Darrell W Cockburn, Ph.D.

Darrell W Cockburn, Ph.D.

  • Assistant Professor of Food Science
428 Rodney A. Erickson Food Science Building
University Park, PA 16803

Areas of Expertise

  • Human Gut Microbiome
  • Carbohydrate Active Enzymes
  • Dietary Fiber
  • Resistant Starch


  • BSc University of Guelph, Canada
  • PhD University of Guelph, Canada


Lab Website
Google Scholar
Research Gate 

Research Interests

Our interests center around the processing of dietary fiber by the human gut microbiome. This fiber is composed primarily of the undigested carbohydrates in our diet. Humans can really only directly use the polysaccharide starch (mostly, see below), the disaccharides lactose, sucrose and maltose and their constituent monosaccharides glucose, galactose and fructose. All other carbohydrates are untouched by human digestive enzymes and instead serve as substrates to be fermented by our gut microorganisms. 

Resistant Starch

We are particularly interested in resistant starch, a term for all the various forms of starch that cannot be broken down by human enzymes. Almost all cooked starches are easily digested by humans, but many raw starches such as uncooked potato starch (even uncooked, wheat starch is easily digested) require specialized bacteria for their digestion. Whole grains (the starch is hidden away), retrograded (cooked and cooled starch) and some chemically modified starches are also types of resistant starch. You can see that there are a number of things that can make starch resistant and we study the bacteria and the mechanisms they use to degrade these polysaccharides. But why do we care? Resistant starch has a potent ability to shape the microbiome and has the potential to shift the populations of bacteria so that they produce health boosting compounds like butyrate, regulate the immune system and prevent infection by pathogenic bacteria. However, not everyone's microbiome responds in the same way to each type of resistant starch. This suggests that we need to customize aspects of the diet like fiber and resistant starch to a particular person's microbiome. This development of personalized diets dictated by the microbiome is a major thrust of our lab. Thus using a combination of in vitro assays and feeding trials with humans we are trying to develop the methods of determining how you can get the most health benefits out of your personal microbiome.   


Microscopic assessment of the degradation of millet starch granules by endogenous and exogenous enzymes during mashing
Carbohydrate Polymers, Ledley, Andrew, Ziegler, Gregory, Elias, Ryan, Cockburn, Darrell W., 2023

Evaluating the Role of Mashing in the Amino Acid Profiles of Worts Produced from Gluten-Free Malts
Beverages, Ledley, Andrew J., Elias, Ryan J., Cockburn, Darrell W., 2023

Affinity Electrophoresis for Analysis of Catalytic Module-Carbohydrate Interactions
Methods in Molecular Biology, Cockburn, Darrell W., Wilkens, Casper, Svensson, Birte, 2023

Surface Plasmon Resonance Analysis for Quantifying Protein-Carbohydrate Interactions
Methods in Molecular Biology, Møller, Marie Sofie, Cockburn, Darrell W., Wilkens, Casper, 2023

Impact of mashing protocol on the formation of fermentable sugars from millet in gluten-free brewing
Food Chemistry, Ledley, Andrew, Elias, R, Cockburn, Darrell, 2023

Additional Resistant Starch from One Potato Side Dish per Day Alters the Gut Microbiota but Not Fecal Short-Chain Fatty Acid Concentrations
Nutrients, DeMartino, P, Johnston, E, Petersen, Kristina, Kris-Etherton, Penny, Cockburn, Darrell W., 2022

Effect of processing on the anti-inflammatory efficacy of cocoa in a high fat diet-induced mouse model of obesity
Nutrition Reports International, Weikart, D., Indukuri, V., Racine, K., Coleman, K., Kovac, Jasna, Cockburn, Darrell, Hopfer, Helene, Neilson, A., Lambert, Joshua D., 2022

Structure and substrate recognition by the Ruminococcus bromii amylosome pullulanases
Journal of Structural Biology, Cockburn, Darrell W., Kibler, Ryan, Brown, Haley A., Duvall, Rebecca, Moraïs, Sarah, Bayer, Edward, Koropatkin, Nicole M., 2021

Characterization of Microbial Dynamics and Volatile Metabolome Changes During Fermentation of Chambourcin Hybrid Grapes From Two Pennsylvania Regions
Frontiers in Microbiology, Wang, Hung Li, Hopfer, Helene, Cockburn, Darrell W., Wee, Josephine, 2021

Resistant starch: impact on the gut microbiome and health
Current Opinion in Biotechnology, DeMartino, Peter, Cockburn, Darrell W., 2020

Zippia, Cockburn, Darrell, 2020

5 things you can do to make your microbiome healthier
The Conversation, Cockburn, Darrell, Rogers, C, 2019

Resistant starch: impact on the gut microbiome and health
Current Opinion in Biotechnology, DeMartino, P, Cockburn, Darrell, 2019

Structural basis for the flexible recognition of α-glucan substrates by Bacteroides thetaiotaomicron SusG
Protein Science, Arnal, Gregory, Cockburn, Darrell W., Brumer, Harry, Koropatkin, Nicole M., 2018

Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch-degrader Ruminococcus bromii
Environmental Microbiology, Mukhopadhya, Indrani, Moraïs, Sarah, Laverde-Gomez, Jenny, Sheridan, Paul O., Walker, Alan W., Kelly, William, Klieve, Athol V., Ouwerkerk, Diane, Duncan, Sylvia H., Louis, Petra, Koropatkin, Nicole, Cockburn, Darrell, Kibler, Ryan, Cooper, Philip J., Sandoval, Carlos, Crost, Emmanuelle, Juge, Nathalie, Bayer, Edward A., Flint, Harry J., 2018

Novel carbohydrate binding modules in the surface anchored α-amylase of Eubacterium rectale provide a molecular rationale for the range of starches used by this organism in the human gut
Molecular Microbiology, Cockburn, Darrell W., Suh, Carolyn, Medina, Krizia Perez, Duvall, Rebecca M., Wawrzak, Zdzislaw, Henrissat, Bernard, Koropatkin, Nicole M., 2018

Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch-degrader Ruminococcus bromii.
Environmental Microbiology, Mukhopadhya, I, Moraïs, S, Laverde-Gomez, J, Sheridan, P, Walker, A, Kelly, W, Klieve, A, Ouwerkerk, D, Duncan, S, Louis, P, Koropatkin, N, Cockburn, Darrell, Kibler, R, Cooper, P, Sandoval, C, Crost, E, Juge, N, Bayer, E, Flint, H, 2018

Affinity electrophoresis for analysis of catalytic module-carbohydrate interactions, Cockburn, Darrell, Wilkens, Casper, Svensson, Birte, 2017

Lysozyme activity of the Ruminococcus champanellensis cellulosome
Environmental Microbiology, Moraïs, Sarah, Cockburn, Darrell W., Ben-David, Yonit, Koropatkin, Nicole M., Martens, Eric C., Duncan, Sylvia H., Flint, Harry J., Mizrahi, Itzhak, Bayer, Edward A., 2016

Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease
Journal of Molecular Biology, Cockburn, Darrell W., Koropatkin, Nicole M., 2016

Using carbohydrate interaction assays to reveal novel binding sites in carbohydrate active enzymes
PLoS One, Cockburn, Darrell, Wilkens, Casper, Dilokpimol, Adiphol, Nakai, Hiroyuki, Lewińska, Anna, Hachem, Maher Abou, Svensson, Birte, 2016

An efficient arabinoxylan-debranching α-l-arabinofuranosidase of family GH62 from Aspergillus nidulans contains a secondary carbohydrate binding site
Applied Microbiology and Biotechnology, Wilkens, Casper, Andersen, Susan, Petersen, Bent O., Li, An, Busse-Wicher, Marta, Birch, Johnny, Cockburn, Darrell, Nakai, Hiroyuki, Christensen, Hans E.M., Kragelund, Birthe B., Dupree, Paul, McCleary, Barry, Hindsgaul, Ole, Hachem, Maher Abou, Svensson, Birte, 2016

The Sus operon: a model system for starch uptake by the human gut Bacteroidetes
Cellular and Molecular Life Sciences, Foley, Matthew H., Cockburn, Darrell W., Koropatkin, Nicole M., 2016

Surface binding sites in amylase have distinct roles in recognition of starch structure motifs and degradation
International Journal of Biological Macromolecules, Cockburn, Darrell, Nielsen, Morten M., Christiansen, Camilla, Andersen, Joakim M., Rannes, Julie B., Blennow, Andreas, Svensson, Birte, 2015

Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale
Molecular Microbiology, Cockburn, Darrell W., Orlovsky, Nicole I., Foley, Matthew H., Kwiatkowski, Kurt J., Bahr, Constance M., Maynard, Mallory, Demeler, Borries, Koropatkin, Nicole M., 2015

Analysis of surface binding sites (SBS) within GH62, GH13, and GH77
Journal of Applied Glycoscience, Wilkens, C, Cockburn, Darrell, Andersen, S, Petersen, B, Ruzanski, C, Field, R, Hindsgaul, O, Nakai, H, McCleary, B, Smith, A, others, None, 2015

Analysis of surface binding sites (SBSs) in carbohydrate active enzymes with focus on glycoside hydrolase families 13 and 77 - a mini-review
Biologia (Poland), Cockburn, Darrell, Wilkens, Casper, Ruzanski, Christian, Andersen, Susan, Willum Nielsen, Jonas, Smith, Alison M., Field, Robert A., Willemoës, Martin, Abou Hachem, Maher, Svensson, Birte, 2014