Microbial Rewilding in the Gut Microbiomes of Captive Ring-Tailed Lemurs (Lemur catta) in Madagascar

19 January 2023by Barış Özdinç

The gut microbiome is critical to good animal health and environmental factors are influential on the microbiome. Environmental variations such as altered ecosystems, degraded habitats, deforestation or captivity may have negative impacts on host-microbiome communities, and cripple host fitness, making it a vital issue for ecology research.


In this blog, we will explore the latest research into how microbial rewilding could be used to restore gut microbiomes in captive ring-tailed lemurs (Lemur catta) in Madagascar. By understanding the impact of our environment on these animals, we can ensure their health and well-being for generations to come.

Why does microbial rewilding in the gut microbiomes of lemurs matter?

The microbiome-host links of animals under captivity are particularly interesting for conservation purposes. The Microbiome Rewilding Hypothesis (MRH) suggests that the restoration of ‘green’ habitats and promotion of diverse environmental microbiomes in urban settings can improve human gut microbiome and health. 


However, humans are heavily studied animals, and findings on humans cannot always be extrapolated to conservation animals. 


To understand if the MRH could be expanded from humans to conservation animals, the study of Bornbusch et al. (2023) collected fecal samples from captive lemurs, wild lemurs and lemurs which were recently transferred to a naturalistic rescue center in Madagascar from captivity.

What does the research say?

Understanding the gut taxonomic and functional gut microbiome variations in lemur cohorts required accurate profiling and quantification of fecal microbes and functional genes. 


The gut taxonomic variation in lemurs was characterized by both amplicon and shotgun sequencing. Functional gene profiling was done using the shotgun sequencing data. All lemur fecal samples were subjected to amplicon sequencing of the 16S rRNA gene V4 region before a subset of samples were sequenced by paired-end shotgun sequencing with a read length of 150 base pairs by CosmosID Inc.(Germantown, MD). 


Downstream analysis of the shotgun metagenomic data was performed on the CosmosID bioinformatics platform, the CosmosID-HUB (CosmosID Inc, Germantown, MD), to characterize cross-kingdom microbial and functional metagenomic compositions.

What were the findings?

According to the study, analysis of the fecal taxonomic and functional metagenomics data of lemurs from wild, captivity and rescue centers illustrated different areas of evidence in favor of MRH in lemurs. 


A lemur’s exposure duration to the naturalistic rescue center settings significantly correlated with the convergence to the gut communities of wild lemurs, decreased proportions of antibiotic resistance genes that were likely acquired via human contact during human captivity, and greater covariation with soil microbiomes from natural habitats. 


Beyond the inherent psychosocial value of naturalistic environments, the authors found that specific actions, such as providing appropriate diets, minimizing contact with humans, and increasing exposure to natural environmental consortia, such as soil microbiota, may assist in maximizing host-microbe homeostasis in conservation animals. 


To read more about the original paper highlighting implications for animals under conservation, please check out the original study

How did CosmosID support this research? 

CosmosID’s comprehensive microbial identification and data analysis platform proved to be a valuable resource for the research team. Utilizing CosmosID’s integrated analytics, the researchers were able to accurately interpret all of their data for further downstream interpretation.


The powerful combination of CosmosID’s microbiome sequencing services, such as amplicon sequencing and shotgun sequencing, provided the researchers with comprehensive profiling of the lemur gut microbiome. At the same time, CosmosID’s integrated analytics enabled downstream analysis to characterize and compare taxonomic and functional metagenomic compositions across different cohorts.


In conclusion, the research team was able to confirm the MRH in lemurs from this study, demonstrating that animals can benefit from appropriate care and exposure to naturalistic environments. By providing insights into the impact of human contact and captive living conditions on the microbial composition, this study provides a valuable contribution to our understanding of conservation animal health.

Discover the benefits of using CosmosID for your research…

CosmosID provides powerful and comprehensive microbial analysis services that enable you to quickly and accurately identify microbes, characterize their relationships, and gain insights into the role of microorganisms in health and disease.


Our integrated analytics allow for quick downstream analysis of taxonomic composition, functional composition, antibiotic resistance genes and more. Additionally, our microbiome sequencing services provide versatile and high-quality data for a wide range of applications. Our workflow automation, accessible web platform, and highly experienced bioinformatics team provide seamless support from sample collection to results interpretation.

Contact us today to learn more about our services and how CosmosID can help you reach the next level in microbial ecology research.

Barış Özdinç

Barış Özdinç analyzes microbiome research with his educational background in genetics and evolution. As a research analyst for CosmosID, he combines metagenomics and data analyses to identify microbial biomarkers in disease cohorts and evaluate microbiome research tools. His work involves curating microbiome data and creating interesting microbiome content for newsletters and blog posts. Barış Özdinç received his bachelor’s degree in genetics and master’s degree in biodiversity, evolution, and conservation from University College London (UCL). Currently, he lives in Istanbul, Turkey, where he lives with his cat, Delight, and mentors female students in their STEM career pursuits.