Author: Kevin Dudley

Benjamin Callahan, BRC member and Associate Professor of Department of Population Health and Pathobiology, has been selected to receive the 2023 Microbiome Data Prize by the American Society for Microbiology. Dr. Callahan is widely known for the development of the DADA2 package for sample inference from amplicon data, which has received over 12.000 citations. More generally, he has been instrumental in developing standard and reproducible workflows for handling metagenomic data.

Callahan joined the faculty of North Carolina State University in Jan. 2017 as a Chancellor’s Faculty Excellence Program cluster hire in microbiomes and complex microbial communities. Callahan’s research program at N.C. State focuses on microbomes and the high-throughput methods used to characterize them, in particular marker-gene and metagenomic sequencing. He develops new statistical and bioinformatic methods to better characterize microbial communities from high-throughput biological data. Callahan uses those methods to study important problems, such as the relationship between the maternal microbiome and preterm birth and the barriers to reproducibility and interoperability between microbiome measurements made in different laboratories. Callahan and his group also develop and support software used by the wider microbiome research community in a wide variety of applications.

Additional details about DADA2 and Dr. Callahan’s research are described here: https://asm.org/Articles/2022/October/Advancing-Microbiome-Data-Analysis-with-Benjamin-C

David Reif was named to the U.S. Environmental Protection Agency (EPA) Science Advisory Committee on Chemicals (SACC) for a four-year term by Administrator Michael Regan. The Science Advisory Committee on Chemicals provides independent scientific advice, information and recommendations to the EPA Office of Pollution Prevention and Toxics on the scientific basis for risk assessments, methodologies and pollution prevention measures or approaches. Its major objectives are to provide expert advice and recommendations to the EPA on risk assessments, models, tools, guidance documents, chemical category documents and other chemical assessment and pollution prevention products as deemed appropriate.

The COVID-19 Pandemic Vulnerability Index (PVI)

Dr. David Reif has led teams at North Carolina State University, NIEHS, and Texas A&M University in developing the Pandemic Vulnerability Index (PVI) dashboard, which offers a view and real-time analysis of county-level U.S. data on the coronavirus pandemic. “The dashboard helps officials allocate resources and update responses, as well as providing both county-level and a nationwide overview of various statistics” explained Dr. Reif.  The team developed risk profiles, called PVI scorecards, are available for every county in the United States. The resource has now been added to the COVID Data Tracker resources curated on the U.S. Centers for Disease Control and Prevention website

( https://covid.cdc.gov/covid-data-tracker/#pandemic-vulnerability-index), and was featured in the Environmental Factor (https://factor.niehs.nih.gov/2021/2/feature/1-feature-pandemic/index.htm)

The original publication appeared  in Environmental Health Perspectives (https://ehp.niehs.nih.gov/doi/10.1289/EHP8690).

Additional NC State co-authors include Dr. Yi-Hui Zhou, Dr. Fred A. Wright, and Kuncheng Song.

Dr. Yi-Hui Zhou and colleagues reported on the potential dangers of popular energy drinks in the March 2021 issue of Food and Chemical Toxicology. The study, led by Dr. Ivan Rusyn, a professor in the Veterinary Integrative Biosciences at Texas A&M University, showed that cardiomyocytes – human heart cells grown in a laboratory – exposed to some energy drinks showed an increased beat rate and other factors affecting cardiac function. Dr. Zhou used complex patterns from mass spectrometry to show that certain chemical profiles from the energy drink constituents were associated with aspects such as QT prolongation,  which is associated with serious human heart conditions. “This was a great collaboration showing the power of machine learning methods to learn features of the data that have direct relevance to human health,” explained Dr. Zhou. The project has gained considerable media attention, due to the popularity of energy drinks, which has a $61 billion worldwide market. “Many consumers don’t realize that energy drinks are marketed as regular beverages or dietary supplements, and as such don’t really undergo extensive safety testing” said Dr. Zhou.  “Some ingredients may be available from natural sources but still have worrisome effects on heart function.  Further research should be performed, as some people, even children, consume these drinks every day.”

Link to the article : https://www.sciencedirect.com/science/article/abs/pii/S0278691521000132

Other NC State authors include Fred A. Wright and Erin Baker.