Introduction to Microbes
Today, out of an estimated 1 trillion species on Earth, 99.999 percent are considered microbial — bacteria, archaea, viruses, and single-celled eukaryotes. For much of our planet’s history, microbes ruled the Earth, able to live and thrive in the most extreme of environments. Researchers have only just begun in the last few decades to contend with the diversity of microbes — it’s estimated that less than 1 percent of known genes have laboratory-validated functions.
Meet Yunha Hwang
An environmental microbiologist and computer scientist by training, new MIT faculty member Yunha Hwang is interested in the novel biology revealed by the most diverse and prolific life form on Earth. In a shared faculty position as the Samuel A. Goldblith Career Development Professor in the Department of Biology, as well as an assistant professor at the Department of Electrical Engineering and Computer Science and the MIT Schwarzman College of Computing, Hwang is exploring the intersection of computation and biology.
Research Focus
Hwang’s research focus is on studying microbes in extreme environments. Extreme environments are great places to look for interesting biology. The biggest challenge in studying microbes is that a majority of them cannot be cultivated, which means that the only way to study their biology is through a method called metagenomics.
Studying Microbes in Silico
Hwang’s latest work is genomic language modeling. We’re hoping to develop a computational system so we can probe the organism as much as possible “in silico,” just using sequence data. A genomic language model is technically a large language model, except the language is DNA as opposed to human language. It’s trained in a similar way, just in biological language as opposed to English or French. If our objective is to learn the language of biology, we should leverage the diversity of microbial genomes.
Advancing Understanding of Microbial Genomes
Given how diverse microbes are and how little we understand about them, studying microbes in silico, using genomic language modeling, can advance our understanding of the microbial genome. A genome is many millions of letters. A human cannot possibly look at that and make sense of it. We can program a machine, though, to segment data into pieces that are useful. That’s sort of how bioinformatics works with a single genome.
Applications of Microbe Research
Hwang’s research can be applied to harnessing the functional potential of microbes. Microbes are possibly the world’s best chemists. Leveraging microbial metabolism and biochemistry will lead to more sustainable and more efficient methods for producing new materials, new therapeutics, and new types of polymers. Understanding how microbes work, and being able to understand their genomic makeup and their functional capacity, will also be really important as we think about how our world and climate are changing.
Real-World Implications
A majority of carbon sequestration and nutrient cycling is undertaken by microbes; if we don’t understand how a given microbe is able to fix nitrogen or carbon, then we will face difficulties in modeling the nutrient fluxes of the Earth. On the more therapeutic side, infectious diseases are a real and growing threat. Understanding how microbes behave in diverse environments relative to the rest of our microbiome is really important as we think about the future and combating microbial pathogens.
Conclusion
In conclusion, microbes are the most diverse and prolific life form on Earth, and studying them can lead to a better understanding of the world and its many complexities. By using computational approaches and genomic language modeling, researchers like Yunha Hwang can advance our understanding of microbial genomes and harness the functional potential of microbes.
FAQs
Q: What is metagenomics?
A: Metagenomics is a method of studying the biology of microbes that cannot be cultivated in a lab.
Q: What is genomic language modeling?
A: Genomic language modeling is a computational system that uses sequence data to probe the organism and understand its biology.
Q: What are the potential applications of microbe research?
A: The potential applications of microbe research include more sustainable and efficient methods for producing new materials, new therapeutics, and new types of polymers, as well as a better understanding of how microbes behave in diverse environments.
Q: Why is it important to study microbes?
A: It is important to study microbes because they are the most diverse and prolific life form on Earth, and understanding them can lead to a better understanding of the world and its many complexities.
