The microbiome of the indri, a critically endangered lemur, has been described

Joint research between the Department of Medicine and Life Sciences (MELIS) at Pompeu Fabra University and the University of Trento (Italy) has, for the first time, ascertained the composition of the intestinal microbiome of the indri, a critically endangered lemur only found in the north-east of Madagascar. In addition to determining up to 47 hitherto unknown species of bacteria, the study has concluded that the indri’s microbiome is transmitted within their social group. This could have implications for the preservation of their habitats. 

Indri indri, or babakoto in the local language, is an arboreal lemur endemic to Madagascar that lives in the tropical forests of the north-east of the island and feeds on leaves, fruit, seeds, flowers, bark, and sometimes soil. According to the red list of the International Union for Conservation of Nature (IUCN), the indri is in critical danger of extinction due to the loss of its habitat as a result of climate change and human activity. 

Indris live in small families –stable social groups– of between two and five individuals. They are monogamous and live in a matriarchal society forming long-term bonds. Interaction between individuals of different groups is minimal as each group occupies a well-delimited territory. In addition, it has never been possible to keep the species in captivity. 

The study, published in the journal ISME of the International Society for Microbial Ecology, has analysed the microbiome of faecal and soil samples from the regions inhabited by six families of indri. By assembling genomes, the research team has identified 48 species of bacteria that make up the microbiome of the indri. Almost all the sequenced species (47) had not been described to date and are specific to the microbiome of these lemurs. “The only known species that has been identified is E.coli and it has been found mainly in indri populations living closer to areas frequented by humans”, explains Mireia Vallès Colomer, a researcher at MELIS-UPF, who led the study. 

“We have discovered that the vast majority of bacterial species in the indri microbiome are new and specific to these lemurs. So, if the Indri becomes extinct, so too will the bacteria that compose their microbiota”, Vallès-Colomer points out. 

In addition, the researchers have determined that the microbiome is transmitted between indri of the same social group and that they do not obtain any species from the ground, despite ingesting soil. “All indri have the same species of bacteria, but bacterial strains vary from one social group to another. Each “family” has unique bacterial strains, and the genetic distance between the strains correlates with the distance between the populations of lemurs that live isolated from each other”, notes Nicola Segata of the University of Trento, who co-led the study. 

Despite being a preliminary study –due to the sample size studied– “we hope that the description of the indri microbiome will be another tool to preserve its increasingly fragmented habitat and help keep the species from extinction”, Segata concludes.