Honors & Awards


  • ASMS Career Development Award, American Society of Mass Spectrometry (June 2023)
  • Richard Armstrong Prize for Research Excellence in Chemical Biology, Vanderbilt University (August 2022)
  • Outstanding Independent Research Proposal, Vanderbilt University (May 2022)
  • Outstanding Chemistry Forum Presentation, Vanderbilt University (May 2021)
  • Department of Chemistry and Biochemistry Leadership Award, University of Notre Dame (May 2018)

Professional Education


  • Doctor of Philosophy, Vanderbilt University (2022)
  • Bachelor of Science, University of Notre Dame (2018)
  • Ph.D., Vanderbilt University, Chemistry (2022)
  • B.S., University of Notre Dame, Chemistry, Philosophy (2018)

Stanford Advisors


All Publications


  • Clostridioides difficile infection induces a rapid influx of bile acids into the gut during colonization of the host CELL REPORTS Wexler, A. G., Guiberson, E. R., Beavers, W. N., Shupe, J. A., Washington, M., Lacy, D., Caprioli, R. M., Spraggins, J. M., Skaar, E. P. 2021; 36 (10): 109683

    Abstract

    Clostridioides difficile is the leading cause of nosocomial intestinal infections in the United States. Ingested C. difficile spores encounter host bile acids and other cues that are necessary for germinating into toxin-producing vegetative cells. While gut microbiota disruption (often by antibiotics) is a prerequisite for C. difficile infection (CDI), the mechanisms C. difficile employs for colonization remain unclear. Here, we pioneered the application of imaging mass spectrometry to study how enteric infection changes gut metabolites. We find that CDI induces an influx of bile acids into the gut within 24 h of the host ingesting spores. In response, the host reduces bile acid biosynthesis gene expression. These bile acids drive C. difficile outgrowth, as mice receiving the bile acid sequestrant cholestyramine display delayed colonization and reduced germination. Our findings indicate that C. difficile may facilitate germination upon infection and suggest that altering flux through bile acid pathways can modulate C. difficile outgrowth in CDI-prone patients.

    View details for DOI 10.1016/j.celrep.2021.109683

    View details for Web of Science ID 000693615400026

    View details for PubMedID 34496241

    View details for PubMedCentralID PMC8445666

  • High-throughput identification of gut microbiome-dependent metabolites. Nature protocols Han, S., Guiberson, E. R., Li, Y., Sonnenburg, J. L. 2024

    Abstract

    A significant hurdle that has limited progress in microbiome science has been identifying and studying the diverse set of metabolites produced by gut microbes. Gut microbial metabolism produces thousands of difficult-to-identify metabolites, which present a challenge to study their roles in host biology. In recent years, mass spectrometry-based metabolomics has become one of the core technologies for identifying small metabolites. However, metabolomics expertise, ranging from sample preparation to instrument use and data analysis, is often lacking in academic labs. Most targeted metabolomics methods provide high levels of sensitivity and quantification, while they are limited to a panel of predefined molecules that may not be informative to microbiome-focused studies. Here we have developed a gut microbe-focused and wide-spectrum metabolomic protocol using liquid chromatography-mass spectrometry and bioinformatic analysis. This protocol enables users to carry out experiments from sample collection to data analysis, only requiring access to a liquid chromatography-mass spectrometry instrument, which is often available at local core facilities. By applying this protocol to samples containing human gut microbial metabolites, spanning from culture supernatant to human biospecimens, our approach enables high-confidence identification of >800 metabolites that can serve as candidate mediators of microbe-host interactions. We expect this protocol will lower the barrier to tracking gut bacterial metabolism in vitro and in mammalian hosts, propelling hypothesis-driven mechanistic studies and accelerating our understanding of the gut microbiome at the chemical level.

    View details for DOI 10.1038/s41596-024-00980-6

    View details for PubMedID 38740909

    View details for PubMedCentralID 5541232

  • Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics. Cell reports Voogdt, C. G., Tripathi, S., Bassler, S. O., McKeithen-Mead, S. A., Guiberson, E. R., Koumoutsi, A., Bravo, A. M., Buie, C., Zimmermann, M., Sonnenburg, J. L., Typas, A., Deutschbauer, A. M., Shiver, A. L., Huang, K. C. 2023; 43 (1): 113519

    Abstract

    The critical role of the intestinal microbiota in human health and disease is well recognized. Nevertheless, there are still large gaps in our understanding of the functions and mechanisms encoded in the genomes of most members of the gut microbiota. Genome-scale libraries of transposon mutants are a powerful tool to help us address this gap. Recent advances in barcoded transposon mutagenesis have dramatically lowered the cost of mutant fitness determination in hundreds of in vitro and in vivo experimental conditions. In an accompanying review, we discuss recent advances and caveats for the construction of pooled and arrayed barcoded transposon mutant libraries in human gut commensals. In this review, we discuss how these libraries can be used across a wide range of applications, the technical aspects involved, and expectations for such screens.

    View details for DOI 10.1016/j.celrep.2023.113519

    View details for PubMedID 38142398

  • A mutant fitness compendium in Bifidobacteria reveals molecular determinants of colonization and host-microbe interactions. bioRxiv : the preprint server for biology Shiver, A. L., Sun, J., Culver, R., Violette, A., Wynter, C., Nieckarz, M., Mattiello, S. P., Sekhon, P. K., Friess, L., Carlson, H. K., Wong, D., Higginbottom, S., Weglarz, M., Wang, W., Knapp, B. D., Guiberson, E., Sanchez, J., Huang, P. H., Garcia, P. A., Buie, C. R., Good, B., DeFelice, B., Cava, F., Scaria, J., Sonnenburg, J., Sinderen, D. V., Deutschbauer, A. M., Huang, K. C. 2023

    Abstract

    Bifidobacteria commonly represent a dominant constituent of human gut microbiomes during infancy, influencing nutrition, immune development, and resistance to infection. Despite interest as a probiotic therapy, predicting the nutritional requirements and health-promoting effects of Bifidobacteria is challenging due to major knowledge gaps. To overcome these deficiencies, we used large-scale genetics to create a compendium of mutant fitness in Bifidobacterium breve (Bb). We generated a high density, randomly barcoded transposon insertion pool in Bb, and used this pool to determine Bb fitness requirements during colonization of germ-free mice and chickens with multiple diets and in response to hundreds of in vitro perturbations. To enable mechanistic investigation, we constructed an ordered collection of insertion strains covering 1462 genes. We leveraged these tools to improve models of metabolic pathways, reveal unexpected host- and diet-specific requirements for colonization, and connect the production of immunomodulatory molecules to growth benefits. These resources will greatly reduce the barrier to future investigations of this important beneficial microbe.

    View details for DOI 10.1101/2023.08.29.555234

    View details for PubMedID 37693407

    View details for PubMedCentralID PMC10491234

  • Rapid Multivariate Analysis Approach to Explore Differential Spatial Protein Profiles in Tissue JOURNAL OF PROTEOME RESEARCH Sharman, K., Patterson, N., Weiss, A., Neumann, E. K., Guiberson, E. R., Ryan, D. J., Gutierrez, D. B., Spraggins, J. M., Van de Plas, R., Skaar, E. P., Caprioli, R. M. 2022

    Abstract

    Spatially targeted proteomics analyzes the proteome of specific cell types and functional regions within tissue. While spatial context is often essential to understanding biological processes, interpreting sub-region-specific protein profiles can pose a challenge due to the high-dimensional nature of the data. Here, we develop a multivariate approach for rapid exploration of differential protein profiles acquired from distinct tissue regions and apply it to analyze a published spatially targeted proteomics data set collected from Staphylococcus aureus-infected murine kidney, 4 and 10 days postinfection. The data analysis process rapidly filters high-dimensional proteomic data to reveal relevant differentiating species among hundreds to thousands of measured molecules. We employ principal component analysis (PCA) for dimensionality reduction of protein profiles measured by microliquid extraction surface analysis mass spectrometry. Subsequently, k-means clustering of the PCA-processed data groups samples by chemical similarity. Cluster center interpretation revealed a subset of proteins that differentiate between spatial regions of infection over two time points. These proteins appear involved in tricarboxylic acid metabolomic pathways, calcium-dependent processes, and cytoskeletal organization. Gene ontology analysis further uncovered relationships to tissue damage/repair and calcium-related defense mechanisms. Applying our analysis in infectious disease highlighted differential proteomic changes across abscess regions over time, reflecting the dynamic nature of host-pathogen interactions.

    View details for DOI 10.1021/acs.jproteome.2c00206

    View details for Web of Science ID 000830838200001

    View details for PubMedID 35849531

  • Multimodal Imaging Mass Spectrometry of Murine Gastrointestinal Tract with Retained Luminal Content JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY Guiberson, E. R., Good, C. J., Wexler, A. G., Skaar, E. P., Caprioli, R. M., Spraggins, J. M. 2022; 33 (6): 1073-1076

    Abstract

    The gastrointestinal tract, including luminal content, harbors a complex mixture of microorganisms, host dietary content, and immune factors. Existing imaging approaches remove luminal content and only visualize small regions of the GI tract. Here, we demonstrate a workflow for multimodal imaging using matrix-assisted laser desorption/ionization imaging mass spectrometry, autofluorescence, and bright field microscopy for mapping intestinal tissue and luminal content. Results comparing tissue and luminal content in control murine tissue show both unique molecular and elemental distributions and abundances using multimodal protein, lipid, and elemental imaging. For instance, lipid PC(42:1) is 2× higher intensity in luminal content than tissue, while PC(32:0) is 80× higher intensity in tissue. Additionally, some ions such as the protein at m/z 3443 and the element manganese are only detected in luminal content, while the protein at m/z 8564 was only detected in tissue and phosphorus had 2× higher abundance in tissue. These data highlight the robust molecular information that can be gained from the gastrointestinal tract with the inclusion of luminal content.

    View details for DOI 10.1021/jasms.1c00360

    View details for Web of Science ID 000807481600019

    View details for PubMedID 35545232

    View details for PubMedCentralID PMC9264265

  • Spatially Targeted Proteomics of the Host-Pathogen Interface during Staphylococcal Abscess Formation ACS INFECTIOUS DISEASES Guiberson, E. R., Weiss, A., Ryan, D. J., Monteith, A. J., Sharman, K., Gutierrez, D. B., Perry, W. J., Caprioli, R. M., Skaar, E. P., Spraggins, J. M. 2021; 7 (1): 101-113

    Abstract

    Staphylococcus aureus is a common cause of invasive and life-threatening infections that are often multidrug resistant. To develop novel treatment approaches, a detailed understanding of the complex host-pathogen interactions during infection is essential. This is particularly true for the molecular processes that govern the formation of tissue abscesses, as these heterogeneous structures are important contributors to staphylococcal pathogenicity. To fully characterize the developmental process leading to mature abscesses, temporal and spatial analytical approaches are required. Spatially targeted proteomic technologies such as micro-liquid extraction surface analysis offer insight into complex biological systems including detection of bacterial proteins and their abundance in the host environment. By analyzing the proteomic constituents of different abscess regions across the course of infection, we defined the immune response and bacterial contribution to abscess development through spatial and temporal proteomic assessment. The information gathered was mapped to biochemical pathways to characterize the metabolic processes and immune strategies employed by the host. These data provide insights into the physiological state of bacteria within abscesses and elucidate pathogenic processes at the host-pathogen interface.

    View details for DOI 10.1021/acsinfecdis.0c00647

    View details for Web of Science ID 000609249400009

    View details for PubMedID 33270421

    View details for PubMedCentralID PMC7796985

  • Fundamentals of Mass Spectrometry-Based Metabolomics Toxic Chemical and Biological Agents Rivera, E. S., Jones, M. A., Guiberson, E. R., Norris, J. L. Springer Dordrecht. 2020: 61-81