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Benjamin J Callahan

Associate Professor

Dept of Population Health & Pathobiology

North Carolina State University

Raleigh, NC 27607


Phone: (919) 515-8536


Twitter: @bejcal



PhD in Physics

University of California, Santa Barbara

Evolution on an interacting fitness landscape: The effects of the interplay of epistasis and recombination on genetic structure


BS in Physics and Math, Minor in Linguistics

Iowa State University


2022 -

Associate Professor, Microbiomes and Complex Microbial Communities

Department of Population Health & Pathobiology

North Carolina State University, College of Veterinary Medicine

2017 - 2022

Assistant Professor, Microbiomes and Complex Microbial Communities

Department of Population Health & Pathobiology

North Carolina State University, College of Veterinary Medicine

2014 - 2016

Research Associate

Stanford University, Department of Statistics

2010 - 2013

Postdoctoral Scholar

Stanford University, Department of Applied Physics


Google Scholar profile:

Huang C#, Callahan BJ, Wu MC, Holloway ST, Brochu H, Lu W, Peng X, Tzeng JY^ (2022). Phylogeny-Guided Microbiome OTU-Specific Association Test (POST). Microbiome, 10, 86. 

Tedersoo L^, Albertsen M, Anslan S, Callahan B (2021). Perspectives and benefits of high-throughput long-read sequencing in microbial ecology. Applied and Environmental Microbiology, 87(17), e00626-21. 

Callahan BJ^, Grinevich D#, Thakur S, Balamotis MA, Yehezkel TB (2021). Ultra-accurate Microbial Amplicon Sequencing with Synthetic Long Reads. Microbiome, 9, 130. 

Halleran JL, Callahan BJ, Jacob ME, Sylvester HJ, Prange T, Papich MG, Foster DM^ (2021). Effects of danofloxacin dosing regimen on gastrointestinal pharmacokinetics and fecal microbiome in steers. Scientific Reports, 11(1), 1-3. 

Thanissery R, McLaren MR#, Rivera A, Reed AD, Betrapally NS, Burdette T, Winston JA, Jacob M, Callahan BJ, Theriot CM^ (2020). C. difficile carriage in animals and the associated changes in the host fecal microbiota. Anaerobe, 66, 102279. 

McLaren MR#, Callahan BJ^ (2020). Pathogen resistance may be the principal evolutionary advantage provided by the microbiome. Phil. Trans. R. Soc. B, 375, 20190592. 

Kolodny O, Callahan BJ, Douglas AE (2020). The role of the microbiome in host evolution. Phil. Trans. R. Soc. B, 375, 20190588. 

Muñana K^, Jacob J, Callahan BJ (2020). Evaluation of fecal Lactobacillus populations in dogs with idiopathic epilepsy: A pilot study. Animal Microbiome, 2, 19. 

Berman HL#, McLaren MR#, Callahan BJ^ (2020). Understanding and Interpreting Community Sequencing Measurements of the Vaginal Microbiome. BJOG: An International Journal of Obstetrics & Gynaecology, 127, 139-146. 

Foster DM^, Jacob M, Farmer K, Callahan B, Theriot C, Kathariou S, Cernicchiaro N, Prange T, Papich M (2019). Ceftiofur formulation differentially affects the intestinal drug concentrations, resistance of fecal Escherichia coli, and the microbiome of steers. PLoS One, 14(10), e0223378. 

McLaren MR#, Willis AD, Callahan BJ^ (2019). Consistent and correctable bias in metagenomic sequencing experiments. eLife, 8, e46923. 

Bolyen E*, Rideout JR*, Dillon MR*, Bokulich NA*, [......12 authors......], Callahan BJ, [......91 authors......], JG Caporaso^ (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37, 852–857. 

Callahan BJ^, Wong J, Heiner C, Oh S, Theriot CM, Gulati AS, McGill SK, Dougherty MK (2019). High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Research, 47, e103. 

Davis NM*, Proctor D*, Holmes SP, Relman DA, Callahan BJ^ (2018). Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome, 6, 226. 

Jeganathan P, Callahan BJ, Proctor DM, Relman DA, Holmes SP^ (2018). The Block Bootstrap Method for Longitudinal Microbiome Data. arXiv, 1809.01832 [stat.ME].

Ferguson K,  Jacob M, Theriot C, Callahan B, Prange T, Papich M, Foster D^ (2018). Dosing Regimen of Enrofloxacin Impacts Intestinal Pharmacokinetics and the Fecal Microbiota in Steers. Frontiers in Microbiology, 9, 2190. 

Ghaemi MS, DiGiulio DB, Contrepois K, Callahan B, Ngo T, Lee-McMullen B, Lehallier B, Robaczewska A, Mcilwain D, Rosenberg-Hasson Y, Wong RJ, Quaintance C, Culos A, Stanley N, Tanada A, Tsai A, Gaudilliere D, Ganio E, Han X, Ando K, McNeil L, Tingle M, Wise P, Maric I, Sirota M, Wyss-Coray T, Winn VD, Druzin ML, Gibbs R, Darmstadt GL, Lewis DB, Nia VP, Agard B, Tibshirani R, Nolan G, Snyder MP, Relman DA, Quake SR, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B, Aghaeepour N^ (2018). Multiomics Modeling of the Immunome, Transcriptome, Microbiome, Proteome, and Metabolome Adaptations During Human Pregnancy. Bioinformatics, 35(1), 95-1037. 

McLaren MR#, Callahan BJ^ (2018). In nature, there is only diversity. mBio, 9:e02149-17. 

Callahan BJ*, DiGiulio DB*, Goltsman DSA, Sun CL, Costello EK, Jeganathan P, Biggio JR, Wong RJ, Druzin ML, Shaw GM, Stevenson DK, Holmes SP, Relman DA^ (2017). Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women. Proceedings of the National Academy of Sciences USA, 114(37), 9966–9971. PMCID: PMC5604014. 

Callahan BJ^, McMurdie PJ, Holmes SP (2017). Exact sequence variants should replace operational taxonomic units in marker gene data analysis. The ISME Journal, 11, 2639–2643. PMCID: PMC5702726. 

Mayer-Blackwell K, Fincker M, Molenda O, Callahan BJ, Sewell H, Holmes S, Edwards E, Spormann A^. 1,2-dichloroethane exposure alters the population structure, metabolism, and kinetics of a trichloroethene-dechlorinating Dehalococcoides mccartyi consortium (2016). Environmental Science & Technology, 50, 12187–12196. PMID: 27809491.

Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP^ (2016). Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000 Research, 5, 1492. PMCID: PMC4955027. 

Callahan BJ^, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP (2016). DADA2: High resolution sample inference from Illumina amplicon data. Nature Methods, 13, 581–583. PMCID: PMC4927377. 

Bik EM, Costello EK, Switzer AD, Callahan BJ, Holmes SP, Wells RS, Carlin KP, Jensen ED, Venn-Watson S, Relman DA^ (2016). Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nature Communications, 7, 10516. PMCID: PMC4742810. 

Callahan BJ, Proctor D, Relman DA, Fukuyama J, Holmes SP^ (2016). Reproducible research workflow in R for the analysis of personalized human microbiome data. Pacific Symposium on Biocomputing, 21, 183-194. PMCID: PMC4873301. 

DiGiulio DB*, Callahan BJ*, McMurdie PJ, Costello EK, Lyell DJ, Robaczewska A, Sun CL, Goltsman DSA, Wong RJ, Shaw G, Stevenson DK, Holmes SP, Relman DA^ (2015). Temporal and spatial variation of the human microbiota during pregnancy. Proceedings of the National Academy of Sciences USA, 112(35), 11060-11065. PMCID: PMC456827. 

Callahan BJ^, Fukami T, Fisher DS (2014). Rapid Evolution of Adaptive Niche Construction in Experimental Microbial Populations. Evolution, 68(11), 3307-3316. PMID: 25138718. 

Walker SI*^, Callahan BJ*, Arya G, Barry JD, Bhattacharya T, Grigoryev S, Pellegrini M, Rippe K, Rosenberg SM (2013). Evolutionary Dynamics and Information Hierarchies in Biological Systems. Annals of the New York Academy of Sciences, 1305(1), 1-17. PMID: 23691975


Rosen MJ^, Callahan BJ, Fisher DS, Holmes SP (2012). Denoising PCR-amplified metagenome data. BMC bioinformatics, 13(1), 283. PMCID: PMC3563472. 


Callahan BJ (2012). The length scale of selection in protein evolution. Fly, 6(1), 16-20. PMID: 22198524


Sellis D, Callahan BJ, Petrov DA^, Messer PW (2011). Heterozygote advantage as a natural consequence of adaptation in diploids. Proceedings of the National Academy of Sciences USA, 108(51), 20666-20671. PMCID: PMC3251125. 


Callahan BJ^, Neher RA, Bachtrog D, Andolfatto PA, Shraiman BI (2011). Correlated evolution of nearby residues in Drosophilid proteins. PLoS Genetics, 7(2), e1001315. PMCID: PMC3044683. 


Callahan BJ, Thattai M, Shraiman BI^ (2009). Emergent gene order in a model of modular polyketide synthases. Proceedings of the National Academy of Sciences USA, 106, 19410-19415. PMCID: PMC2780807. 

Cheung MS, Finke JM, Callahan BJ, Onuchic JN^ (2003). Exploring the interplay between topology and secondary structural formation in the protein folding problem. Journal of Physical Chemistry B, 107, 1193-11200. 

* equal contributions                ^ corresponding                # lab member


Callahan BJ, McMurdie PJ, Holmes SP (2022). dada2: Accurate, high-resolution sample inference from amplicon sequencing data. R package version 1.22.0.

        Over 10,000 citations (Google Scholar, Jul 2022)

        Top 5% most downloaded Bioconductor packages.

Callahan BJ, Davis NM (2022). decontam: Identify contaminants in marker-gene and metagenomics sequencing data. R package version 1.14.0.

        Over 1,000 citations (Google Scholar, Jul 2022)

Funded Grants

2019 - 2024


Quantitative Metagenomics and the Vaginal Microbiome of Preterm Birth

Total Costs: $1,442,610

2019 - 2022

USDA National Institute of Food and Agriculture (PI)

FACT: Rapid Detection and Tracking of Foodborne Pathogens with Long-read Amplicon Sequencing

Total Costs: $493,921

2021 – 2023

NIH NICHD F31HD104353 (Sponsor, Grad Student: Berman)

Understanding Intraspecific Diversity of Gardnerella vaginalis in the Vaginal Microbiome (Hanna Berman)

Total Costs: $111,672

2019 - 2022

American Kennel Club (Co-I, PI: Munana)

Is Gut Dysbiosis Associated with Canine Idiopathic Epilepsy?

Total Costs: $104,453

2021 – 2024

US Army Research Office (Co-I, PI: Meiklejohn)

Validating DNA Metabarcoding for Characterization of Pollen from Surface Soils

Total Costs: $450,000.00


(no cost extension)

NCSU Research and Innovation Seed Funding Program (Co-I)

Medieval Monks Meet Modern Science: Using Genetics to Unlock the Secrets of Medieval Parchment Books and their Makers

Total Costs: $18,750 (plus $6,250 matching funds from the CVM)

2020 – 2021

(no cost extension)

Triangle Center for Evolutionary Medicine (Co-I)

Drivers of the gut microbiome in children and animals in urban Ethiopia

Total Costs: $12,000

2017 - 2019


Plant Soil Microbial Community Consortium (PI)

Extension and validation of maximum resolution amplicon bioinformatics methods to fungal marker-gene data

Total Costs: $55,000

Invited Talks


East Carolina University, Dept. of  Microbiology and Immunology Seminar, Greenville NC


Kavli Institute of Theoretical Physics Program on The Ecology and Evolution of Microbial Communities, Santa Barbara CA


Microbiome Data Congress 2021


Aarhus University, Denmark


University of Nebraska - Lincoln, Advanced Food Science Seminar


DNAQUA International Conference, Data Analysis & Storage Session Keynote


Duke University Marine Laboratory


Loop Genomics, Live Webinar


University of Innsbruck, Austria


Microbiome Movement - Maternal & Infant Health Summit, Virtual Seminar


University of South Florida, Virtual Seminar


FDA, Virtual Seminar


NIEHS, Research Triangle Park NC


University of Louisville, Louisville KY


NIST Workshop on Standards for Microbiome Measurements, Gaithersburg MD


Microbiome Movement - Maternal & Infant Health Summit, Boston MA


Simons Foundation 3rd Workshop on Statistical and Algorithmic Challenges in Microbiome Data Analysis, New York City NY


Triangle Microbial Interactions Meeting, Chapel Hill NC


UNC-Charlotte Bioinformatics Seminar Series, Charlotte NC


UNC Bioinformatics & Computational Biology Seminar, Chapel Hill NC


VCU Microbiology & Immunology Research Seminar, Richmond VA


International Metagenomics and Microbiome Standards Alliance, Webinar


Physical Principles Governing the Organization of Microbial Communities, Aspen Center for Physics, Aspen CO


Symposium on the Microbiome: Hype and Hope, Fred Hutchinson Cancer Research Center, Seattle WA


Kavli Foundation Microbiome Seminar, Ohio State, Columbus OH


UNC First Friday Microbiome Seminar, Chapel Hill NC


BASF Seminar, Research Triangle Park NC


Joint Statistical Meetings, Baltimore MD


University of Idaho Seminar for the Center for Modeling Complex Interactions (CMCI) and the Institute for Bioinformatics and Evolutionary Studies (IBEST)


UNC Biostatistics Department Seminar, Chapel Hill NC


Bioinformatics for the Microbiome Symposium, Stanford CA


Challenges in Microbiome Data Analysis, Simons Foundation, NYC NY


Microbiome Workshop, Johnson & Johnson, Webinar


REvolution - Transcending the Past Symposium, Stanford CA


Seminar, Vienna Institute of Science and Technology, Vienna Austria


Bay Area Population Genomics Meeting, UC Berkeley


Seminar, Princeton University, Princeton NJ

Honors and Awards


Academic Service Award, Genetics & Genomics Academy at NC State


Goodnight Early Career Innovator Award, NC State


Pacific Symposium on Biocomputing Travel Award


American Society of Naturalists Conference

Best Postdoc Talk (2nd place)

2003 - 2005

Broida Fellowship for Graduate Studies in Physics, UCSB

before 2002

Phi Beta Kappa, Tau Beta Pi, National Merit Scholarship

Professional Activities

Editor: Guest editor for Philosophical Transactions B special issue on “The Role of the Microbiome in the Evolution of the Host” (2020).

Reviewer (journals): Bioinformatics, BJOG, Environmental Microbiology, Frontiers in Genetics, Genetics, Gigascience, Microbiome, mSphere, mSystems, Nature, Nature Communications, Nature Ecology & Evolution, Nature Methods, Nature Microbiology, New Phytologist, PeerJ, PLoS Comp Bio, PLoS One, PNAS, Proceedings of the Royal Society B, Science, Theoretical Population Biology.

Reviewer (grants): NIH EMNR Study Section (Mar 2022), NIH CHHD-W Study Section (Oct 2021), NIH K99 Study Section (Nov 2020), NIH BDMA Study Section (Feb 2020).

Advisor: Michael McLaren (postdoc - completed), Dmitry Grinevich (postdoc), Craig Gin (postdoc), Naga Betrapally (postdoc - completed), Caizhi Huang (PhD), Hanna Berman (PhD), Taylor Gin (PhD), Ozge Kuddar (PhD), Jorden Rabasco (PhD).

Workshop Instruction: Strategies and Techniques for Analyzing Microbial Population Structures at Woods Hole (2015, 2017, 2019, 2020-Canceled, 2022), Harvard Workshop on Metagenomics (2015), Microbe Analysis in R at ASM Microbe (2018, 2019), QCBS BIOME Workshop on Metabarcoding at University of Montreal (2018, Lead Instructor), Microbiome Analysis with DADA2 and R Workshop at NC State (2018, Lead Instructor)