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Understanding the complex ecosystem that is our gut microbiome: how new technologies are identifying undiscovered species

Many studies that look at the microbiome assess how the microbiome changes due to a certain illness or condition, or how the microbiome of a sick person differs from a healthy person. So we see if certain species increase or decrease. However, what if we don’t even know about all the types of bacteria in the microbiome? How can we be sure we are assessing the right things? Well, this year alone, about 2000 new types of bacteria have been discovered in the gut microbiome!

 

A very recent study discovered about 100 new types of bacteria and developed a resource for other researchers to understand which bacteria are present in their microbiome samples.

 

Researchers used faecal samples from twenty people in the UK and Canada, and then grew and determined the DNA sequences of 737 different types of bacteria. These included 173 species that had never had their DNA sequenced, and 105 that had never been grown before.

 

Once we have successfully grown these bacteria and put their DNA sequences in a database like the one described above, it helps researchers all over the world to better characterise the microbiome and how it relates to whatever they are studying. This may include gastrointestinal disorders as well as things like mood disorders and diseases like cancer.

 

If you are like me, you probably assumed all bacteria had been discovered long ago. So how, and why are we only discovering new types now? The main issue is that many types of bacteria that live in the gut are extremely difficult to grow in a laboratory. This can be to do with oxygen and pH levels, along with other issues. Additionally, it is tremendously difficult to try and recapitulate the exact conditions the bacteria grows in the environment.

 

Even once we have worked out how to grow and sequence the DNA of these new bacteria, we still need to learn what they do. For example, some bacteria in the gut produce a compound called butyrate, which the cells in our intestine use for energy. Other bacteria break down food that our own bodies can’t break down. Knowing what our gut bacteria do is really helpful in understanding why our microbiome changes in disease. For example, just knowing that bacterium X changes when we eat a lot of junk food is not that interesting. But, knowing that bacterium X has a special function that helps our body get nutrients from our food is a lot more useful.

 

So this new study used new culture (bacteria growing) techniques to make it cheaper and easier to understand these new types of bacteria. Hopefully we see more of these techniques becoming accessible to all researchers soon. Another study used specialised computational tools to discover many new species, and the authors noted an interesting point: many microbiome studies have looked at European and North American populations, however the small number of South American and African datasets they examined in this study were really different to the other populations. More research in people from these areas may reveal many more new bacterial species.

 

So it seems every day we get closer to understanding the whole gut microbiome. However, under-researched populations may require more analysis to gain an accurate picture of the changing microbiome world-wide.

 

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