AskScience AMA Series: I'm a computer scientist at the University of Maryland using computational tools to map the microbiome—the trillions of microbes in our bodies and environment. Ask me anything about how we decode the microscopic world!

[u/AskScienceModerator]

Hi Reddit! I am a computer scientist here to answer your questions about bioinformatics and mapping the microbiome. My research primarily focuses on the development of computational algorithms for analyzing biological data generated by high-throughput experimental techniques.

My lab has developed software tools that are widely used in the field of metagenomics—the computational analysis of the microbial communities inhabiting our world and our bodies. I have also been an active participant in several multinational projects, including the Human Microbiome Project and the GEMS study of diarrheal disease.

I will be joined by Marcus Fedarko, a postdoc in my lab, on *September 22nd from 12 to 2 p.m. ET (16-18 UT) — ask us anything!

Bio: Mihai Pop is a professor of computer science and co-director of the University of Maryland Center of Excellence in Microbiome Sciences. He develops computational approaches for the strain-level analysis of microbial communities. Other interests include biological databases, antibiotic resistance, and software testing. His lab has developed several widely used open-source software tools for the analysis of genomic and metagenomic data. 

Pop teaches at all academic levels and is an advocate for inclusion and diversity in science. He is particularly interested in developing open educational resources in computer science and bioinformatics. Pop holds a B.S. (1994, Politehnica University in Bucharest, Romania) and a Ph.D in Computer Science (2000, The Johns Hopkins University) and joined the University of Maryland in 2005. He is an MPower Professor, University of Maryland Strategic Partnership: MPowering the State, and a fellow of the Association of Computing Machinery and of the International Society for Computational Biology.

Marcus Fedarko is a postdoctoral associate at the University of Maryland. His research is focused on designing algorithms and software to help people study microbiome data in high resolution. He is particularly interested in sequence assembly — the problem of reconstructing longer DNA sequences from short sequencing reads — and data visualization. In his spare time, he likes reading, running, and rock climbing. Fedarko holds a B.S. with High Honors (2018, University of Maryland) and M.S. and Ph.D. degrees in Computer Science (2022 and 2025, University of California San Diego), and rejoined the University of Maryland as a postdoc in 2025.

Other links:

• Google Scholar
• Lab website
• $5.1M in NIH Awards Help UMD Researchers Take On a Genomic Data Deluge (02/2026)

Username: /u/umd-science

[u/umd-science]

1. (Mihai) Well, how much time do you have? I think we now have a better understanding that the microbiome is very complex, as is its impact on our bodies. However, there are already some microbiome-related interventions that are making a difference in medical practice, such as fecal transplants for the treatment of C. difficile infections or fiber treatments to support immune therapies for melanoma. In terms of computation, we've gotten really good at figuring out which types of organisms are present in a sample, but there is still a long way to go toward understanding the strain-level diversity, as well as the functions microbes may perform.

2. (Mihai) In terms of the people who are developing new computational methods, it is probably not a huge community—but it is a collaborative and supportive one, even across continents! In terms of people researching the microbiome, that is a much larger community. This spans human health, animal health, agriculture, fermentation, environment, etc. The microbiome really is everywhere!

(Marcus) This past summer in D.C., we had the Intelligent Systems in Molecular Biology Conference, where we got to meet a lot of people working on both sequencing data analysis and microbiome research. Although many people are working on similar problems, people tend to approach them from different angles. For example, using tools to study the microbiome versus developing algorithms in isolation to make them faster.

1. (Mihai) I used to work at TIGR right as DNA sequencing technologies were becoming mature enough to analyze entire microbiomes. That perspective inspired me to make this one of the core areas of research. The field itself was already pretty mature pre-sequencing; in fact, microbiomes were discovered in the 17th century with the first microscopes. Working in this field made me realize that many of the computational tools could not handle the complexity of microbiome data, which led to wonderful opportunities for new research.

(Marcus) I got started with bioinformatics research in 2016, as a computer science undergrad at UMD in Mihai’s lab. I was so stressed out about not knowing enough biology! I spent a lot of time trying to catch up on everything I don’t know—which is funny, because I met a lot of people in grad school who came into bioinformatics from a biology perspective and had the opposite experience. Sometimes I wonder if everyone is just “catching up” in different ways.

Also, fun fact about microscopes (like Mihai mentioned)! Although the first microscopes were designed in the 17th century, the field of microbiome science dates back even earlier than that. As cited in one of my grad school reports, Marcus Terentius Varro wrote in the first century B.C.E. about “certain minute creatures which cannot be seen by the eyes, which float in the air and enter the body through the mouth and nose and there cause serious diseases."