Author

B. D. Merrill

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 8

Signature Assays, Organisms & Methods

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Approach:experimental assay· 6 Research Focus:host-pathogen & immune response· 5 Organism:human· 5 Assay:metagenomics· 4 Organism:mouse· 4 Research Focus:cell type annotation· 2 Approach:deep learning· 2 Research Focus:gene regulatory network inference· 2

Frequent Co-Authors

J. L. Sonnenburg· 6 shared A. J. Hryckowian· 3 shared D. Dahan· 3 shared F. B. Yu· 3 shared A. R. Jha· 2 shared E. C. Martens· 2 shared E. D. Sonnenburg· 2 shared M. A. Fischbach· 2 shared

Activity by Year

2019-2022 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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6 shared papersMicrobiology

J. L. Sonnenburg

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8 papers

Recent·Most cited

Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles

M. R. Olm, D. Dahan, M. M. Carter, B. D. Merrill, B. Yu, S. Jain, X. D. Meng, S. Tripathi, H. Wastyk, N. Neff, S. Holmes, E. D. Sonnenburg, A. R. Jha, J. L. Sonnenburg

This study compares infant gut microbiome assembly in Hadza hunter-gatherers and industrialized infants, finding distinct microbial trajectories and functional differences.

bioRxiv · Mar 30, 2022Microbiology

Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes

B. D. Merrill, M. M. Carter, M. R. Olm, D. Dahan, S. Tripathi, S. P. Spencer, F. B. Yu, S. Jain, N. Neff, A. R. Jha, E. D. Sonnenburg, J. L. Sonnenburg

The paper uses ultra-deep metagenomic sequencing to analyze the gut microbiome of Hadza hunter-gatherers, revealing many microbes absent from existing datasets and highlighting differences in microbial dynamics compared to industrialized populations.

bioRxiv · Mar 30, 2022 · PreprintMicrobiology

Gut Microbiota-Targeted Diets Modulate Human Immune Status

H. C. Wastyk, G. K. Fragiadakis, D. Perelman, D. Dahan, B. D. Merrill, F. B. Yu, M. Topf, C. Gonzalez, J. L. Robinson, J. E. Elias, E. Sonnenburg, C. D. Gardner, J. Sonnenburg

This study examines how plant-based fiber and fermented food diets affect the gut microbiome and immune system in healthy adults over 17 weeks.

Cell · Aug 1, 2021Peer-reviewedMicrobiology

Independent host- and bacterium-based determinants protect a model symbiosis from phage predation

J. B. Lynch, B. D. Bennett, B. D. Merrill, E. G. Ruby, A. J. Hryckowian

The paper identifies host- and bacterium-based mechanisms that protect a symbiotic relationship from phage predation.

bioRxiv · Jul 9, 2021Microbiology

A metabolomics pipeline enables mechanistic interrogation of the gut microbiome

S. Han, W. Van Treuren, C. R. Fischer, B. D. Merrill, B. C. DeFelice, J. M. Sanchez, S. K. Higginbottom, L. Guthrie, L. A. Fall, D. Dodd, M. A. Fischbach, J. L. Sonnenburg

The paper develops a metabolomics pipeline to identify microbiota-dependent metabolites and explores their links to host phenotypes using machine learning and comparative genomics.

bioRxiv · May 25, 2021Microbiology

Multiple phase-variable mechanisms, including capsular polysaccharides, modify bacteriophage susceptibility in Bacteroides thetaiotaomicron

N. T. Porter, A. J. Hryckowian, B. D. Merrill, J. J. Fuentes, J. O. Gardner, R. W. P. Glowacki, S. Singh, R. D. Crawford, E. S. Snitkin, J. L. Sonnenburg, E. C. Martens

This study shows that capsular polysaccharides and other phase-variable cell surface structures in Bacteroides thetaiotaomicron influence bacteriophage susceptibility, enabling bacterial persistence through phase variation.

bioRxiv · Mar 26, 2020 · PreprintMicrobiology

Bacteroides thetaiotaomicron-infecting bacteriophage isolates inform sequence-based host range prediction

A. J. Hryckowian, B. D. Merrill, N. T. Porter, W. Van Treuren, E. J. Nelson, R. A. Garlena, D. A. Russell, E. C. Martens, J. L. Sonnenburg

The paper isolates and analyzes 27 bacteriophages infecting Bacteroides thetaiotaomicron, identifies phage structural gene alleles linked to infectivity, and highlights unexplored phage diversity in the human gut.

bioRxiv · Mar 4, 2020Microbiology

Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs

K. M. Ng, A. Aranda-Diaz, C. Tropini, M. R. Frankel, W. W. Van Treuren, C. O'Laughlin, B. D. Merrill, F. B. Yu, K. M. Pruss, R. A. Oliveira, S. K. Higginbottom, N. F. Neff, M. A. Fischbach, K. B. Xavier, J. L. Sonnenburg, K. C. Huang

The paper investigates how gut microbiota recovers after antibiotics, showing diet and environmental factors influence resilience and recovery patterns.

bioRxiv · Aug 8, 2019Microbiology