lack of proximity to or interaction with the Australian marsupial, but could not identify the Indian wolf native to their backyard.
For children living in communities that come in close contact with wildlife, their perception of the animals is often one of fear. Karanth said the curiosity and empathy that WildShaale nurtures is critical to creating communities that have a net positive relationship with their animal neighbors. By fostering this empathy, violence becomes a last resort when dealing with wildlife conflicts.
After Karanth’s talk, I grabbed a chai latte from Beyu Cafe and sat down in Penn Pavilion for New York Times columnist Bret Stephens’ chat on cross-partisan conversation. At the time, I didn’t see much connection between the two events, but in retrospect, it is there. Both talks touched on that attempt at harmony, respect, and civil discourse I so often find myself craving: for Karanth, it’s between animals and people; for Stephens, people and people.
As I got ready to write this article, I turned on my GE digital clock radio to keep me company. I debated switching to a podcast, but then the host mentioned elephants and — given their relevance to task — I leaned in a little closer.
WUNC was playing this week’s segment of the TED Radio Hour, which centered on finding resolutions in situations of conflict. The woman being interviewed was discussing her own solution to elephant-human conflict in Kenya: beehives.
I will leave it to the reader to find out how, but the remainder of the segment drove home my key takeaway from hearing Karanth speak: Seeking out simple, yet innovative answers to human-wildlife conflict, a life or death issue, can teach us a lot about the importance of finding solutions to interpersonal conflict.
On a sunny Friday in September, Dr. Nicki Cagle led a herpetology walk in the Duke Forest with the Wild Ones. The Wild Ones is an undergraduate club focused on increasing appreciation for the natural world through professor-led outings. Herpetology is the study of reptiles and amphibians.
Dr. Cagle is a senior lecturer in the Nicholas School of the Environment at Duke and the Associate Dean of Diversity, Equity, and Inclusion. Along with teaching courses on environmental education and natural history, she is also the science advisor for a citizen science project focused on reptiles and amphibians, or herpetofauna, in the Duke Forest. Volunteers monitor predetermined sites in the Duke Forest and collect data on the reptiles and amphibians they find.
“We get a sense of abundance, seasonality… and how the landscape is affecting what we’re seeing,” Dr. Cagle says. There is evidence that herp populations in the Duke Forest and elsewhere are decreasing.
The project relies on transects, “a sampling design… where you have a sampling spot at various intervals” along a line of a predetermined length. In this case, the sampling spots are “traps” meant to attract reptiles and amphibians without harming them. Each site has a large board lying on the ground. “Different herps are more likely to be found under different objects,” Dr. Cagle explains, so the project uses both wooden and metal cover boards.
But why would snakes and other herps want to hide under cover boards, anyway? Reptiles and amphibians are “cold-blooded” animals, or ectotherms. They can’t regulate their own body temperature, so they have to rely on their environment for thermoregulation. Snakes might sun themselves on a rock on cold days, for instance, or hide under a conveniently placed wooden board to escape the heat.
Salamanders that use the cover boards might be attracted to the moist environment, while “snakes will tend to go under cover boards either to hide — like if they’re about to molt and they’re more vulnerable — to look for prey, or just to maintain the proper temperature,” Dr. Cagle says.
Citizen scientists typically check the boards once a week and not more than twice a week. Volunteers have to avoid checking the traps too often because of a phenomenon called “trap shyness,” where animals might start avoiding the traps because they’ve learned to associate them with pesky humans flipping the boards over and exposing their otherwise cozy resting places. By checking the traps less frequently, scientists can reduce the likelihood of that and minimize disturbance to the animals they’re studying.
Dr. Cagle gave the Wild Ones a behind-the-scenes tour of some of the cover boards. Using a special, hooked tool conveniently stashed in a PVC pipe next to the first cover board, we flipped each board over and looked carefully underneath it for slithery movements. We didn’t find any under the first several cover boards.
But then, under a large sheet of metal, we saw a tiny snake squirming around in the leaf litter. There was a collective intake of breath and exclamations of “snake!”
Dr. Cagle captured it and held it carefully in her hands. Snakes, especially snakes as young as this one, can be all too easily crushed. We gathered around to look more closely at the baby snake, a species with the adorable name “worm snake.” It was dark above with a strikingly pink underside. The pink belly is a key field mark of worm snakes. Earth snakes are also found around here and look similar, but they tend to have tan bellies.
After a minute or two, the worm snake made a successful bid for freedom and wriggled back under the board, disappearing from sight almost immediately.
Some of the cover boards revealed other animals as well. We found a caterpillar chrysalis attached to one and several holes — probably made by small mammals — under another.
Whatever made the holes, we can safely assume it wasn’t a snake. According to Dr. Cagle, the term “snakehole” is misleading. Most snakes don’t make their own holes, though some of them do use existing holes made by other animals. One exception is the bull snake, which is known for digging.
We found a young five-lined skink sunning itself on top of one of the metal cover boards. (Thermoregulation!) Juvenile five-lined skinks are colloquially known as blue-tailed skinks, but the name is somewhat misleading — the adults don’t have blue tails at all.
The snakes we were looking for, meanwhile, were often elusive. Some vanished under the leaf litter before we could catch them. Sometimes it was hard to tell whether we were even looking at a snake at all.
“What are you?” Dr. Cagle muttered at one point, crouching down to get a better look at what was either a stick-esque snake or a snake-esque stick. “Are you an animal? Or are you just a wet something?” (Just a wet something, it turned out.)
Later on, we found at least three young ring-necked snakes (Diadophis punctatus) under different cover boards. One of them was particularly cooperative, so we passed it around the group. (“All snakes can bite,” Dr. Cagle reminded us, but “some have the tendency to bite less,” and this species “has the tendency not to bite.”) Its small, lithe body was surprisingly strong. The little snake wrapped tightly around one of my fingers and seemed content to chill there. A living, breathing, reptilian ring. That was definitely a highlight of my day.
If you’ve ever wondered if snakes have tails, the answer is yes. The official cut-off point, Dr. Cagle says, is the anal vent. Everything below that is tail. In between flipping over cover boards and admiring young snakes, we learned about other herps. Near the beginning of our walk, someone asked what the difference is between a newt and a salamander.
“A newt is a type of salamander,” Dr. Cagle says, “but newts have an unusual life cycle where they spend part of their life cycle on land… and that is called their eft phase.” As adults, they return to the water to breed.
We learned that copperheads “tend to be fatter-bodied for their length” and that spotted salamanders cross forest roads in large numbers on warm, rainy nights in early spring when they return to wetlands to breed.
Perhaps the most interesting herp fact of the day came near the end of our walk when one of the students asked how you can tell the sex of a snake. Apparently there are two ways. You can measure a snake’s tail (males usually have longer tails), or you can insert a metal probe, blunted at the end, into a snake’s anal vent. Scientists can determine the sex of the snake by how deep the probe goes. It goes farther into the anal vent if the snake is a male. Why is that? Because male snakes have hemipenes — not two penises, exactly, but “an analogous structure that allows the probe to slide between the two and go farther” than it would in a female snake. The more you know…
Disclaimer: Handling wild snakes may result in snake bites. It can also be stressful to the snakes. Furthermore, some snakes in this area are venomous, and it’s probably best to familiarize yourself with those before getting close to snakes rather than afterward. Snakes are amazing, but please observe wildlife safely and responsibly.
Hello, my name is Jakaiyah Franklin, and I am a sophomore here at Duke University. In terms of my major, I am undecided, but I do know my passion lies in biology, science communication, and environmental science.
Outside of classes, I am the treasurer for the Duke Chapter of the NAACP and LLC leader for the Stem Pathways for Inclusion, Readiness, and Excellence (SPIRE) program. Last year I was the stage manager for two Hoof n Horn productions.
This year, I will start a research position along with this research blogging position.
In a more personal sense, I am the youngest of three and a proud aunt. Right now, I say I am from Texas, even though I have lived in Georgia, South Carolina, Germany, and presently North Carolina. If someone ever asked me, I would say that Germany holds my most memorable memories; however, I have grown into a better version of myself in each place I have lived. Other than school, I like to read and watch House of the Dragon and the earlier seasons of The Game of Thrones. I prefer to study outside or in a place where natural light is abundant. I also love learning new things pertaining to science, specifically infectious diseases.
I find diseases fascinating, and I believe they are our natural predators. I want to be able to not only understand them, but also, I want to help prevent them. If one were to have a favorite type of disease to study, mine would be zoonotic diseases. They are interesting because the act of a virus being able to jump from a host like a rat to a human is captivating to me.
After graduating from Duke, I want to earn a master’s in public health or a Ph.D. in epidemiology, virology, or infectious disease to feed my curiosity about diseases. However, before I can even decide what Ph.D. or master’s I want to earn, my current goal is to decide on my major.
I do like to think ahead, so, for my very distant career, I know I want to be able to see infectious diseases in both the lab and in the places where they are infecting populations. I want my research to be digestible for the general population because, as seen with both COVID and Monkeypox, science can be easily misinterpreted if not delivered appropriately. I want to prevent this occurrence from happening to me by learning more about science communication and actively improving my communication skills.
I hope this blogging position will expose me to infectious disease research or general public health research. With this new understanding of the research, I hope this position will also educate me on how to inform others so that they can enjoy and understand the science.
New research shows that lemurs and their food trees are tightly linked in ecological networks, and that the extinction of lemurs will have cascading effects on ecosystem functions.
Lemurs are the primates found only on Madagascar. They are unique in many ways, and like many organisms, they fit in complex ecological networks. These networks include interactions between lemurs and their food trees. Many interactions are beneficial, or mutualistic; for example, lemurs eat the fruits of trees and disperse their seeds, providing a critical service to the trees. If lemurs go extinct — 98% of species are threatened with extinction due to human activities — the links in the ecological network will be severed, with potentially negative impacts on the trees.
Research published in the Journal of Animal Ecology by Ph.D. student Camille DeSisto, of the Duke University Nicholas School of the Environment, and James Herrera, from the Duke Lemur Center, shows how tightly linked lemurs and trees are in their interaction networks, and the negative impacts of extinction on network resilience. If lemurs do in fact disappear, many trees will be left without a way to disperse their seeds, and may not be able to reproduce effectively.
DeSisto and Herrera used advanced techniques in social network analysis, including exponential random graph models, to test which traits of lemurs and trees predict their probability of interaction. The lemurs with the highest probability of interactions with trees were large, fruit-eating species with a short gestation length, occurring in arid habitats, and with a threat status of Least Concern. Closely related plants were more likely to interact with the same lemur species than distantly related plants, but closely related lemurs were not more likely to interact with the same plant genus.
Simulated lemur extinction tended to increase network structure in some properties, including connectance (% of realized interactions out of all possible interactions) and modularity (how many unique cliques or subcommunities form in the network), but decrease nestedness (the tendency for specialists which feed on only a few trees to be a subset of generalists which feed on many trees) and robustness (tolerance to future extinctions), compared to pre‐extinction networks. Networks were more tolerant to plant than lemur extinctions.
By simulating the loss of lemur and plant species, the authors could predict how network structure will erode over time if threatened lemurs and trees go extinct. The results showed that if the most well-connected lemurs in the network were to disappear, the percentage of trees with interactions would quickly decline, compared to scenarios in which lemurs were removed randomly or if the least-well connected lemurs went extinct. Given the threat status and geographic range size of lemurs, the percentage of trees that would lose their interacting lemurs would be greater than that expected if lemur extinctions were random.
Results also showed that if lemurs go extinct, the resilience of the networks to further disturbance would decrease. This indicates that the current links between lemurs and trees are critical to the stability of these complex ecological networks.
To prevent the loss of key ecosystem functions like seed dispersal, it is critically important to protect lemurs and trees, which depend so crucially on one another for survival. DeSisto is currently conducting field research in Madagascar, studying how well seeds germinate when eaten by lemurs. She created a tree nursery in the forest to grow the seeds obtained from lemur feces, and already has several species germinating. Interestingly, she is also showing how lemurs disperse the seeds of vines, which are an important yet understudied food source when tree fruits are not available. She will continue her research across multiple seasons, to determine how changes in plant phenology affect seed dispersal patterns.
Many conservation programs are currently striving to safeguard Madagascar forests and the diverse species found only in these natural habitats. The Duke Lemur Center has an active conservation program in the northeast, called the DLC-SAVA Conservation Initiative. This program takes a community-based approach to conservation, partnering closely with local stakeholders and actors to develop projects that address the needs of both lemurs and people. By co-creating projects that include alternative and sustainable livelihood strategies, both nature and people benefit from conservation. Natural ecosystems provide important services for people, including locally, such as protecting watersheds and pollinators, as well as globally, such as carbon sequestration. Without the native forests, and the lemurs that call those forests home, people would lose the valuable and irreplaceable services forests provide.
CITATION: “Drivers and Consequences of Structure in Plant–Lemur Ecological Networks,” Camille DeSisto and James Paul Herrera. Journal of Animal Ecology, July 15, 2022. DOI: 10.1111/1365-2656.13776.
DURHAM, N.C. — A jungle. A rainforest. A wetland. A wilderness. Researchers have used various metaphors to describe the complex, interconnected community of microbes (most of them bacteria) living inside your body, and all over it too.
If you were to count up all the trillions of cells inside and out, we are more bacteria than human. Fortunately, perhaps, the microbes that make a cozy home inside your nose, or clinging to your teeth, aren’t the same ones that are living behind your ear or busily multiplying in your belly button.
Lemurs rely on gut microbes to digest their leafy diets, explains Greene, a research scientist at the Duke Lemur Center. Microbes in lemurs’ GI tracts help ferment plant fiber, detoxify plant chemical defenses, and synthesize vitamins and nutrients that lemurs can’t make for themselves. Our own gut bugs do many of the same things for us.
Greene and McKenney study how lemur gut bacteria are shaped by what lemurs eat, how they evolved and the complexity of the route microbes travel through the body. They hope to better understand how these microorganisms keep lemurs healthy, or — when they’re out of balance — make them sick.
Researchers who do this kind of work spend a lot of time collecting poop. For good reasons, says McKenney, an assistant professor at North Carolina State University. Scientists can learn about lemurs by what they leave behind, and poop can be collected repeatedly without harming the animals. But for this study the team tried something different, made possible by a one-of-a-kind biobank:
When an animal dies at the Duke Lemur Center, veterinary staff determine the cause of death, and blood and tissue samples that might be important for research or education are collected and preserved.
Today, the collection holds thousands of samples, collected over decades from more than two dozen species of rare and endangered primates, which the center stores in super cold freezers in their headquarters in North Carolina. It’s a frozen ark maintained at up to minus 80 degrees Celsius, with redundant backup power.
In the event that any one of these species goes extinct, and the last living parts of them are gone, future generations will still be able to study the genetic and other information they left behind.
Using this bank, the team sampled several sites in the bowels of 52 deceased lemurs, including dwarf lemurs, aye-ayes, ruffed lemurs, bamboo lemurs, brown lemurs, ring-tailed lemurs and sifakas.
A trip through a lemur’s GI tract is a journey through a varied landscape. The long, twisting route from the stomach through the small intestine to the colon serves numerous functions, filtering, digesting, absorbing, detoxifying, fermenting.
Not all lemur guts work the same: Fruit-eaters, like ruffed lemurs, generally have short, simple guts. If you stretched them out, they’d be five times their body length — not much shorter than ours, relative to body size. Leaf-eaters like sifakas have more complex GI tracts with relatively longer colons and a leaf-fermentation pouch called a cecum. Their guts are the lemur champions — up to 16 times body length.
Having whole lemurs to study instead of just poo enabled the researchers to sample different regions of the gut to figure out what kinds of microbes were present in each spot. They used genetic sequencing technology to identify microbes and compare their relative abundance in different sites.
Sampling along the digestive tract, they found that different spots along this long, twisting pathway have their own communities of bacteria doing different kinds of jobs. The complex ecosystem lurking in a lemur’s small intestine, for example, isn’t the same as the microbial menagerie setting up camp in their colon.
Levels of biodiversity varied too. The stomach supports less microbial life because fewer species can tolerate its acidic digestive juices. But if the upper regions of the gut are a garden, the lower regions are more like a tropical rainforest. About two dozen types of bacteria were more abundant in the cecum and colon than elsewhere. Lemurs with relatively longer lower guts host the richest microbiomes, to better ferment high-fiber foods.
“We probably couldn’t have detected these relationships without such an extensive comparative dataset,” McKenney said.
“This kind of lemur research can really only be done at the Duke Lemur Center,” Greene said.
This research was supported by the National Science Foundation (DBI PRFB 1906416) and by a Duke Lemur Center Director’s fund.
CITATION: “Gut Site and Gut Morphology Predict Microbiome Structure and Function in Ecologically Diverse Lemurs,” Lydia K. Greene, Erin A. McKenney, William Gasper, Claudia Wrampelmeier, Shivdeep Hayer, Erin E. Ehmke, & Jonathan B. Clayton. Microbial Ecology, May 14, 2022. DOI: 10.1007/s00248-022-02034-4
An April symposium at Grainger Hall, People and Nature, brought a diverse set of speakers, both from Duke and other U.S. institutions, to examine the relationship between human culture and land and to discuss pressing issues such as environmental justice. The session was organized by PhD students Nicholas School of the Environment and the biology department.
Professor Paul Manos of Duke Biology told us how oaks, ubiquitous tree species in temperate regions, can make people think about nature. A walk in the woods looking at the different oaks can result in a fascinating journey of natural history. For those who are curious enough, an inquiry into the lives of oaks will take them deep into topics such as evolutionary history, leaky species boundaries, plant-animal interactions, among others, Manos said. Keeping true to the theme of the symposium, Manos explored some hypotheses about the first time that humans had contact with oaks, and how this relationship unfolded ever since.
Associate Professor Orou G. Gaoue of the University of Tennessee, Knoxville, took us through a detailed case study of human and plant interactions with long-term data from the country of Benin, in Africa. He showed how the harvest of the African mahogany (Khaya senegalensis) affects human demography and even the marriage dynamics of the Fulani people, with many other insights into the intertwined relationship of the locals and their harvest.
Central to the morning sessions were the rights of nature and the granting of personhood to non-humans, which is common in the cosmology of many indigenous cultures. For instance, Andrew Curley, assistant professor at the University of Arizona, mentioned in his talk that the O’odham people in the Sonoran Desert confer the Saguaro cactus personhood status. His talk exposed how colonial dynamics have created climate catastrophes and drought around the Colorado River, how indigenous peoples have to navigate these foreign systems, and how they understand their relationship with the land and water.
Michelle Carter, a first-year Masters of Environmental Management (MEM) student at Duke, examined the feasibility of the rights of nature in the US legal system. These rights allow certain natural features (e.g. rivers) to stand as a sole party in litigation and recover damages on their behalf. However, effective application and the enforcement of policy have been lacking.
The second part of the symposium focused on environmental justice. Duke Ph.D. student Maggie Swift presented a land acknowledgement which was divided into three parts: recognition of the violent history of the past; an understanding of the present with a celebration of the lives and achievements of current indigenous peoples; and a call to action so that participants were encouraged to financially support native-led organizations. Links for donations and more information can be found on the symposium website. The land acknowledgement was followed by a brief presentation on the project Unearthing Duke Forest that explores the human history surrounding Duke Forest.
Assistant professor Christine Folch, from Duke’s Department of Cultural Anthropology provided an analysis of the discourse around climate change. At the center was the question “do you believe in climate change?” which has ingrained the element of doubt and the ability of the speaker to say “no, I don’t.”
Associate professor Louie Rivers III, from NC State University, gave a talk on perceived environmental risks and their influence on social justice. He pointed out that these questions could be dismissed by certain groups such as black farmers, who are concerned and disproportionally affected by environmental issues but might not relate to how the question is addressed.
Sherri White-Williamson, Environmental Justice Policy director at NC Conservation Network, explained the concept of environmental justice and provided concrete examples of how certain policies (e.g. federal housing/lending policies or interstate highway systems) can create inequalities that leave communities of color to bear the exposure of environmental degradation. She also made us aware that this year is the 40th anniversary of the birth of the US environmental justice movement that started when an African-American community in Warren County, North Carolina organized to fight a hazardous waste landfill.
No exploration of people and nature would be complete without including the seas. A team of three students at the Duke University Marine Lab, undergrad Maddie Paris, second-year MEM Claire Huang, and Ph.D. student Rebecca Horan, presented two case studies of social and ecological outcomes linked to education and outreach interventions conducted in tropical marine environments.
Their first case study was on turtle education in Grenada, West Indies. Here a 10-week summer program for local children ages 9-12 created an improved understanding of marine turtle biology and its connection to the health of the ocean and their communities. The second case study was a 4-week training course for fisher people and fisheries officers in Mtwara, Tanzania. These participants increased their skills in monitoring the local reefs and were better equipped to educate their communities on marine environmental issues.
The symposium ended with two open questions for the audience, which should be considerations for anyone doing environmental research: Why is it important to jointly consider people and nature in your work? What insights do you gain in your work by taking this approach?
Guest post by Rubén Darío Palacio, Ph.D. 2022 in Conservation Biology from the Nicholas School of the Environment, and science director of conservation non-profit Fundacion Ecotonos in Colombia.
Emily Levy studies how the physical and social environments that baboons experience affect their physiology and life outcomes. The Massachusetts native, who works under advisor Susan Alberts (PhD), is in the final year of her Biology PhD and will defend her thesis later this Spring.
Though Duke’s in-person classes have been delayed until next week, I caught up with Levy over Zoom. The wall of her home office displays a fascinating Russian map of Chicago from the cold war era that shows bridges with their weight capacity. Levy tells me that she had no idea how her husband, who is from Evanston, found the map.
“Something that I really appreciate about Susan and the way she runs the lab is that she starts first-year grad students on a starter project,” Levy told me. Following a discussion about Levy’s interests, this project led to her first work on dominance rank, stress levels, and what this means physiologically for baboons. Levy also “poked around” at how scientists study dominance rank and found that the methods used for assessing rank “matter a lot.”
In her more recent project, Levy is trying to figure out what early life environments mean for adulthood in baboons. “So, we know that baboons that experience a really harsh early life, if they survive to adulthood, have really, really reduced lifespans as adults – like half as long – as baboons that had no adverse events,” Levy said.
“I’m focusing on two hypotheses to get at what might be happening under the skin that could have something to do with longer term effects on health and mortality.” One hypothesis is that a tough early life environment, especially nutritional stress, could stunt baboon growth and impinge adult activities like foraging or maintaining dominance rank. The other hypothesis proposes that early life adversity disrupts immune development, leading to an immune system that is either always inflamed or produces an overpowering inflammatory response when a baboon does get sick.
The second hypothesis is one that has been supported by human research, but Levy’s preliminary results “are the exact opposite.” This highlights one facet of the importance of her research: Its implications and parallels to human health and mortality. But Levy says her research is also “cool because it’s just cool” and appreciates what her work may add to basic science beyond human application.
In her journey to Duke, Levy said that she “tried a few ways of studying” animals before arriving at the work she conducts now. Levy, who really liked animals, enjoyed time outside, and was “hooked on biology” in high school, began her undergraduate career at Williams College with this in mind. “In college, I took biology and neuroscience and then took animal behavior my sophomore year and was like Oooo, this is cool!,” Levy exclaimed with a big smile on her face, “And it felt sort of light-bulby.”
Along the journey to her PhD, Levy studied plants and insect pollinators and spent a few weeks in Madagascar in a tent filled with fleas. Though Levy said that these experiences of field work became “one of my favorite things about my job,” they also helped shape her trajectory as a scientist as she figured out which model systems and research questions “did and did not spark her joy.”
It was during her undergraduate thesis assessing social behavior in rats that she felt a strong “click” for studying social behavior in animals. Taking a couple years to work in a clinical research lab that conducted work on autism in humans, Levy enjoyed working on research to aid in special needs people. “But pretty quickly,” Levy said, “I was like, Alright, I don’t want to study humans for my whole life.”
“I’d basically been crossing things off my list up until this point,” Levy continued, “I now knew I wanted to study social animal behavior in non-human animals.” In her year away from research, Levy worked as an outdoor educator in Wyoming while she applied to grad school with this study plan in mind. Her time in Jackson Hole, Wyoming narrowed her interests even more, pushing her towards behavioral ecology because of her observation of an amazing, unbroken natural ecosystem.
Levy says she ultimately ended up at Duke because “the Baboon Project is amazing,” “Susan Alberts is amazing,” and “the Duke Biology Department is really wonderful.”
While Levy enjoys working with Alberts and mentoring undergraduates, as well as using grant writing as a “fun way to develop really exciting ideas and hypotheses,” she also shared some of her frustrations with me. “Science is very slow — often, not always — and a project from start to finish takes a long time. And the publication process is so long. I struggle with that pace sometimes” Additionally, as someone who was raised to never take herself too seriously, Levy also said that she has felt a lot of pressure in grad school to take herself more seriously than she should as part of academic culture.
Levy loves teaching and her hope is to become a faculty member at a small liberal arts college or undergraduate institution following a post-doc, for which she is currently in the application process. Through this future work, Levy aspires to “bring undergrads through the scientific process.”
In her time away from the lab and science, Emily is an avid baker. “One of my goals in grad school has been to acknowledge and own what I am good at, and I know I am good at baking,” Levy said with a grin. Chocolate chip cookies are her specialty.
If she could give any aspiring science PhDs a word of advice, Levy offered that you should have fun and “pay attention to the non-intellectual, as well as intellectual, things that you enjoy most.” As exemplified by her path to figuring out what exactly it was in science that inspired her, Levy says not to worry as much about figuring out where you are going, and when, but reaping the lessons and insights of the experiences along the way.