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Clay Swackhamer

Researcher at Oregon State

CV

I'm a researcher in the Dallas lab at Oregon State studying the effect of milk processing on health using in vitro digestion systems like SHIME. I want to learn more about how digestion affects the gut microbiome, and in particular how mathematical modeling can be used to understand the dynamics of the gut microbial community to design better prebiotics or probiotics.

  • Research Associate at Oregon State in the lab of Dr. David Dallas
  • Postdoc (USDA-NIFA fellowship, 2022-2024) at Purdue in the lab of Dr. Bruce Hamaker
  • PhD (2022) from UC Davis in Biological Systems Engineering in the lab of Dr. Gail Bornhorst
  • BS (2015) from Penn State in Biological and Agricultural Engineering
  • PE (Agricultural Engineer)

    • Research

    Fiber structure
    2025 → Proposed system to standardize dietary fiber products (review article)

    C. Swackhamer, S. Jang, B-R Park, B. Hamaker, S-K Jung. “Structure-based standardization of prebiotic soluble dietary fibers based on monosaccharide composition, degree of polymerization, and linkage composition.” 2025. Carbohydrate Polymers. 123949. 10.1016/j.carbpol.2025.123949

    Fracture props of model foods
    → Foods broke down by different mechanisms depending on their fracture properties

    C. Swackhamer, R. Doan, Y. Lu, N. Nitin, G. M. Bornhorst. “Fracture and rheological properties of standardized, model solid foods influence their breakdown mechanisms during in vitro gastric digestion with simulated peristalsis.” 2025. Food Hydrocolloids. 111580. 10.1016/j.foodhyd.2025.111580

    Digestion of porridges
    → Stunted and healthy toddlers could both digest and obtain energy from sorghum porridge with thick texture

    F. Cisse, C. Swackhamer, H. Diall, A. Rahmanifar, M. Sylla, A.R. Opekun, M.A. Grusak, A. H-M. Lin, E.A. Pletsch, A. M.R. Hayes, R. Quezado-Calvillo, B.L. Nichols, B. R. Hamaker, “Stunted African toddlers digest and obtain energy from energy-dense thick sorghum porridge.” 2025. European Journal of Clinical Nutrition. 10.1038/s41430-025-01632-y

    Metabolic flexibility
    → Slowly digestible carbohydrates enhanced metabolic flexiblity in mice

    A. Hayes, C. Swackhamer, R. Quezado-Calvillo, N.F. Butte, E.E. Sterchi, B.L. Nichols, B.R. Hamaker “Moderating carbohydrate digestion rate in mice promotes fat oxidation and metabolic flexibility revealed through a new approach to assess metabolic substrate utilization.” 2025. European Journal of Nutrition. 10.1007/s00394-025-03585-1

    Peristaltic Simulator
    2023 → A new device to study the effect of peristalsis on fluid flow and food breakdown during digestion

    C. Swackhamer, T. Bedane, S. Keppler, A. Poltorak, K. Cheung, N. Awais, F. Marra, G. Bornhorst, “Development and Analysis of a Multi-Module Peristaltic Simulator for Gastrointestinal Research." 2023. Food Research International. 112877. 10.1016/j.foodres.2023.112877

    FBCS model foods
    2022 → We created 4 model foods with very different breakdown rates but minimal differences in formulation

    C. Swackhamer, R. Doan, G. Bornhorst, “Development and characterization of standardized model, solid foods with varying breakdown rates during gastric digestion." 2022. Journal of Food Engineering. 316:110827. 10.1016/j.jfoodeng.2021.110827

    Gastric secretion rate
    2021 → Changing the secretion rates in the Human Gastric Simulator affected protein hydrolysis

    Y. Mennah-Govela, C. Swackhamer, G. Bornhorst, “Gastric secretion rate and protein concentration impact intragastric pH and protein hydrolysis during dynamic in vitro gastric digestion." 2021. Food Hydrocolloids for Health. 10.1016/j.fhfh.2021.100027

    Teaching
    → Remote teaching of engineering design course

    C. Swackhamer, J. Mullin, “Emergency Transition of Intro Communication and Design Course to Remote Teaching." 2021. American Society of Engineering Education Conference. 10.18260/1-2--37025

    Couscous digestion
    2019 → Slow gastric emptying of couscous is likely driven by slower starch hydrolysis

    A. Hayes, C. Swackhamer, Y. Mennah-Govela, M. Martínez, A. Diatta, G. Bornhorst. B. Hamaker. “Pearl millet (Pennisetum glaucum) couscous breaks down faster than wheat couscous in the Human Gastric Simulator, though has slower starch hydrolysis." 2020. Food & Function. 11: 111-122. 10.1039/C9FO01461F

    Almond digestion
    → Peristalsis was necessary to break down almond particles during in vitro digestion

    C. Swackhamer, Z. Zhang, A. Taha, G. Bornhorst. “Fatty acid bioaccessibility and structural breakdown from in vitro digestion of almond particles." 2019. Food & Function. 10: 5174-5187. 10.1039/C9FO00789J

    Fracture properties
    → Fracture properties of foods influence their breakdown during chewing (review article)

    C. Swackhamer, G. Bornhorst. “Fracture properties of foods: Experimental considerations and applications to mastication." 2019. Journal of Food Engineering. 263: 213-226. 10.1016/j.jfoodeng.2019.07.002

    Other Projects

    mancuso_analysis
    → Re-analysis of a mathematical model to study the effect of disturbances to an ecosystem on its biodiversity

    Project report for a bioinformatics course at Purdue (audited)

    Pie cooling
    → World's simplest method to see how long it takes to cool a slice of pie

    Project from a math course at UC Davis

    Undergrad thesis
    → A green fluorescent protein optimized using different schemes had different translation elongation rates

    Undergrad thesis in the Schreyer Honors College at Penn State

    Miscellaneous

    "...it would appear to be a pointless and doubtful exercise to examine and disentangle the apparently random appearing bacteria in normal feces and the intestinal tract, a situation that seems controlled by a thousand coincidences... Yet I have nevertheless devoted myself now for a year virtually exclusively to this special study, it was with the conviction that the accurate knowledge of these conditions is essential, for the understanding of not only the physiology of digestion..., but also the pathology and therapy of microbial intestinal diseases."

    - Theodor Escherich (1888)

    Contact

    swackhac [at] oregonstate.edu