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

Education

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

Websites

Lab Website
Google Scholar
LinkedIn
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.   

Publications

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

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

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

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

A bacterial glucanotransferase can replace the complex maltose metabolism required for starch to sucrose conversion in leaves at night
Journal of Biological Chemistry, Ruzanski, Christian, Smirnova, Julia, Rejzek, Martin, Cockburn, Darrell, Pedersen, Henriette L., Pike, Marilyn, Willats, William G.T., Svensson, Birte, Steup, Martin, Ebenhöh, Oliver, Smith, Alison M., Field, Robert A., 2013

Binding Interactions Between α-glucans from Lactobacillus reuteri and Milk Proteins Characterised by Surface Plasmon Resonance
Food Biophysics, Diemer, Silja K., Svensson, Birte, Babol, Linnéa N., Cockburn, Darrell, Grijpstra, Pieter, Dijkhuizen, Lubbert, Folkenberg, Ditte M., Garrigues, Christel, Ipsen, Richard H., 2012

Modulating the pH-activity profile of cellulase A from Cellulomonas fimi by replacement of surface residues
Protein Engineering, Design and Selection, Cockburn, Darrell W., Clarke, Anthony J., 2011

Direct visualization of the enzymatic digestion of a single fiber of native cellulose in an aqueous environment by atomic force microscopy
Langmuir, Quirk, Amanda, Lipkowski, Jacek, Vandenende, Chris, Cockburn, Darrell, Clarke, Anthony J., Dutcher, John R., Roscoe, Sharon G., 2010

Modulating the pH-activity profile of cellulase by substitution
Biochemistry, Cockburn, Darrell, Vandenende, Chris, Clarke, Anthony J., 2010