Untangling Microbiomes

Dr. Dariia Vyshenska

Have you ever had to deal with tangled cords? What if computers could do it for us? Wrestling recently with wires, I thought: “This is so similar to what I do at work except I am working with microbes instead of wires”. As our gadgets are connected to each other with wires, microbes are connected through the consumption and production of nutrients. And my job is to automate untangling these microbial connections.

Bacterial communities are essential to our lives: with their help, we produce food, generate gas, and even train our immune system. But we use it as a black box without a clear understanding of how microbes are connected and what each of them does. As with tangled headphones, there is little we can do with it. But if we understand microbial connections, we can unleash a hidden potential of artificial microbiomes. We’ll be able to engineer microbial communities to produce useful chemical compounds, clean environment, and even improve human health.

Good news, there is one method that can help - Stable Isotope Probing, or simply SIP. If we take a nutrient, let’s say, glucose, and substitute all 6 Carbon atoms in the molecule with stable non-radioactive isotope, then this molecule of glucose will become 6 neutrons heavier than the regular glucose. We can then take a microbiome, separate it into two portions, feed one portion with regular glucose – our control, and feed the other portion with the heavier glucose – our treatment. Bacteria that ate heavy glucose will incorporate heavy Carbon in its DNA. By comparing control and treatment, we then can find which species of bacteria in the microbiome consumed the nutrient.

Unfortunately, SIP is costly and the results are often inconsistent. To overcome these issues, I designed a universal SIP data analysis pipeline. Now our team uses robots for sample processing. Then, I use computers for streamlined data analysis. And this protocol includes a multi-step control system to exclude mishandled samples. Next year, our pipeline will become available to anyone in the world. So even though we don’t yet have access to a pocket-robot that would untangle our cords, soon we will have access to an automated SIP pipeline for untangling microbial connections!