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Current Research on the Cheetah Microbiome

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A microbiome is a community of microorganisms that share our body space and play an important part in our physiology and health. Most of these organisms inhabit our gastrointestinal tract, but natural microorganism communities also live on our skin, in our mouths and elsewhere in our bodies. It is estimated that there are 10 times as many microbial organisms (about 100 trillion organisms) on and in the human body than actual human cells. Each of us is therefore a walking ecosystem rather than an individual entity.

Recent research has shown that these microbes play an important part in food digestion, immune systems development and function and the synthesis of various vital nutrients. It is becoming evident that imbalances or changes in the composition of these microbial communities may play an important role in the development of several chronic diseases and increase our susceptibility to infections.

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In the past, it was rather difficult to identify all the microbes in these communities, because most cannot be cultured artificially in a laboratory. Recent DNA sequencing technology has however enabled us to identify the genes of different bacteria, fungi and other microorganisms. The gene sequences provide a kind of fingerprint for each species or group of species, allowing us to establish a library of microbial genetic data.

An individual’s microbiome is influenced by several factors, including their own genetic makeup, diet, exposure to antibiotics and level of personal hygiene. This variation makes it difficult to evaluate a "normal" or natural microbiome in humans and domesticated animals. Free-living animals however, that live in a relatively unaltered environment, eat a near natural diet and are not exposed to antibiotics, provide researchers with an opportunity to study their more pristine or natural microbial communities. Such studies have only recently started to appear in the scientific literature. One such study on the faecal microbiome of free-ranging cheetahs and black backed jackals, was recently published in the journal – Frontiers in Microbiology (Menke et al 2014 – available online at: ).

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Bacteria present in fresh faecal samples fairly accurately reflect the population composition of these species in the colon of the animals from which the samples were obtained. In this study, fresh faecal samples were collected from these two species at various locations in Namibia. Cheetahs are strict carnivores and eat a smaller range of prey species than the more omnivorous black backed jackals. It was therefore no surprise that the cheetah faeces contained a smaller variety of bacterial species than that of the black backed jackals. Unfortunately only a small amount of microbiome data is currently available on other captive or free-ranging carnivores, but already this study was able to demonstrate that major faecal microbiome differences exist between samples obtained from captive or domestic carnivores and those obtained from carnivores in the wild.

There is however a long way to go before we get a clearer understanding of how these differences relate to the actual health of individual animals. At the AfriCat foundation microbiome research is already being undertaken to understand the role that microorganisms play in the health of both captive and free-ranging carnivores. Dr Holly Ganz from the University of California, Davis, Dr Adrian Tordiffe from the National Zoological Gardens of South Africa, Dr Gerhard Steenkamp from the University of Pretoria and others, have already collected samples from cheetahs, lions and leopards from AfriCat’s Care Centre and from the wild-roaming cats in the Okonjima Nature Reserve for the initial microbiome research in these species. Various grants will hopefully provide more funding for much larger studies, including research on the influence of diet composition on the cheetah gastrointestinal microbiome in the future.


Oligotyping reveals differences between gut 'microbiomes' of free-ranging sympatric Namibian carnivores (Acinonyxjubatus,Canismesomelas) on a bacterial species-like level.

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