Hi MO BIO community! I’m Lydia Greene, a Ph.D. student in the Ecology program at Duke University. My dissertation research is focused on the gut microbiomes of lemurs, you know, those bug-eyed primates from Madagascar that happen to be the most threatened group of mammals on earth. I specifically work with indriids, a group of critically endangered lemurs that include the indris, woolly lemurs, and sifakas. Go google them, seriously. They are some of the most exotic and stunning animals on the planet.
Madagascar is chock full of stunning wildlife and scenery. The island is enormous: It’s the fourth largest island on earth, behind only Greenland, New Guinea, and Borneo. Because of its large size, Madagascar comprises varied climates and ecosystems, ranging from tropical rainforests to deciduous and mangrove forests, spiny deserts, and plateaus. Madagascar has been isolated from other land masses for about 88 million years, which has allowed for some crazy evolutionary history. The island’s endemism levels are unmatched with 80% of the flora and 90% of the fauna found nowhere else on earth. Besides the ~80 species of endemic lemur, the Malagasy fossa, tenrecs, and chameleons, as well as the hundreds of endemic orchid species and six endemic species of Baobab tree are well worth a google. Unfortunately, Madagascar’s wildlife is under intense pressure from deforestation due to slash-and-burn agriculture and illegal logging: An estimated 90% of the island’s forests are now gone.
But enough about Madagascar’s history and back to lemurs. Indriids, the lemurs I study, are folivorous (leaf eaters). To survive on a primarily leaf-based diet, they have a highly specialized gastrointestinal system that includes long intestines, an enormous sacculated cecum (a glorious pocket the appendix dreams of becoming), and a lot of gut bacteria that help convert plant material into usable energy. In my research, I’m trying to understand how indriid gut microbiomes facilitate host dietary flexibility, by helping their hosts extract nutrients from diverse food substrates. Likewise, I’m examining if indriid gut microbes promote host health by clearing pathogens or potential toxins from the intestinal tract. I hope that my research will not only illuminate the symbiotic relationship between lemurs and their gut bacteria but will also inform conservation strategies for both captive and wild lemurs.
What this all means is that I collect a lot of lemur poop. Luckily, fecal samples can be collected non-invasively, which is a definite bonus when working with endangered species. I collect poop from wild indriids living in both intact and disturbed Eastern rainforest habitats to compare how microbiomes change with forest quality. I am also sampling a captive population of ~30 sifakas housed at the Duke Lemur Center (DLC). The DLC is a unique facility in Durham, NC that is dedicated to the conservation and study of lemurs and maintains the largest and most diverse collection of lemurs outside of Madagascar. At the DLC, I can study how different or specialized sifaka diets result in different or specialized gut microbial consortia. True story: I collect so much lemur poop that I am now referred to as a ‘poop ninja’ by the DLC research coordinator.
And this is where MO BIO comes in. I have to be able to extract genomic DNA (gDNA) from fecal samples in order to determine which microbes or microbial genes comprise a lemur’s gut microbiome. Specifically, I’m sequencing the 16S rRNA gene, a gene common to all bacteria with enough variability to allow me (and many others) to determine the taxa present in a microbial community. Successful sequencing begins with high-quality gDNA extracted from fecal samples. Indriids are folivorous and because of this, their fecal samples are hard and pelleted, and most closely resemble goat poop. MO BIO’s PowerSoil®DNA Isolation Kit may have ‘soil’ in its name, but it’s also optimized for fecal samples and has been able to break apart the fibrous samples I work with to produce excellent quality gDNA. Lemur guts, like human guts, are densely populated with microbes, thus, I only need to use a tiny amount of feces- 0.1g, which is about half a sifaka pellet. This means I have plenty of sample leftover for backup extractions or for other types of assays! This is terrific because I will also be using shotgun metagenomics down the road. Shotgun sequencing will allow me to determine the genes that are present in a sample, rather than just the bacterial taxa. Although I’m not sure what the results of my dissertation will ultimately reveal, I do know that my project wouldn’t be possible without good-quality gDNA. Thanks, MO BIO!