The gopher tortoise gut microbiome

A gopher. Not a gopher tortoise. From the movie Caddyshack.

A few weeks ago I wrote about a study on socially structured gut microbiomes in wild baboons. Well, now I’m here to tell you about a new study that examined the population structure of tortoise gut microbiomes.

Gopher tortoises are zero part gopher and 100% tortoise (they get their names from their burrowing behavior). A threatened species that live in the southeastern United States, gopher tortoises are obligate herbivores and hindgut fermenters. This last bit of information was the primary reason that Michael Yuan and colleagues opted to study the gut microbiota of these interesting reptiles.

Gopher tortoise entering burrow (from Wikimedia commons)

In their study, recently published in Molecular Ecology, Yuan et al. used the ever-popular sequencing of 16s rRNA to examine whether or not gopher tortoises had similar gut microbiota to those present in mammalian herbivores. What they found was pretty interesting:

“The relative abundances of microbial phyla in gopher tortoise feces were more similar to those reported in a diverse assemblage of hindgut-fermenting mammals”

They also found 16s regions that were members of a group of microbes that are found in termite guts: called “Termite Group 3”. Yuan told me:

“It’s cool because, to our knowledge, members of TG3 have never been reported in vertebrates – even transiently in myrmecophagous (termite-eating) mammals. While it is possible possible that these bacteria are just surviving the journey through a tortoise gut and actually come from a tortoise accidentally eating a termite. But that seems unlikely given the fact that this group was found in the guts of almost all of our study individuals. So we think that these microbes are part of the same cellulose digesting mechanism in tortoises as they are in termites.”

The authors also looked at how age, genetic background, geography, and kinship influenced the gut microbiome. In short, they found that:

“Although host genetic structure did not explain variation in microbial composition and community structure, we found that fine-scale spatial structure, inbreeding, degree of relatedness, and possibly ontogeny shaped patterns of diversity in fecal microbiomes of gopher tortoises.”

Specifically, close kin had more similar gut microbiota, which could be due to vertical transfer from mother to offspring or through sibling association (and possibly coprophagy). And juvenile tortoises exhibit comparatively less richness than adults. Yuan gave me two possible explanations for this observation: 1) that juvenile tortoises are much more selective in their foraging, and/or 2) juveniles are born with simple gut microbial communities and have to “diversify” as they grow up. But he also said that this finding should be interpreted with caution as they only had a sample size of three juveniles “because it’s [expletive]-ing hard to find baby tortoises.” Ah, the difficulties of field work!

Yuan ML, Dean SH, Longo A V, Rothermel BB, Tuberville TD & Zamudio KR (2015) Kinship, inbreeding, and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise. Mol. Ecol. doi: 10.1111/mec.13169


About Noah Snyder-Mackler

I'm a postdoctoral fellow in the department of Evolutionary Anthropology at Duke University. Broadly, I study non-human primate genetics and genomics. More specifically, I'm interested in the interaction between behavior, genotype, and gene expression in response to social stress.
This entry was posted in community ecology, genomics, natural history, next generation sequencing, population genetics, Uncategorized and tagged , , . Bookmark the permalink.