Mass extinction also happens in your gut
Our world is in the midst of its sixth mass extinction. Up to 50% of all plant and animal species are likely heading towards extinction by 2050. It’s well known that human activities greatly impact the biodiversity around us, but we also must be aware of how the invisible diversity living inside us, our microbiome, is also experiencing drastic disturbances.
Our gut microbiome – whose composition is strongly influenced by our diet, genetic background, and lifestyle - has a crucial role in bodily functions like metabolism and immune responses. A growing number of studies highlight that people living in non-industrialized and rural lifestyles possess a more diverse gut microbiome, with critical differences in bacterial species diversity and functions, in comparison to people living in urban and industrialized lifestyles. Additionally, lower species diversity and/or high compositional disturbances in the gut microbiome are associated with several non-communicable diseases, such as metabolic syndrome and inflammatory bowel diseases. Such ecological perturbations occurring inside our own organism are concerning, and are likely to cause or amplify disease phenotypes (severity of disease). Thus, further investigations are needed to fully understand their impact on host-microbe interactions and health.
Since bacterial organisms have developed resistance mechanisms to face changing environments and have colonized every single ecosystem on the planet, it is often thought, even among communities of microbiologists and geneticists, that bacterial lineages cannot undergo extinction. However, recent studies provided a quantification of extinction rates in bacteria and confirmed that bacterial lineages go extinct almost as frequently as they emerge.
From left to right: (1) African Elephant and (2) African paradise flycatcher, Lake Manyara National Park, Tanzania (3) Human gut bacteria grown on a blood agar plate under anaerobic conditions
Credits: Christopher Corzett – Mathilde Poyet
Just as global warming, deforestation, and environmental pollution impoverish ecosystems of the planet, the consumption of processed food and the abusive use of antibiotics and sanitizers contribute to the decrease of human-associated bacterial diversity. As a result, some commensal microbes that have co-evolved with us for millennia – and which represent an integral facet of human health and history – may soon go extinct. We already find many gut bacterial species that now exist almost exclusively among members of non-industrialized, isolated human populations; yet these populations, along with their lifestyle and culture, are under threat from globalization and climate change.
A long-term safeguard against extinctions of human-associated microbes
As scientists engaged in the Global Microbiome Conservancy (GMbC), we strongly support efforts to conserve human-associated microbial diversity where it naturally exists by educating the public about the negative effects of processed foods and antibiotic consumption. In parallel, since major losses are already happening at a global scale, we are committed to collecting the diversity of gut microbiomes, and preserving it within laboratory repositories for the health of future generations.
Since 2016, the GMbC consortium has been collecting and preserving microbiomes from diverse human populations around the world, ranging from fully urbanized populations to highly isolated groups who have historically been overlooked by basic and biomedical science. To date, fecal samples of over 1,000 individual adults living in 32 distinct regions across the globe have been collected. In aiming to capture the full diversity of human gut microbiomes, we are promoting the inclusion of populations living non-industrialized lifestyles, such as rural farmers, pastoralists, fishermen, and hunter-gatherers.
The inclusion of underrepresented groups is essential. Existing microbiome collections are historically limited to industrialized ‘majority’ populations. Additionally, the gut microbiomes of industrialized human populations are significantly less diverse than those of non-industrialized populations and thus do not reflect the full diversity of human gut microbes. Imbalances in microbiome knowledge and resource then further amplify healthcare inequities, with underrepresented groups being less likely to benefit from scientific and medical advances tailored to well-studied populations.
Left to right: (1) Man of a Moors village leaving in a warm, sandy, desert area at the border between Senegal and Mauritania. (2) Women of a Hmong village, wearing the traditional outfit at an annual festival in the area of Mae Sot, North-Western Thailand. (3) Women of a Datoga pastoralist village mainly relying upon close association with their livestock, near the Lake Eyasi in Tanzania. Credits: Christopher Corzett – Mathilde Poyet
For a very long time, the vast majority of gut bacterial species were considered to be “unculturable” under laboratory conditions. With recent technological and microbiological advancements, we are now capable of growing a wide range of intestinal microbes, mostly in oxygen-free environments. The GMbC collection of bacterial cells - maintained as a secure public library – currently contains 16,000+ bacterial lineages, including dozens of human gut bacterial species that had never been successfully cultured before. Every single sample brings to light a new set of poorly characterized and unknown bacterial species, leading us to realize just how little we know about the existing microbial diversity colonizing humans. If anything, it strongly motivates us to continue our collection work to better understand the microbes that live in symbiosis with humans.
The GMbC biobank will continuously be enriched over the years to capture the full biodiversity of the human gut microbiome – and by safeguarding this endangered biodiversity, we aim to advance our understanding of this critical facet of human health. By building this resource and making it available to scientists, we wish to advance microbiome research and ultimately human health worldwide.
Mathilde Poyet and Mathieu Groussin are senior post-doctoral associates in Eric Alm Laboratory, Massachusetts Institute of Technology. By developing advanced methodologies, they investigate bacterial species associated with humans. In 2016 they co-founded the Global Microbiome Conservancy to preserve this particular and vital biodiversity and to understand how microbiomes impact human health.
Malaysia, 2019 Thailand, 2019