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How to efficiently predict the structure of microbial communities

Work done in the lab of Dr. Narendra Dixit at The Chemical Engineering department of the Indian Institute of Science.

About author

Aamir Ansari is a 25-year-old scientist from Nagpur. He did his bachelor’s in Chemical engineering from Visvesvaraya National Institute of Technology, Nagpur. He continued in the same discipline to persue his Master’s from Indian Institute of Science, Bangalore. Currently he is pursuing Ph.D. at the University of Minnesota, USA. He aspires to become a professor.

Interview

How would you explain your research outcomes to the non-scientific community?

Our body is home to many microbes, which function as a community to help us fight against bad microbes, train our immune system and even influence our mental health. However, predicting the behavior of these microbial communities is challenging due to the presence of a large number of inter-species interactions. Traditionally, these interactions are estimated using a bottom-up approach by examining all microbes alone followed by all pairs of microbes, all triads of microbes, and so on. This prediction method however becomes increasingly intractable as the number of species in the community increases and becomes practically impossible for a real microbial community that has hundreds of microbes. To solve this problem, we proposed a reverse, top-down approach to estimate the interactions. As opposed to the traditional, bottom-up approach, our method requires examining only monocultures and leave-one-out sub communities. Leave-one-out sub communities are obtained by dropping one species at a time from the original community. This enables our method to be applied to real microbial communities that have hundreds of microbes. Finally, to rigorously validate our method, we applied it to millions of computer generated synthetic communities and two real communities and found that our method performs impressively well in each case.

“I believe that leveraging research aptitude from a young age and investing in improving research infrastructure are the two most important ways to help advancement of science in India.”

What was the exciting moment during your research?

The most exciting moment during this research was when our method was able to correctly predict the structure of real communities.

What do you hope to do next?

As the next step, we would hope to apply this method to more communities to understand what kinds of interactions are necessary to maintain microbial community stability.

Where do you seek scientific inspiration from?

I seek inspiration from scientists across the globe. In one or another way, each one of us is striving to solve as many problems in the world.

How do you intend to help Indian science improve?

I believe that leveraging research aptitude from a young age and investing in improving research infrastructure are the two most important ways to help advancement of science in India. I can certainly help in the former by inspiring young kids and graduate students to pursue and make careers in science. I wish that the government would take the charge of the later.

Reference

Ansari, A.F., Reddy, Y.B.S., Raut, J. et al. An efficient and scalable top-down method for predicting structures of microbial communities. Nat Comput Sci 1, 619–628 (2021). https://doi.org/10.1038/s43588-021-00131-x

Edited by: Pratibha Siwach

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