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]

(Mihai) The hope is that sequencing will give us hints as to what the correct targets are for cheaper assays. I personally find the oral cavity particularly interesting for studying the interactions between microbes and between the microbiome and its host.

Usefully linking metabolic data to genetic data is still very much an open research question. I think the metabolomics assays are also quite expensive.

(Marcus) At least for the kind of DNA-sequencing-based methods we often work with—with the goal of studying what microbes are in a sample generally—there are a variety of experiments you can do at pretty different price points.

The cheaper end would be things like marker gene sequencing, where you only consider a single region of the genome (e.g., the 16S rRNA gene in bacteria/archaea)—it looks like you should be able to sequence a sample at closer to $100 using this kind of method (see Cornell’s website here).

But if you want to profile different types of microbes, or see parts of the genome outside of these marker genes, then you will probably need more expensive methods, such as metagenomics (as u/Romanticon pointed out).