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Keystone Species in the Gut

Key Players in Human Health


Among the trillions of microbes that live in our intestines, scientists have found a few species that seem to play a key role in keeping us healthy.

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In an ecosystem like our gut microbiota, bacteria rely on each other and work together for normal functioning and health. Some bacteria are redundant and their function can be easily replaced by other bacteria. However, some species are crucial to the functioning of the ecoystem. These crucial species are also called “keystone” species. In the gut, keystone species play an important role in maintaining the structure of the gut microbiota and maintaining human health. They seem to be indispensable since their functionalities are not easily taken over by other species. When a keystone species becomes extinct, the well-being of other species will be affected as well, which can result in an overall loss of microbial biodiversity. It has been shown that many human diseases affecting westernized countries are associated with dysbiosis and loss of microbial diversity in the gut microbiota, which highlights an important role for keystone species in human health.



All animals are equal, but some animals are more equal than others


George Orwell, Animal Farm

Sophisticated microbial detection research tools have provided us with better understanding of which bacteria are present and how they function. These technologies have helped us to identify the species that are associated with the onset of a variety of diseases. Examples of bacterial species that are nowadays internationally recognised as essential to maintain proper gut microbiome functioning are species such as Ruminococcus bromii, Faecalibacterium prausnitzii, Akkermansia muciniphila and Eubacterium hallii. 




R. bromii

Ruminococcus bromii is an important keystone species in the breakdown of resistant starch in the human large intestine. The bacterium also supports other bacteria in their functioning, as can be seen in the graph. It has been shown, that when Ruminococcus bromii is grown on resistant starch the bacterium shows excellent growthThis in contrast with another common gut bacterium, Anaerostipes hadrus that is barely able to grow on resistant starch. However, when the two species are combined (co-cultured), both species show excellent growth indicating that Anaerostipes hadrus is able to utilize the metabolites resulting from the degradation of resistant starch by Ruminococcus bromii






Ruminococcus=Rb, Anaerostipes hadrus=Ah

F. prausnitzii 

F. prausnitzii is one of the most dominant bacteria in the human gut microbiota and can make up to 5-10% of the total number of bacteria detected in stool samples of healthy humans. Low counts of F. prausnitzii have been correlated with several pathological disorders, such as chronic inflammatory intestinal disorders (Crohn's disease, Ulcerative Colitis, IBS)  and colon cancer. 




A. muciniphila

Akkermansia muciniphila is an important bacterium in metabolic health. The anaerobe bacterium resides in the mucus layer and supports the proper functioning of the intestinal barrier. The bacterium has been associated with the development of diabetes, autism, obesity, metabolic disorders and IBD.




Future plans

Keystone bacteria could offer a potential treatment strategy in treating the autoimmune, allergic and inflammatory disorders that have increased in recent decades. Winclove is now looking into the possibilities to bring probiotic formulations to the market containing these keystone species. However, one of the difficulties with these gut-derived species is that most of them are strictly anaerobic and thus hard to grow under standard culture conditions. We are in the unique position to have experts in house who have in-depth knowledge on these keystone species and are able to optimize (anaerobic) fermentation processes. Another challenge we face is a regulatory challenge since most of these keystone species are not on the Qualified Assumption of Safety (QPS) list. We are exploring the possibilities to guarantee safety of such strains and  bring them to the market.



  Among Trillions of Microbes in the Gut, a Few Are Special  




An alternative to increasing the keystone species in the gut by (re)-introducing them, is to stimulate their growth in the gut. This goal can be achieved with prebiotics. Prebiotics are non-digestible, fermentable food ingredients, defined as “selectively fermented ingredients that allow specific changes, both in the composition and/or activity of the gastro-intestinal microflora that confer benefits upon host well-being and health”. Prebiotics are usually carbohydrates or fibres, but not all carbohydrates are prebiotics. Many of the species residing in the gut are saccharolytic, which means that they need carbohydrates (e.g. sugars) to grow on. These species derive most of their energy from the food that we ingest.  Since not all bacterial species are the same, one can imagine that each species has their own preference for which specific carbohydrate(s) (and which prebiotic)s it can use for growth.

Winclove has introduced two prebiotic formulations on the market and at the moment we are looking into formulations that focus even more on stimulating keystone species and short chain fatty acid production. 






Key stone species

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