What zoo animals teach us about a healthy microbiome

Extensive comparative study at Kiel University on the composition of bacterial colonization in zoo animals provides new insights into the loss of microbial diversity in the human body

For several years, life science and medical research has focused on how the microorganisms living in and on a body influence key life processes and thus the health and disease of their host organisms. Scientists at Kiel University, among others, have been able to gather numerous pieces of evidence that there are connections between the entire microbial colonization of the body, the so-called microbiome, and the development of diseases. Specifically, inflammatory bowel disease (IBD) is closely linked to the composition and balance of the microbiome. Together with numerous other so-called environmental diseases, their incidence has increased sharply in recent decades. Researchers see one possible cause in the massive decline in the microbial biodiversity of the human microbiome. The impoverishment of the microbiome is probably due to the radical change in living conditions in Western society, which are characterized by industrially produced foods, comprehensive hygiene measures, massive use of antibiotics and socially isolated lifestyles, among other things. Researchers see great potential in future interventions to restore a healthy microbiome. Important clues to define such a healthy state are provided by comparative microbiome studies – both with pristine human societies and with animals.

Researchers at Kiel University have now analyzed a total of 368 stool samples from 38 different animal species ranging from ruminants to primates in an extensive comparative analysis as part of the Collaborative Research Center (CRC) 1182 “Origin and Function of Metaorganisms” to investigate the influences of evolutionary relationships among the different species and external living conditions on the composition of the microbiome. They collected the sample material from seven German zoos and compared it both with each other and with human samples by determining the microbial species contained therein by genome sequencing and were thus able to characterize the different microbiome compositions of the various animal species in each case. The research team from the Institute of Clinical Molecular Biology (IKMB), led by Professor Andre Franke, found that the occurrence of certain bacterial species is declining in some monkey species, for example, but also in humans, and that their microbiome is apparently becoming depleted, particularly in adaptation to changes in their living conditions. The researchers, who are also involved in the DFG research group miTarget, recently published their findings in the journal BMC Microbiology.

Lifestyle influences the microbiome in humans and animals

The composition of the microbiome depends on many different factors. These include diet, environmental influences or the kinship relationships among host organisms. To obtain their data under controlled conditions, the Kiel researchers collected samples from captive animals fed according to uniform standards in zoos in Hamburg, Berlin and Neumünster, among others. Such collaborations are of great value to science, as they can provide easily accessible sample material and thus important data sources for a whole range of research questions. In the current work, for example, the sample material collected in the zoos forms the basis of a novel biobank, some of which contains completely unknown microbial species and is therefore of great scientific interest. “When analyzing the microbiome data, we first found that geography does not seem to have a major influence on bacterial colonization of the gut and that the composition of microorganisms is largely independent of location,” says first author Dr. Corinna Bang, head of the microbiome lab at the IKMB. “In contrast, phylogeny, i.e. the evolutionary relationships of living organisms – and thus also their own genetic makeup – fundamentally plays the most important role in microbiome composition. The more closely different species are related to each other, the more similar their microbiome is, because it has developed largely in parallel over long evolutionary periods,” CRC 1182 member Bang adds.

Under certain circumstances, however, it can happen in the animal kingdom that this actually determining factor recedes into the background and is overshadowed by the effects of special living conditions. The researchers of SFB 1182 were able to shed light on this aspect when they compared the microbiome data of certain African monkey species with those of monkeys from South America. Although they are relatively closely related, their lifestyles differ greatly: In the case of the African animals, they live in large social associations on the ground; their South American relatives, especially in zoos, live in trees in relatively isolated small groups. Surprisingly, their contrasting lifestyles were also reflected in marked differences in the composition of their respective microbiomes. “Thus, the differences in lifestyle here override the influence of relatively close kinship. Specifically, this means that there is a marked decline in characteristic individual bacterial species in the South American monkeys compared to the African animals. We suspect that this impoverishment of their microbiome is related to their comparatively low-contact lifestyle,” Bang continues.

In this aspect, the Kiel researchers see an important parallel to the development of the human microbiome. “The loss of certain bacterial species in the microbiome – particularly Spirochaeta and Prevotella, which help digest fiber-rich, plant-based food components – is observed not only in South American monkeys, but also in humans. These consistent patterns support the notion that microbiome depletion may be related to rapidly changing human living conditions,” emphasizes Louise Thingholm, Ph.D., a bioinformatician at the IKMB.

Promoting a healthy microbiome

From an evolutionary perspective, the transition to an industrial and urban lifestyle in the Western world has occurred in a very short period of time in recent decades. One hypothesis of the researchers is therefore that human microbial communities – having changed little over millennia, as in the animal kingdom – were unable to adapt to the abrupt emergence of the Western lifestyle. This, he said, explains the drastic decline in microbial diversity with its numerous health consequences. “A fundamental task for future microbiome research will therefore be to define precisely which components of the body’s original bacterial colonization need to be restored in order to alleviate or prevent certain microbiome-associated diseases,” summarizes miTarget spokesperson Franke, who also leads a subproject in CRC 1182. “On the one hand, this could be done in the future through targeted interventions in the microbiome by therapeutic means. However, it will be equally important to promote a preventive lifestyle that allows for more microbial diversity again,” Franke added. In identifying therapeutic targets in the microbiome, research is currently in its infancy, despite promising prospects. A microbiome-friendly lifestyle, on the other hand, can already be realized today and essentially consists of at least mitigating the aspects of the Western lifestyle that are problematic from a microbiological point of view and allowing more contact with microorganisms again in a variety of ways

Original article:
Louise B. Thingholm, Corinna Bang, Malte C. Rühlemann, Annika Starke, Florian Sicks, Verena Kaspari, Anabell Jandowsky, Kai Frölich, Gabriele Ismer, Andreas Bernhard, Claudia Bombis, Barbara Struve, Philipp Rausch and Andre Franke (2021): Ecology impacts the decrease of Spirochaetes and Prevotella in the fecal gut microbiota of urban humans. BMC Microbiology First published 11. October 2021 DOI: 10.1186/s12866-021-02337-5

More information:

By analysing 368 stool samples from 38 different animal species, the Kiel researchers investigated the influences of kinship relationships and external living conditions on the microbiome composition.

© Dr Corinna Bang / A. Starke

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