Researchers at Arizona State University have developed new tools to help scientists better understand the microscopic organisms that are crucial to human health and ecosystems. These advances address ongoing challenges in identifying microbes and mapping their relationships, even with the use of modern DNA sequencing.
The research team, led by Qiyun Zhu from ASU’s Biodesign Center for Fundamental and Applied Microbiomics and School of Life Sciences, introduced two main tools. One is designed to improve the construction of microbial family trees, while the other is an open-source software library used globally for biological data analysis.
“Our team builds open-source software tools because we believe that when everyone can access and extend scientific tools, the entire community benefits and discovery accelerates,” said Qiyun Zhu, lead author of the new studies.
The first study appears in Nature Communications and focuses on a tool called TMarSel (Tree-based Marker Selection). This tool automates the process of selecting marker genes—DNA segments used to trace evolutionary history—by searching thousands of gene families. It then selects those that produce the most reliable evolutionary trees, making it possible to work effectively with large groups of organisms or incomplete genomes.
The second study, published in Nature Methods, describes scikit-bio, a comprehensive open-source software library. Scikit-bio provides over 500 functions for analyzing large biological datasets. Its features include comparing microbial communities, calculating diversity, transforming compositional data, analyzing genetic sequences, building phylogenetic trees, and preparing data for machine learning applications. The project is supported by more than 80 contributors worldwide and has been cited extensively across fields such as medicine, ecology, climate science, and cancer biology.
These developments support large-scale microbiome research as well as efforts in disease tracking and environmental monitoring. They also reinforce ASU’s growing role at the intersection of biology and computational sciences. As DNA sequencing becomes more accessible and affordable, these tools are expected to help researchers convert increasing amounts of data into scientific insight.
ASU has been recognized for its innovative contributions; it was named number one in innovation for eight consecutive years by U.S. News & World Report. The university was also ranked among top institutions for undergraduate business, nursing, and engineering programs according to this ranking (https://news.asu.edu/20220911-university-news-asu-no-1-innovation-us-news-world-report-eighth-year?utm_source=twitter&utm_medium=asu&utm_campaign=ASURankings&utm_term=USNWR).
In addition to these advancements in microbiology research tools, ASU collaborates with technology startups such as Argos Vision through partnerships like those with the City of Phoenix Street Transportation Department. These collaborations aim to develop smart traffic cameras capable of collecting extensive data for public safety improvements (https://www.phoenix.gov/newsroom/street-transportation/2420).
With continued progress in both research infrastructure and external partnerships, Arizona State University remains active in driving innovation across scientific disciplines.
