by Kristin Neumann

Shedding some light into the black box of the microbiome

„I had a philosophic moment when thinking of the microbiome which is still kind of a black box.“
„I had a philosophic moment when thinking of the microbiome which is still kind of a black box.“

An interview with Olaf Larsen

Microbiome science is very fresh and scientists all over the world try to understand how we can manipulate our microbiome in the best way for our health. Something I found very interesting was a totally different approach to the understanding of the microbiome by the Biophysicist Olaf Larsen, who understands the vast complexity of the microbiome and approaches it with tiny little steps but in a systematic way. I was very lucky to meet him at the Microbiome Conference in Rotterdam and to get an interview:

„I had a philosophic moment when thinking of the microbiome which is still kind of a black box. We have a reservoir of bacteria and apply something to it, such as a diet or antibiotics and we are having an outcome, a signal, a drop in butyrate, psychological changes or whatever“. Olaf’s idea was to create a very simple way of shedding at least a little bit of light into this black box of our microbiome. He worked on a mechanism which models the interactions between the bacteria on a very basic level. In his latest publication he started with a very simple model, consisting of three bacteria (nodes) which can interact with each other. In his first approach the interactions between the bacteria were undirected. Considering every possible interaction-network, a bacterial community consisting of three species only results in 8 different possible interaction-networks. In his mechanistic approach Olaf added one bacterium after the other to the system, up until 7 bacteria. The number of possible interaction-networks goes up very fast upon introducing more species.

Only 7 different species correspond already to about 2.1 million possible interaction-networks!

By calculating for each interaction-network all paths going from species 1 to the last species in the network (respectively 2, 3, …, 7) Olaf could show that, diversity of the bacterial species results in the system becoming more efficient in performing its specific task. This means, that the higher the bacterial diversity in a system is, the less each single bacterium has to interact with other species to get the same signal out of the system in the end. This means that each bacterium needs to spend less energy because less interactions are necessary in order to get the same result – the species are more in a „relaxed“ state. According to Olaf’s calculations, redundancy sets in when the system reaches ~6 species. This means that a system of 7 (or more) species can „loose“ one (or more) species, without losing its efficiency. In other words, the removal of one (or more) bacterial species in a diverse system doesn’t add additional burden to interact with the bacterial species which are left behind.

This mathematical/mechanistic approach to the understanding of interactions within our microbiome, although kept very simple, nicely demonstrates that a high ecological diversity is necessary to stabilize an ecological system. A system may be beneficial to our health but some might also be detrimental to our body: „IBD (Inflammatory Bowel Disease) is also very stable but is also very detrimental to your health“.

These results from such small model systems are a very first step in understanding the tremendously complex microbiome, and what happens when we trigger it through diets, antibiotics, stress and so on.

Dr. Olaf Larsen and Dr. Kristin Neuman at the Microbiome Conference in Rotterdam
Dr. Olaf Larsen and Dr. Kristin Neuman at the Microbiome Conference in Rotterdam, March 2018

Olaf is already working on the next publication in which he will refine his model closer to nature, in order to ultimately model natural systems and get quantitative information. Let’s hope that Olaf’s computer won’t break down due to the gigantic processing power needed for his calculations!

I am very excited about the future research from Olaf on the microbiome.

Thank you Olaf for the interview and for your patience explaining the very abstract calculation to a simple biologist like me!

Dr. Kristin Neumann
Dr. Kristin Neumann

I was always curious about how life works in its tiny details and ended up spending a lot of time in the lab, working with these bacteria and getting a PhD in Microbiology. I always had the idealistic idea of working on something that changes peoples live for the better …

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