Bonham Lab

Publications

Papers where Kevin Bonham is an author, sorted by year.

2026

  1. Amso D., Fahur Bottino G., Forest T. T., Bonham K. S., Zieff M. R., Patel F., Miles M., Herr D., Team K. S. A. D. C., Espinoza-Heredia C., D'Amato C. L., Ren J., Gladstone M., Mbale E., Alexander D. C. C., Jones D. K., Williams S. C. R., Fifer W. P. P., Gabard-Durnam L. J., Donald K. A. A., Klepac-Ceraj V.

    Microbiome-Behavior Coupling Shapes Infant Adaptation to Early Maternal Unpredictability

    Frontiers in Microbiology 17. doi:10.3389/fmicb.2026.1830339

2025

  1. Bonham K. S., Margolis E. T., Fahur Bottino G., Sobrino A. C., Patel F., McCann S., Zieff M. R., Miles M., Herr D., Davel L., others undefined.

    Codevelopment of Gut Microbial Metabolism and Visual Neural Circuitry over Human Infancy

    mBio , e00835-25. doi:10.1128/mbio.00835-25

  2. Fahur Bottino G., Bonham K. S., Patel F., McCann S., Zieff M., Naspolini N., Ho D., Portlock T., Joos R., Midani F. S., others undefined.

    Early Life Microbial Succession in the Gut Follows Common Patterns in Humans across the Globe

    Nature Communications 16, 660. doi:10.1038/s41467-025-56072-w

  3. Harker S. A., Bonham K. S., McCann S. H., Volpe A. R., Zhu Q., D'Sa V., Koinis-Mitchell D., Deoni S. C. L., Klepac-Ceraj V., Lewis C. R.

    Associations between Relative Abundances of Bifidobacterium Species in the Gut and DNA Methylation of Cortisol-Related Genes in a Pediatric Population

    Frontiers in Microbiology 16. doi:10.3389/fmicb.2025.1558809

  4. Liu T., Kress A. M., Debelius J., Zhao N., Smirnova E., Bandyopadhyay S., Bonham K., Comstock S. S., Gill S., Gern J. E., others undefined.

    Maternal Vaginal and Fecal Microbiota in Later Pregnancy Contribute to Child Fecal Microbiota Development in the ECHO Cohort

    iScience 28. doi:10.1016/j.isci.2025.112211

  5. Naspolini N. F., Schüroff P. A., Vanzele P. A., Pereira-Santos D., Valim T. A., Bonham K. S., Fujita A., Passos-Bueno M. R., Beltrão-Braga P. C., Carvalho A. C., others undefined.

    Exclusive Breastfeeding Is Associated with the Gut Microbiome Maturation in Infants According to Delivery Mode

    Gut Microbes 17, 2493900. doi:10.1080/19490976.2025.2493900

2024

  1. Deoni S. C., D'Sa V., Beauchemin J., Huentelman M., Lewis C., Carnell S., Bonham K., Klepec-Ceraj V., Bruchhage M., Volpe A.

    The Developing Myeloarchitecture of the Human Cortex: Relationships between Intra-Cortical Myelination and Developing Cognitive Function

    . doi:10.1016/j.neuroimage.2021.118142

  2. Laue H. E., Bonham K. S., Coker M. O., Moroishi Y., Pathmasiri W., McRitchie S., Sumner S., Hoen A. G., Karagas M. R., Klepac-Ceraj V., others undefined.

    Prospective Association of the Infant Gut Microbiome with Social Behaviors in the ECHO Consortium

    Molecular Autism 15, 21.

2023

  1. Bonham K. S., Fahur Bottino G., McCann S. H., Beauchemin J., Weisse E., Barry F., Cano Lorente R., Consortium \. R., Huttenhower C., Bruchhage M., others undefined.

    Gut-Resident Microorganisms and Their Genes Are Associated with Cognition and Neuroanatomy in Children

    Science advances 9, eadi0497. doi:10.1126/sciadv.adi0497

  2. Schoenborn A. A., Yannarell S. M., MacVicar C. T., Barriga-Medina N. N., Bonham K. S., Leon-Reyes A., Riveros-Iregui D., Klepac-Ceraj V., Shank E. A.

    Microclimate Is a Strong Predictor of the Native and Invasive Plant-Associated Soil Microbiome on San Cristóbal Island, Galápagos Archipelago

    Environmental Microbiology 25, 1377-1392.

  3. Thompson K. N., Bonham K. S., Ilott N. E., Britton G. J., Colmenero P., Bullers S. J., McIver L. J., Ma S., Nguyen L. H., Filer A., others undefined.

    Alterations in the Gut Microbiome Implicate Key Taxa and Metabolic Pathways across Inflammatory Arthritis Phenotypes

    Science translational medicine 15, eabn4722.

  4. Woodruff M. C., Bonham K. S., Anam F. A., Walker T. A., Faliti C. E., Ishii Y., Kaminski C. Y., Ruunstrom M. C., Cooper K. R., Truong A. D., others undefined.

    Chronic Inflammation, Neutrophil Activity, and Autoreactivity Splits Long COVID

    Nature Communications 14, 4201.

2021

  1. Bonham K. S., Kayisire A. A., Luo A. S., Klepac-Ceraj V.

    Microbiome. Jl and BiobakeryUtils. Jl-Julia Packages for Working with Microbial Community Data

    Journal of Open Source Software 6, 3876.

  2. Gauthier A. E., Chandler C. E., Poli V., Gardner F. M., Tekiau A., Smith R., Bonham K. S., Cordes E. E., Shank T. M., Zanoni I., others undefined.

    Deep-Sea Microbes as Tools to Refine the Rules of Innate Immune Pattern Recognition

    Science immunology 6, eabe0531.

  3. Lewis C. R., Bonham K. S., McCann S. H., Volpe A. R., D'sa V., Naymik M., De Both M. D., Huentelman M. J., Lemery-Chalfant K., Highlander S. K., others undefined.

    Family SES Is Associated with the Gut Microbiome in Infants and Children

    Microorganisms 9, 1608.

  4. Peterson D., Bonham K. S., Rowland S., Pattanayak C. W., Consortium R., Klepac-Ceraj V.

    Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes

    Frontiers in microbiology 12, 670336.

  5. Tso L., Bonham K. S., Fishbein A., Rowland S., Klepac-Ceraj V.

    Targeted High-Resolution Taxonomic Identification of Bifidobacterium Longum Subsp. Infantis Using Human Milk Oligosaccharide Metabolizing Genes

    Nutrients 13, 2833.

2019

  1. Lloyd-Price J., Arze C., Ananthakrishnan A. N., Schirmer M., Avila-Pacheco J., Poon T. W., Andrews E., Ajami N. J., Bonham K. S., Brislawn C. J., others undefined.

    Multi-Omics of the Gut Microbial Ecosystem in Inflammatory Bowel Diseases

    Nature 569, 655-662.

  2. Tett A., Huang K. D., Asnicar F., Fehlner-Peach H., Pasolli E., Karcher N., Armanini F., Manghi P., Bonham K., Zolfo M., others undefined.

    Lifestyle Is a Threat to Gut Bacteria: Ötzi Proves It, Study Shows

    .

  3. Tett A., Huang K. D., Asnicar F., Fehlner-Peach H., Pasolli E., Karcher N., Armanini F., Manghi P., Bonham K., Zolfo M., others undefined.

    The Prevotella Copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

    Cell host & microbe 26, 666-679.

2017

  1. Bonham K. S., Wolfe B. E., Dutton R. J.

    Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

    Elife 6, e22144.

  2. Bonham K. S., Stefan M. I.

    Women Are Underrepresented in Computational Biology: An Analysis of the Scholarly Literature in Biology, Computer Science and Computational Biology

    PLoS computational biology 13, e1005134.

2016

  1. Bonham K. S., Stefan M. I.

    Gender Disparity in Computational Biology Research Publications preprint

    bioRxiv : the preprint server for biology , 070631.

2015

  1. Brubaker S. W., Bonham K. S., Zanoni I., Kagan J. C.

    Innate Immune Pattern Recognition: A Cell Biological Perspective

    Annual review of immunology 33, 257-290.

2014

  1. Bonham K. S., Kagan J. C.

    Biochemistry of Toll-like Receptors

    eLS .

  2. Bonham K. S.

    Cellular and Biochemical Events in Toll-like Receptor Signaling

    Harvard University .

  3. Bonham K. S., Kagan J. C.

    Endosomes as Platforms for NOD-like Receptor Signaling

    Cell host & microbe 15, 523-525.

  4. Bonham K. S., Orzalli M. H., Hayashi K., Wolf A. I., Glanemann C., Weninger W., Iwasaki A., Knipe D. M., Kagan J. C.

    A Promiscuous Lipid-Binding Protein Diversifies the Subcellular Sites of Toll-like Receptor Signal Transduction

    Cell 156, 705-716.

2010

  1. Bonham K., Hemmers S., Lim Y., Hill D. M., Finn \. M., Mowen K. A.

    Effects of a Novel Arginine Methyltransferase Inhibitor on T-helper Cell Cytokine Production

    The FEBS journal 277, 2096-2108.

  2. Fathman J. W., Gurish M. F., Hemmers S., Bonham K., Friend D. S., Grusby M. J., Glimcher L. H., Mowen K. A.

    NIP45 Controls the Magnitude of the Type 2 T Helper Cell Response

    Proceedings of the National Academy of Sciences 107, 3663-3668.