Benjamin John Callahan

About

Benjamin Callahan is an Associate Professor in the Department of Population Health and Pathobiology at NC State University and a member of the Bioinformatics Research Center. He joined NC State in January 2017 as part of the Chancellor’s Faculty Excellence Program cluster hire in Microbiomes and Complex Microbial Communities. His research focuses on microbiomes—the complex microbial communities that inhabit and interact with nearly every part of the environment. Callahan has developed new computational methods to more accurately, precisely, and reproducibly characterize these communities, particularly through the use of metagenomic sequencing methods. His work aims to understand the microbial contribution to important health and environmental issues, including the pathophysiology of preterm birth, the development of antimicrobial resistance following antibiotic use, and the epidemiology of C. difficile. Additionally, he is interested in microbial adaptation, which he studies through analytics, simulation, and experimental evolution. Callahan holds a bachelor’s degree in physics and mathematics from Iowa State University and earned his Ph.D. in physics from the University of California, Santa Barbara, under the mentorship of Boris Shraiman. His postdoctoral training includes positions at Stanford University, where he worked with Daniel Fisher on adaptive evolution and with Susan Holmes on quantitative microbiome analysis.

Research topics

• Biology
• Computer Science
• Ecology
• Genetics
• Computational biology
• Microbiology
• Bioinformatics
• Evolutionary biology
• Medicine
• Internal medicine

Selected publications

• Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology

  Applied and Environmental Microbiology · 2021 · 196 citations

  Senior authorCorresponding

  Short-read, high-throughput sequencing (HTS) methods have yielded numerous important insights into microbial ecology and function. Yet, in many instances short-read HTS techniques are suboptimal, for example, by providing insufficient phylogenetic resolution or low integrity of assembled genomes. Single-molecule and synthetic long-read (SLR) HTS methods have successfully ameliorated these limitations. In addition, nanopore sequencing has generated a number of unique analysis opportunities, such…

  DOI

• Ultra-accurate microbial amplicon sequencing with synthetic long reads

  Microbiome · 2021 · 129 citations

  1st authorCorresponding

  BACKGROUND: Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. METHODS: Here, we describe and analytically validate LoopSeq, a commercially availa…

  DOI

• Pathogen resistance may be the principal evolutionary advantage provided by the microbiome

  Philosophical Transactions of the Royal Society B Biological Sciences · 2020 · 116 citations

  Senior authorCorresponding

  To survive, plants and animals must continually defend against pathogenic microbes that would invade and disrupt their tissues. Yet they do not attempt to extirpate all microbes. Instead, they tolerate and even encourage the growth of commensal microbes, which compete with pathogens for resources and via direct inhibition. We argue that hosts have evolved to cooperate with commensals in order to enhance the pathogen resistance this competition provides. We briefly describe competition between co…

  DOI

• A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

  Molecular Ecology Resources · 2023-08-07 · 73 citations

  reviewOpen access

  Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria and eukaryotes. Accordingly, a multitude of metabarcoding data a…

  PublisherOA PDFDOI

• Guidelines for preventing and reporting contamination in low-biomass microbiome studies

  Nature Microbiology · 2025-06-20 · 67 citations

  reviewOpen access
  PublisherOA PDFDOI

Recent grants

• Improving Microbiome Science by Modeling the Measurement Process

  NIH · $1.9M · 2019–2030

Frequent coauthors

• Susan Holmes

  Stanford University

  27 shared

• David A. Relman

  Stanford University

  26 shared

• Megan E. Jacob

  North Carolina State University

  18 shared

• Derek M. Foster

  North Carolina State University

  13 shared

• Luke Thompson

  Mississippi State University

  12 shared

• Mark G. Papich

  North Carolina State University

  12 shared

• Timo Prange

  North Central State College

  12 shared

• Daniel B. DiGiulio

  Stanford University

  12 shared

Education

• Ph.D., Physics

  University of California, Santa Barbara

  2009

• Bachelors of Science, Physics, Math

  Iowa State University

  2002

Similar researchers at North Carolina State University

• José Alonsoh-94
• Anastasios A Tsiatish-80
• David C Muddimanh-71