Food Microbiology Commons^™

Amorphous Calcium Phosphate Maintains Casein Microarchitecture While Modulating Bacterial Growth Kinetics, Vuk Uskoković, Michael Ibba, Lorenzo Eugenio Leiva

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Casein, the primary source of protein in ruminant milk, represents a family of proteins that self-assemble into globules composed of finer spherical subunits and stabilized by calcium phosphate (CP) nanoparticles. These globules act as holdase-type chaperones for unfolded or partially folded proteins, preventing their aggregation. Simultaneously, by integrating CP nanoparticles, they enable the bioavailability of calcium and phosphate beyond their solubility limits, thereby enhancing the nutritional value of milk. Using a range of physicochemical and biological characterization techniques, including scanning and transmission electron microscopy, organic and inorganic elemental analyses, SDS-PAGE, and vibrational, UV/Vis and NMR spectroscopies, it is demonstrated that …

Evaluating Variety- And Market-Class-Specific Effects Of Dietary Pulses On Human Health, Jiayu Tang

Department of Food Science and Technology: Dissertations, Theses, and Student Research

While pulses are globally recognized for their high levels of dietary fibers, protein, and polyphenols, research often focuses on characterizing the physiological effects of a single variety. This approach overlooks the substantial genetic and compositional diversity that exists across pulse varieties and individual market classes, which can differ extensively in nutrient content and structure. These compositional differences have the potential to produce distinct physiological and microbial responses in humans, yet variety- and market-class-specific effects remain poorly characterized.

This thesis uses two complementary research methodologies to investigate the health-relevant effects of different pulse varieties and market classes, providing foundational knowledge to …

Evaluating Relationships Between Immunometabolism And Excess Adiposity Using Anthropometric And Body Composition Measurements, Corina Grimaldo

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Metabolic dysfunction is a key contributor to the development of chronic disease and is associated with excessive adiposity. Though body mass index (BMI) is a common screening tool used to identify possible metabolic dysfunction, it does not consider fat distribution. Other tools are needed to assess body composition and determine fat distribution. In recent studies, it has been suggested that alterations in metabolic processes may occur prior to a clinical diagnosis, and the combination of body composition and blood-based markers can help identify those early changes. The overall objective of this study is to identify low-cost indicators of metabolic dysregulation …

Evaluating The Impact Of Region, Vintage, And Carbon Dioxide-Based Winemaking Techniques On Wine Quality Of Mediterranean Varietals, Coleman R. Imrisek

Master's Theses

Changing Vitis vinifera ripening patterns as a result of increasing climate variability has provided challenges against the production of wines with a balanced sensory profile, with adequate acidity, color, aroma, and texture. This thesis aimed to evaluate the ripening patterns and wine profiles of potentially climate-adaptive Mediterranean varietals in two different California Central Coast climates. Additionally, different carbon-dioxide based winemaking techniques were also assessed. Viognier and Grenache Noir grapes were sourced from the warmer, diurnal Paso Robles AVA and the cooler, marine Santa Maria AVA during the 2024 and 2025 growing seasons, with Syrah and Grenache Blanc grapes being only …

Advancing Targeted Food Allergen Detection: Extraction Optimization And Sample Preparation Method Comparison Using Lc-Ms/Ms, Zhenhao Wang

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Accurate quantification of food allergens in processed foods by liquid chromatography-tandem mass spectrometry (LC-MS/MS) requires effective protein extraction and sample cleanup. However, no single sample preparation workflow has shown consistent performance across diverse food matrices. This study evaluated extraction buffer formulations and post-extraction cleanup strategies for quantification of milk, soy, and peanut allergens in multiple processed food matrices.

Six extraction buffers with varying combinations of SDS, urea, and thiourea alongside a common Tris-HCl/DTT/PVPP base were evaluated across five food matrices. No significant differences in extraction efficiency were observed among buffer formulations for nonfat dry milk (NFDM), non-roasted soy flour, peanut …

Detection And Quantification Of Allergen Cross-Contact In Shared Frying Oil Using Targeted Mass Spectrometry, Francisca Asigri

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Cow’s milk and egg allergies are prevalent IgE-mediated food allergies that pose significant public health concerns worldwide. Although strict avoidance remains the primary management strategy, unintended exposure can still occur through allergen cross-contact, particularly in commercial and industrial food operations that utilize shared frying oils. The objective of this study was to identify and quantify allergen transfer in shared frying oil and assess the robustness of existing targeted mass spectrometry methods (LC-MS/MS) for detecting milk and egg proteins in heated oil matrices.

Heated oil spikes were developed by incorporating non-fat dry milk (NFDM) and whole egg powder (WEP) into oil …

Defining The Causal Contribution Of The Gut Microbiota To Cardiomyopathy Pathogenesis As A Basis For Developing Microbiome-Targeted Therapies, Xu Shi

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Heart failure (HF) is a leading cause of morbidity and mortality worldwide, placing substantial clinical and economic burdens on society. Although advances in therapy have improved patient outcomes, the biological mechanisms that drive HF onset and progression remain incompletely understood. Increasing evidence suggests that the gut microbiota, the trillions of microorganisms residing in the gastrointestinal tract, plays a key role in some forms of heart disease, especially cardiovascular disease. Moreover, gut microbial dysbiosis has been associated with systemic inflammation, metabolic imbalance, and immune dysregulation, all of which contribute to the pathophysiology of HF. Cardiomyopathy, a primary disorder of the heart …

Comparative Analysis Of Probiotic Viability In Alcoholic And Non-Alcoholic Kombucha, Isabella N. Cerrone, Brooke Pirkle, Danielle Williamson, Gianna Vendrell, Chloe Kraft

Humboldt Journal of Microbiology

Kombucha is a fermented tea beverage valued for its probiotic and antimicrobial properties that arise from complex molecular interactions between yeast, acetic acid bacteria (AAB), lactic acid bacteria (LAB), and metabolic byproducts of fermentation. With the rising demand for non-alcoholic versions of traditionally alcoholic kombucha beverages, ethanol reduction methods have become common, though their impact on probiotic viability and antimicrobial properties remains poorly understood. This study investigates the effects of ethanol removal on kombucha’s functional properties, including probiotic survival, antimicrobial activity, and organic acid composition (pH). We compared alcoholic and non-alcoholic versions of JuneShine kombucha across five flavors. Probiotic viability …

Assessment Of Microbial Quality And Safety, Including Aflatoxin B1, In Buckwheat Flour And Groats, La Fontaine Bahatsi

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Buckwheat (Fagopyrum esculentum), a gluten-free pseudocereal, has gained popularity in global food markets for its nutritional value and functional properties. However, despite its health-promoting potential, buckwheat is vulnerable to microbial contamination and mycotoxin accumulation during cultivation, processing, and storage. These factors present significant food safety concerns that remain understudied, particularly in North America.

This study investigated the microbiological quality and mycotoxin contamination of buckwheat flour and groats collected from different suppliers via online sourcing. Samples were collected in two consecutive years (2024-2025). Microbiological quality, including aerobic plate counts (APC), Enterobacteriaceae, coliforms, E. coli, yeasts, and molds, was evaluated …

Cazyme Gene Cluster Diversity In Human Gut Microbiome, Yi Xing

Department of Food Science and Technology: Dissertations, Theses, and Student Research

In gut microbiome research, carbohydrate-active enzyme gene clusters (CGCs) have emerged as key functional units for understanding microbial glycan degradation. Unlike taxonomic or broad pathway annotations, CGCs offer gene-cluster-level resolution and capture substrate-specific microbial functions. However, their diversity and distribution in relation to host metabolic phenotypes, such as obesity, remain poorly characterized. This study tests the hypothesis that the composition and abundance of fiber-targeting CGCs vary between obese and healthy human gut microbiomes, reflecting distinct microbial carbohydrate utilization strategies. To examine this, we constructed a high-quality reference CGC dataset comprising 94,019 clusters from the Unified Human Gastrointestinal Genome and profiled …

Identification Of Antigens For Food Allergy And Food Allergen Detection, Ellenor Sell

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Antibody-based allergen testing is an essential part of allergen management in the food industry. These methods directly detect one or more molecules of the allergenic foodstuff (target’ molecule(s)) and the presence of the allergenic foodstuff is inferred. The identity of these target molecules is crucial to the performance of the method and the interpretation of results. The goal of this study was to develop protein/antibody capture methodology for the identification of antibody binding partners using mass spectrometry.

This study is broken down into three separate projects: the characterization of the antigen-antibody complexes present in sandwich ELISAs, LFDs, and human sera. …

Effects Of Heat Moisture Treatment On Dietary Fiber Utilization By The Gut Microbiota, Yichen Bai

Department of Food Science and Technology: Dissertations, Theses, and Student Research

The present study investigates the impact of heat moisture treatment (HMT) on the utilization of dietary fibers from red lentil hulls and wheat bran and its subsequent effect on gut microbiota and short-chain fatty acid production. HMT significantly decreased the water absorption index in red lentil hulls but increased it in wheat bran. For resistant starch (RS), HMT elevated its content in red lentil hulls but diminished it in wheat bran. In terms of dietary fiber content, HMT increased soluble dietary fiber in red lentil hulls. However, carbohydrate utilization and SCFA production by gut microbiota did not significantly change after …

Development Of Fortified Blended Food Using Great Northern Bean, Aemiro Tadesse Zula

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Undernutrition is a global health challenge affecting people across all stages of life. While everyone is susceptible, certain groups face a significant burden. These include those living in poverty, young children, adolescents, older people, and lactating and pregnant women. Food insecurity is another primary global concern affecting billions of individuals worldwide and is closely associated with undernutrition. Implementing interventions to address these two significant global burdens is critical, and international organizations are playing a crucial role through food aid programs using Fortified Blended Foods such as corn-soy blend (CSB), corn-soy blend plus (CSB+), and corn-soy blend plus plus (CSB++). CSB+ …

Microbial Transfer And Cross-Contamination In Milling Facilities And Pathogen Survival In Milled Products And Baking Mixes, Aryany Leticia Peña-Gomez

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Wheat-based products, traditionally considered low-risk due to their low moisture content, have been involved in numerous foodborne outbreaks in recent decades. Salmonella and Shiga toxin-producing Escherichia coli (STEC) present in these products have caused significant numbers of hospitalizations and massive product recalls. The microbiological quality of flour is highly dependent on the incoming wheat, which is vulnerable to contamination from field to milling. Once pathogens are present in flour, they can survive for extended periods. Implementing strategies to mitigate the risk of pathogen contamination throughout the wheat processing chain is critical.

This study evaluated the distribution of E. coli …

Development And Validation Of Aronia Melanocarpa Berry Recipes For Home Canning: Integrating Thermal Lethality Studies, Microbiological Safety, And Antioxidant Analysis, Juan Diego Villegas Posada

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Aronia melanocarpa, also known as chokeberry, is gaining popularity for its high antioxidant content and health benefits, including reducing oxidative stress and inhibiting cancer gene expression. However, its characteristic bitterness and astringency limit its broader appeal. Chokeberry's low pH places it in the acid foods category, making it ideal for safe home canning. An acidic environment combined with heat treatment inhibits harmful bacteria like Clostridium botulinum. Home canning preserves food by sealing it in airtight containers and heating it to destroy spoilage microorganisms.

Developing safe and palatable recipes is essential for making chokeberries suitable for home canning. A …

The Effect Of Fat Content On The Inactivation And Recovery Of Listeria Spp. In Ready-To-Eat Foods After High Pressure Processing, Yhuliana Kattalina Niño Fuerte

Department of Food Science and Technology: Dissertations, Theses, and Student Research

High-pressure processing (HPP) is recognized by the United States Department of Agriculture Food Safety and Inspection Service (USDA FSIS) as a post-lethality treatment to control Listeria monocytogenes in ready-to-eat (RTE) meat and poultry products. A scoping review of 603 journal articles, which ultimately was narrowed down to 16 articles, revealed that the efficacy of HPP varies with fat content. The studies demonstrated that L. monocytogenes inactivation by HPP tends to be lower in RTE meats with greater than 5% fat content, compared to products with lower than 5% fat. The wide range of HPP parameters used in these studies …

Interactions Between High-Pressure Processing And Natural Antimicrobials In Ground White-Meat Chicken: An Analysis Of Microbial, Textural Charactheristics And Physicochemical Changes, Amalia M. Diaz Alejandro

All Theses

High Pressure processing is an innovative technique for preserving a wide variety of foods, including meat, and this method is increasingly used to satisfy consumer demand for quality food products. High-pressure treatment can impact, negatively or positively, various aspects of meat quality, including color, texture, protein denaturation, and microbial stability, particularly when food products are processed at ambient or low temperatures. By minimizing thermal exposure, appropriate high-pressure ranges help to prevent quality and nutrition degradation, reduce microbial contamination, and enhance tenderness.

The first objective of this research was to examine the influence of high-pressure processing and addition of natural antimicrobials …

Twenty-Three Years Of Pcr-Based Seafood Authentication Assay Development: What Have We Learned?, Maleeka Singh, Robert G. Young, Rosalee S. Hellberg, Robert H. Hanner, Maria G. Corradini, Jeffrey M. Farber

Food Science Faculty Articles and Research

Seafood is a prime target for fraudulent activities due to the complexity of its supply chain, high demand, and difficult discrimination among species once morphological characteristics are removed. Instances of seafood fraud are expected to increase due to growing demand. This manuscript reviews the application of DNA-based methods for commercial fish authentication and identification from 2000 to 2023. It explores (1) the most common types of commercial fish used in assay development, (2) the type of method used, (3) the gene region most often targeted, (4) provides a case study of currently published assays or primer-probe pairs used for DNA …

Utilization Of Probiotics To Compete With Clostridioides Difficile For Nutrient-Niches In A Variety Of In Vitro Contexts, April Elizabeth Johnson

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Clostridium difficile is a major threat to public health and primarily affects at risk groups such as elderly, immunocompromised individuals, and individuals on antibiotics. Many decades of research have been conducted to figure out ways to exclude or reduce C. difficile colonization and toxin production. Two major proposed mechanisms for colonization resistance are production of secondary bile salts and competition for nutrients.

In Chapter 2, we found that antibiotic treatment disrupted bile salt metabolism increasing the levels of the primary bile salt cholate and decreasing the levels of deoxycholate, a secondary bile salt. However, bile salts were not required …

Microbiological And Physicochemical Changes In Rabbit Meat During Ambient Storage, Marielle Gamboa, Dennis Marvin Santiago, April Shayne Sulabo, Mary Ann Torio

The Philippine Agricultural Scientist

This study aimed to evaluate the changes in rabbit meat during storage at ambient temperature (30 ± 1ºC) for nine hours. The study focused on two rabbit muscle parts: the hind leg and the saddle, investigated in terms of microbiological parameters such as aerobic plate count (APC) and total coliform count (TCC); and physicochemical parameters such as pH, color, total myoglobin concentration, and lipid oxidation. Data obtained were subjected to statistical analysis at a 5% significance level (p < 0.05). Results revealed that the pH of both portions of rabbit muscle decreases over time during storage. This decrease is attributed to the growth of acid-producing microorganisms, which ultimately leads to spoilage in rabbit meat. On the contrary, color values (L*, a*, and b*) showed an increasing trend in both muscle portions, indicating a discoloration of rabbit meat during storage. Both lipid oxidation and total myoglobin content of rabbit meat did not change significantly during storage, but lipid oxidation varied between muscle parts. Based on the microbiological analysis of rabbit meat, both aerobic plate count (APC) and total coliform count (TCC) increased significantly during storage in both muscle portions. Results of the study suggest that freshly slaughtered rabbit meat must remain at ambient storage for the shortest time, as this storage condition will cause spoilage of meat, making it unfit for human consumption.

Antioxidant Properties Of Kombucha Beverage Infused With Ganoderma Lucidum And Green Tea From Camellia Sinensis (L.) Kuntze With Several Fermentation Times, Rizki Rabeca Elfirta, Pamungkas Rizki Ferdian, Iwan Saskiawan, Tri Hadi Handayani, Kayla Faza Gustafri Mandalika, Rini Riffiani, Kasirah Kasirah, Ukhradiya Magharaniq Safira Purwanto

Karbala International Journal of Modern Science

Kombucha is a functional beverage produced through the fermentation of infused tea or Camelia sinensis (L.) Kuntze (CS) by a symbiotic culture of bacteria and yeast. Apparently, the substrate of kombucha can be substituted to enhance its functional properties. Ganoderma lucidum (GL) is a potential substrate reported to have health benefits. This study aims to evaluate antioxidant properties by comparing different formulations and fermentation times. The formulations prepared in the present study varied in the compositions of GL and CS substrates, namely F1 (100% GL), F2 (75% GL: 25% CS), F3 (50% GL: 50% CS), F4 (25% GL: 75% CS), …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Thawing And Storage Effects On Quality Of Plant-Based Sausage Patties, Dakota Cook

All Theses

Maintaining sausage analogue quality during a thawing process and storage is important for increasing consumer satisfaction. Following new trends and prevalence of plant-based meats and a flexitarian diet, two experiments were conducted to test how thawing methods (experiment 1) and storage temperatures (experiment 2) affect meat analogue quality. For Experiment 1, Jimmy Dean Original Sausage Patties Made with Pork & Turkey, Morningstar Veggie Original Patties and Beyond Sausage Original Patties were purchased pre-frozen and subsequently thawed in one of three ways: 1. thawed at 4°C for 24 hours, 2. thawed at room temperature (22°C±2°C) for 4 hours and 3. thawed …

Development Of An Intact Mass Spectrometry Method For The Detection And Differentiation Of Major Bovine Milk Proteins, Emily F. Harley-Dowell

Department of Food Science and Technology: Dissertations, Theses, and Student Research

The authentication of products with claims regarding protein sources or compositions is a challenge for traditional analytical methods, which generally lack the required specificity whole protein analysis can provide. For example, the establishment of milk as “A2” is achieved through genetic testing of cows before milk production, with no methods to authenticate milk products themselves. Establishment of A2 milk is completed through genetic testing of the cows before milk production, but with no methods to authenticate the milk products themselves. Intact protein mass spectrometry (MS) has the potential to directly authenticate protein products, including specific proteoform claims. The development of …

Kluyveromyces Marxianus Prepared As A Ready To Use Supplemental Food (Rusf), Zachary Christman

Applied Science Program: Theses

Ready to Use Supplemental Food (RUSF) is a nutrient dense paste or compressed bar used to supplement a person’s nutritional needs because of malnutrition or due to food shortages. The purpose of this article is to demonstrate some methods of how the dairy organism Kluyveromyces marxianus can be used to enrich the protein value of bread or ferment a substrate such as wheat bran into a more digestible form.

Influence Of Overcooking On Food Digestibility And In Vitro Fermentation, Wensheng Ding

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Areas of char or overcooking commonly appear in foods people consume. It has been reported that overcooked food is harmful to human health. However, little research exists on the effect of overcooking on in vitro protein and starch digestibility and gut microbial fermentation. This study aimed to reveal the connection between overcooking and in vitro protein and starch digestibility and gut microbial fermentation. In vitro protein digestibility of an overcooked ground beef patty was almost half that of a standard cooked sample (27 ± 2% versus 48 ± 6%, respectively; p = 0.02). Whole wheat bread protein digestibility was also …

Evaluating Salmonella Cross Contamination In Raw Chicken Thighs In Simulated Post-Chill Tanks, Raziya Sadat

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Salmonella contamination poses a significant risk to food safety, particularly in poultry products and public health. This study aims to investigate the effectiveness of peracetic acid (PAA) treatment in mitigating Salmonella cross-contamination in chicken thighs within simulated post-chill tanks, considering different inoculum concentrations and organic matter (OM) levels.

The experiment involved the use of five distinct Salmonella serovars to inoculate chicken thighs, which were categorized into two groups: higher inoculation level (ca. 7 log CFU/mL) and lower inoculation level (ca, 4 log CFU/mL). These groups underwent treatment with four different solutions, including 540 ppm PAA with 1.5% OM, 540 ppm …

Optimizing Soil Nutrient Management To Improve Dry Edible Bean Yield And Protein Quality, Emily Jundt

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Soil nutrient management is of the utmost importance to ensure crop yields are maximized to feed the world’s growing population. Micro and macronutrient deficiencies can be detrimental to plant growth and cause a drastic reduction in yield. Optimization of nutrient management needs extensive research. Nutrients such as nitrogen increase crop yield, even in legumes capable of using a large amount of nitrogen (N) via biological N fixation. Iron (Fe) fertilizers are also crucial for legumes as they are susceptible to Fe deficiency induced chlorosis.

Dry edible beans (Phaseolus vulgaris) are leguminous plants and excellent dietary protein sources. Great …

The Science Of Baking Bread, Admin Stem For Success

STEM for Success Showcase

Activity plan to teach biology and chemistry using a lesson on the baking of bread.

Isolation And Identification Of Chlorate-Reducing Hafnia Sp. From Milk, William P. Mccarthy, Meghana Srinivas, Martin Danaher, Christine O'Connor, Tom F. O'Callaghan, Douwe Van Sinderen, John Kenny, John T. Tobin

Articles

Chlorate has become a concern in the food and beverage sector, related to chlorine sanitizers in industrial food production and water treatment. It is of particular concern to regulatory bodies due to the negative health effects of chlorate exposure. This study investigated the fate of chlorate in raw milk and isolated bacterial strains of interest responsible for chlorate breakdown. Unpasteurized milk was demonstrated to have a chlorate-reducing capacity, breaking down enriched chlorate to undetectable levels in 11 days. Further enrichment and isolation using conditions specific to chlorate-reducing bacteria successfully isolated three distinct strains of Hafnia paralvei . Chlorate-reducing bacteria were …