Bio

Lab: Microbiome Methods In Health and Disease

Dr. Benjamin Callahan joined NC State in January 2017 as a Chancellor’s Faculty Excellence Program cluster hire in Microbiomes and Complex Microbial Communities. As an Assistant Professor in the Department of Population Health and Pathobiology and a member of the Bioinformatics Research Center, Dr. Callahan’s research focuses on “microbiomes” — the complex microbial communities which inhabit and interact with almost every part of the world around us. He develops new statistical and bioinformatic methods to better characterize microbial communities from high-throughput biological data, and uses those methods to study important problems, such as the relationship between the maternal microbiome and preterm birth.

Dr. Callahan received a B.S. in Physics and Math from Iowa State University, and began to work on problems in quantitative biology while obtaining a Ph.D. in Physics from the University of California, Santa Barbara. After graduation, Dr. Callahan worked as a postdoc in the Applied Physics and Statistics departments at Stanford University, where he studied adaptation in large populations through modeling, comparative genomics and experimental evolution.

CERTIFICATIONS
CFEP- Assistant Professor, Microbiomes and Complex Microbial Communities

AFFILIATIONS

Dr. Benjamin Callahan joined NC State in January 2017 as a Chancellor’s Faculty Excellence Program cluster hire in Microbiomes and Complex Microbial Communities. As an Assistant Professor in the Department of Population Health and Pathobiology and a member of the Bioinformatics Research Center, Dr. Callahan’s research focuses on better understanding various “microbiomes” — the complex microbial communities which inhabit and interact with almost every part of the world around us. He develops new statistical and bioinformatic methods to better characterize microbial communities from high-throughput biological data, and uses those methods to study various interesting problems, for example the relationship between the maternal microbiome and preterm birth.

Dr. Callahan received his Bachelors degree in Physics and Math from Iowa State University, and began to work on problems in quantitative biology while obtaining a Ph.D. in Physics from the University of California, Santa Barbara. After graduation, Dr. Callahan worked as a postdoc in the Applied Physics and Statistics departments at Stanford University, where he studied adaptation in large populations through modeling, comparative genomics and experimental evolution.

CERTIFICATIONS

CFEP- Assistant Professor, Microbiomes and Complex Microbial Communities

 

Area(s) of Expertise

COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, GLOBAL HEALTH, INFECTIOUS DISEASES
COMPUTATIONAL BIOLOGY, INFECTIOUS DISEASES

Publications

• Generating, curating, and evaluating trnL reference sequence databases: Benchmarking OBITools3/ecoPCR, RESCRIPt, and MetaCurator , bioRxiv (Cold Spring Harbor Laboratory) (2026)
• Gut Microbiome Alterations in Canine Idiopathic Epilepsy: A Pairwise Case-Control Study , bioRxiv (Cold Spring Harbor Laboratory) (2026)
• Identify contaminants with decontam on the QIIME 2 Framework , Microbiology Resource Announcements (2026)
• Pathogenic bacterial species and the microbiome of cat fleas (Ctenocephalides felis) inhabiting flea-infested homes , PLoS ONE (2026)
• TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization , bioRxiv (Cold Spring Harbor Laboratory) (2026)
• Assessing contamination in DNA extraction kits commonly used for microbiome research , bioRxiv (Cold Spring Harbor Laboratory) (2025)
• Guidelines for preventing and reporting contamination in low-biomass microbiome studies , Nature Microbiology (2025)
• Gardnerella diversity and ecology in pregnancy and preterm birth , mSystems (2024)
• Impact of florfenicol dosing regimen on the phenotypic and genotypic resistance of enteric bacteria in steers , Scientific Reports (2024)
• Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella , PLoS Pathogens (2024)

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