About

Patrick Gibney is an Associate Professor in the Department of Food Science at Cornell University. His research focuses on a variety of topics that span eukaryotic cell biology to wine microbiology. His lab is interested in understanding fundamental aspects of biology and collaborating with the fermented beverage industry on more applied projects. His areas of expertise include cell biology, electron transport chain, genetics, molecular biology, Saccharomyces cerevisiae, systems biology, trehalose, wine microbiology, and yeast. Dr. Gibney holds a doctorate from the University of Texas Health Science Center at Houston, Graduate School of Biomedical Sciences, obtained in 2009, and a Bachelor of Arts and Bachelor of Science from the University of Northern Iowa, both earned in 2003. He teaches courses related to food science, viticulture, enology, and wine microbiology, including doctoral-level thesis research and undergraduate internships. His contact information is provided as being located at 347 Stocking Hall, Ithaca, NY, with a phone number and email address listed.

Research topics

• Biology
• Biochemistry
• Food science
• Chemistry
• Biotechnology
• Epistemology
• Biochemical engineering
• Philosophy
• Medicine
• Theology
• Pathology

Selected publications

• Dietary grape pomace mitigates high-NSP-induced inflammation and production loss via microbiome-SCFA-immune mediated pathways

  npj Biofilms and Microbiomes · 2026-05-07

  articleOpen access

  The United States poultry industry is transitioning away from antibiotic growth promoters (AGP) to antibiotic-free programs, which may increase the risk of chronic intestinal inflammation due to exposure to multiple factors. Grape pomace (GP), a polyphenol-rich by-product, might be a promising candidate for mitigating such inflammation. This study investigated the fermented and non-fermented GP as potential substitutes for antibiotic growth promoters in broilers. A total of 126 broilers were divided into six treatment groups: (i) standard diet (STD), (ii) high non-starch polysaccharide diet (NSP), (iii) NSP + zinc bacitracin (AGP), (iv) NSP + 0.5% GP (GP), (v) NSP + 0.5% Lactobacillus casei fermented GP (LAB FGP), and (vi) NSP + 0.5% Saccharomyces cerevisiae fermented GP (YST FGP). NSP-fed birds exhibited reduced growth and increased TNF-α and IL-1β expression, indicating chronic inflammation. GP and FGP suppressed cytokine expression, modulated microbial homeostasis, and increased butyrate production, suggesting functional modulation of the cecal microbiome. Exploratory correlation identified the Lactobacillaceae-butyrate-IL-1β pathway, positively associated with growth, microbiome, and SCFA production, and negatively associated with inflammation. Overall, incorporating 0.5% of GP or FGP into the diet may serve as an effective alternative to AGPs in broiler production, with the added benefits of antioxidants and prebiotics.

  PublisherOA PDFDOI

• The Impact of Extended Skin Contact on Phenolic Extraction in Skin-fermented Hybrid White Wines

  Journal of Food and Nutrition Sciences · 2025-06-20

  articleOpen access1st authorCorresponding

  Background. With growing interest in skin-fermented white wines, more winemakers in North America are producing this style of wine with cold-tolerant, interspecific hybrid grape varieties rather than only <i>Vitis vinifera</i> species. Objective. In this study we sought to characterize the level of phenolic extraction using extended skin contact post-fermentation using two hybrid white grape cultivars. Alcoholic fermentations were conducted with Cayuga White and Vidal Blanc separately, followed by five months of extended skin contact post-fermentation. Phenolic compounds and color quantification were monitored over the course of post-fermentative aging on grape skins. The parameters were analyzed using standard UV/Visible spectroscopy and HPLC-MS-based methods. Conclusions. For both hybrid cultivars, there were no significant changes in phenolic content or in brown or yellow color over five months of post-fermentation skin contact. Under the winemaking conditions used in this study, for the interspecific hybrid grape cultivars Cayuga White and Vidal Blanc, we found that extended skin contact did not increase phenolic extraction beyond the level achieved by completion of alcoholic fermentation, providing useful guidance for winemakers to make production decisions regarding potential benefits (increased compound extraction) and risks (increased spoilage or oxidation potential due to longer periods of atmospheric exposure) of extended skin contact post-fermentation.

  PublisherOA PDFDOI

• A Pilot Study for Building Student Metacognitive Skills and Self-Perception in a Food Microbiology Lecture Course

  Teaching & Learning Inquiry The ISSOTL Journal · 2025-03-31

  articleOpen access

  Metacognition, or the monitoring of one’s own learning, is an underutilized tool in STEM education. Previous research suggests instructional strategies that attempt to improve student metacognitive skills could increase student resilience and retention in STEM classes. This pilot initiative aimed to improve student metacognitive skills and self-perception. To do so, metacognitive-based instructional strategies were added to the curriculum of a food microbiology lecture course. These instructional strategies encouraged students to build their metacognitive skills within a supportive classroom community. Student metacognitive skills, self-perception, and learning strategies were assessed throughout the semester. By the end of the semester, over a third of students reported using at least three higher-order learning strategies. Additionally, there were some significant changes in students’ sense of belonging and self-efficacy, with an overall positive improvement compared to their previous science lectures. This study found that metacognitive-based instructional strategies can be an important tool for improving students’ experiences in a food microbiology class.

  PublisherOA PDFDOI

• Electron transport chain disruption leads to failure of glucose derepression via the Snf1/AMPK pathway

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-08

  preprintOpen accessSenior authorCorresponding

  ABSTRACT When Saccharomyces cerevisiae cells transition from a glucose-rich environment to low glucose conditions, the expression of genes that were previously repressed by glucose is derepressed, enabling the cell to adapt metabolic processes to the available carbon source. The Snf1 pathway is one of the primary signaling pathways responsible for orchestrating glucose sensing and signaling. In this study, we investigate the impact of disrupted electron transport chain (ETC) function, a mitochondrial protein complex essential for respiratory energy generation, in glucose derepression. We observe that respiratory incompetent mutants exposed to glucose are unable to subsequently utilize galactose as a carbon source in minimal media. In contrast, ETC mutants that have been generated and maintained on galactose can effectively continue to metabolize galactose until glucose exposure. We define this phenomenon as a F ailure of G lucose D erepression (FGD), wherein respiratory incompetent cells fail to fully reverse glucose repressed gene expression regulation. Through further characterization, we show how irregular localization patterns of crucial proteins within the Snf1 pathway are associated with FGD suggesting a potential novel connection between the ETC and the Snf1 pathway during carbon source transition. SIGNIFICANCE STATEMENT Respiratory incompetent electron-transport chain mutants are capable of metabolizing galactose as a carbon source. However, when ETC mutants encounter glucose, they lose this ability to metabolize galactose. This study demonstrates that failure to derepress glucose repressed genes facilitated by the Snf1/AMPK pathway is primarily responsible for this phenotype in ETC mutants. These results illustrate a novel signaling role for the ETC and suggest a possible metabolic intervention to certain disease phenotypes.

  PublisherOA PDFDOI

• Auxotrophy-Independent Plasmid Shuttle Vectors for Applications in Diverse Yeasts

  Applied Microbiology · 2024-02-28 · 3 citations

  articleOpen accessSenior authorCorresponding

  Plasmid shuttle vectors are a common tool used to study yeast physiology. The majority of yeast plasmids have been optimized for Saccharomyces cerevisiae lab strain compatibility, relying on auxotrophic complementation as their selective property. We sought to construct a series of plasmid shuttle vectors to extend functionality beyond strains with auxotrophic requirements, and test compatibility across a diverse panel of yeasts. We constructed 18 plasmids which were successfully maintained by yeasts from several genera. From a panel of 24 yeast strains, these plasmids were maintained by 18 yeasts, spanning 11 species within the genera Lachancea, Metschnikowia, Pichia, Saccharomyces, and Torulaspora. Additionally, an integrated gene expression reporter was assayed for functional compatibility with the 18 strains. Plasmid-derived gene expression was observed for 13 strains, spanning five species within the Saccharomyces genus, in addition to Torulaspora delbrueckii. These results indicate that this plasmid series is broadly useful for advancements and applications within academia, biotechnology, and the food and fermentation industries for research utilizing diverse Saccharomyces and non-Saccharomyces yeasts.

  PublisherOA PDFDOI

• Agar lot-specific inhibition in the plating efficiency of yeast spores and cells

  G3 Genes Genomes Genetics · 2024-09-23 · 1 citations

  articleOpen access

  The fission yeast Schizosaccharomyces pombe and the budding yeast Saccharomyces cerevisiae are highly diverged (530 mya), single-celled, model eukaryotic organisms. Scientists employ mating, meiosis, and the plating of ascospores and cells to generate strains with novel genotypes and to discover biological processes. Our three laboratories encountered independently sudden-onset, major impediments to such research. Spore suspensions and vegetative cells no longer plated effectively on minimal media. By systematically analyzing multiple different media components from multiple different suppliers, we identified the source of the problem. Specific lots of agar were toxic. We report that this sporadic toxicity affects independently the agar stocks of multiple vendors, has occurred repeatedly over at least three decades, and extends to species in highly diverged taxa. Interestingly, the inhibitory effects displayed variable penetrance and were attenuated on rich media. Consequently, quality control checks that use only rich media can provide false assurances on the quality of the agar. Lastly, we describe likely sources of the toxicity and we provide specific guidance for quality control measures that should be applied by all vendors as preconditions for their sale of agar.

  PublisherDOI

• Utilizing functional genomics in <i>Saccharomyces cerevisiae</i> to characterize food preservative compounds: A pilot study

  Journal of Food Science · 2024-01-15 · 4 citations

  articleSenior authorCorresponding

  Chemical preservatives are ubiquitously used to suppress the growth of or kill microorganisms across numerous industries, including the food industry. Utilizing yeast functional genomic techniques, genes and their functions can be observed at a genomic scale to elucidate how environmental stressors (e.g., chemical preservatives) impact microbial survival. These types of chemical genomics approaches can reveal genetic mutations that result in preservative resistance or sensitivity, assist in identification of preservative mechanism of action, and can be used to compare different preservatives for rational design of preservative mixtures. In this proof-of-concept study, we performed deletion and high-copy genetic expression screens to identify mutants that confer drug resistance to sodium benzoate, potassium sorbate, rosemary extract, and Natamax. By observing overlapping mutant genes between genetic screens, we were able to identify functional overlap between chemical preservatives and begin to explain mechanisms of action for these compounds.

  PublisherDOI

• Evaluating cellular roles and phenotypes associated with trehalose degradation genes in <i>Saccharomyces cerevisiae</i>

  G3 Genes Genomes Genetics · 2024-09-09 · 6 citations

  articleOpen accessSenior author

  In the yeast Saccharomyces cerevisiae, 2 types of trehalase activities have been described. Neutral trehalases (Nth1 and Nth2) are considered to be the main proteins that catalyze intracellular trehalose mobilization. In addition to Nth1 and Nth2, studies have shown that acid trehalase Ath1 is required for extracellular trehalose degradation. Although both neutral and acid-type trehalases have been predominantly investigated in laboratory strains of S. cerevisiae, we sought to examine the phenotypic consequences of disrupting these genes in wild strains. In this study, we constructed mutants of the trehalose degradation pathway (NTH1, NTH2, and ATH1) in 5 diverse S. cerevisiae strains to examine whether published lab strain phenotypes are also exhibited by wild strains. For each mutant, we assessed a number of phenotypes for comparison to trehalose biosynthesis mutants, including trehalose production, glycogen production, cell size, acute thermotolerance, high-temperature growth, sporulation efficiency, and growth on a variety of carbon sources in rich and minimal medium. We found that all trehalase mutants including single deletion nth1Δ, nth2Δ, and ath1Δ, as well as double deletion nth1nth2Δ, accumulated higher intracellular trehalose levels compared to their isogenic wild-type cells. Also, nth1Δ and nth1Δnth2Δ mutants exhibited mild thermal sensitivity, suggesting a potential minor role for trehalose mobilization when cells recover from stress. In addition, we evaluated phenotypes more directly relevant to trehalose degradation, including both extracellular and intracellular trehalose utilization. We discovered that intracellular trehalose hydrolysis is critical for typical spore germination progression, highlighting a role for trehalose in cell cycle regulation, likely as a storage carbohydrate providing glycolytic fuel. Additionally, our work provides further evidence suggesting Ath1 is indispensable for extracellular trehalose utilization as a carbon source, even in the presence of AGT1.

  PublisherDOI

• Identification of the Yeast Mannoprotein Gene <i>HZY1</i> as a Key Genetic Determinant for Yeast-Derived Haze in Beer

  Journal of the American Society of Brewing Chemists · 2024-07-11 · 1 citations

  article
  PublisherDOI

• Patulin contamination of hard apple cider by Paecilomyces niveus and other postharvest apple pathogens: Assessing risk factors

  International Journal of Food Microbiology · 2024-01-05 · 6 citations

  article
  PublisherDOI

Recent grants

• Large Scale Identification and Characterization of Hsf1-mediated Heat Shock Respo

  NIH · $105k · 2011–2013

Frequent coauthors

• David Botstein

  23 shared

• Anqi Chen

  14 shared

• R. Scott McIsaac

  12 shared

• Joshua D. Rabinowitz

  Princeton University

  11 shared

• David G. Hendrickson

  6 shared

• Jeremy R. Smith

  Cornell University

  6 shared

• Jonathan C. Chen

  Massachusetts Institute of Technology

  6 shared

• Patrick H. Bradley

  The Ohio State University

  6 shared

Labs

• Gibney LabPI