Digital Commons Network^™

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 …

Development Of An Egg-Specific Mass Spectrometry Targeted Method For Processed Food Matrices, Liyun Zhang

Dissertations and Doctoral Documents from University of Nebraska-Lincoln, 2023–

Egg is a major food allergen in the United States, causing symptoms from mild reactions to severe anaphylaxis. An egg-free diet remains the only management approach for egg allergy. Therefore, individuals and families living with egg allergies rely heavily on allergen statements on packaged food products for informed food choices. Currently, no labeling regulations exist for unintentionally introduced allergens, posing risks to consumers with egg allergies. Therefore, it is critical to have an accurate and reliable detection method in allergen control and management to determine the concentration of total protein from allergenic food sources. Traditional enzyme-linked immunosorbent assays are routinely …

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 …

Assessment Of Foam Decontamination In Tomato Washing Process, Basim M. Alohali

Dissertations and Doctoral Documents from University of Nebraska-Lincoln, 2023–

The work of the dissertation investigated the efficacy of foam-based decontamination treatments to enhance microbial safety in Roma tomatoes, specifically targeting natural microflora and Salmonella contamination. Growing concerns over foodborne illnesses linked to fresh tomatoes and the limitations of conventional decontamination techniques, such as organic matter built-up and limited microbial reduction, are addressed. The primary objectives were to characterize the physiochemical properties of foams formed using various concentrations of Tween 20 (T20) and sodium dodecyl sulfate (SDS) with and without the addition of sodium hypochlorite (NaOCl) and peracetic acid (PAA), compare the efficacy of foam and traditional dump tank (DT) …

Adaptation To Tolerate High Doses Of Arabinoxylan Is Associated With Fecal Levels Of Bifidobacterium Longum, Edward C. Deehan, Zhengxiao Zhang, Nguyen K. Nguyen, Maria Elisa Perez-Muñoz, Janis Cole, Alessandra Riva, David Berry, Carla M. Prado, Jens Walter

Department of Food Science and Technology: Faculty Publications

Dietary fiber supplements are a strategy to close the ‘fiber gap’ and induce targeted modulations of the gut microbiota. However, higher doses of fiber supplements cause gastrointestinal (GI) symptoms that differ among individuals. What determines these inter-individual differences is insufficiently understood. Here we analyzed findings from a six-week randomized controlled trial that evaluated GI symptoms to corn bran arabinoxylan (AX; n = 15) relative to non-fermentable microcrystalline cellulose (MCC; n = 16) at efficacious supplement doses of 25 g/day (females) or 35 g/day (males) in adults with excess weight. Self-reported flatulence, bloating, and stomach aches were evaluated weekly. Bacterial taxa …

Identification Of Carbohydrate Gene Clusters Obtained From In Vitro Fermentations As Predictive Biomarkers Of Prebiotic Responses, Car Reen Kok, Devin J. Rose, Juan Cui, Lisa Whisenhunt, Robert Hutkins

Department of Food Science and Technology: Faculty Publications

Background Prebiotic fibers are non-digestible substrates that modulate the gut microbiome by promoting expansion of microbes having the genetic and physiological potential to utilize those molecules. Although several prebiotic substrates have been consistently shown to provide health benefits in human clinical trials, responder and non-responder phenotypes are often reported. These observations had led to interest in identifying, a priori, prebiotic responders and non-responders as a basis for personalized nutrition. In this study, we conducted in vitro fecal enrichments and applied shotgun metagenomics and machine learning tools to identify microbial gene signatures from adult subjects that could be used to predict …

Design Of Small-Scale Milk Processing Facility, Luke Bond, Robert Stenzel, Ry Steffen, John Van Nieuwenhuyse, Rossana Villa-Rojas, Terry Howell Jr., Tami M. Brown-Brandl, Forrest Kievit

Department of Biological Systems Engineering: Masters Project Reports

This project was intended to investigate the feasibility of a proposed modular dairy processing facility collocated with a small dairy on the University of Nebraska–Lincoln’s Innovation Campus. Priority was placed upon cost savings for equipment to be used in processing. Process flow diagrams, floor plans, production schedules, risk assessments, and plans for wastewater treatment were all developed to address the needs of the plant should it be built. A Monte Carlo simulation was conducted to evaluate the timeline for breaking even financially, resulting in the potential for a payback period of 4.5 years. The 4.5-year payback period was based on …

Three De Novo Assembled Wild Cacao Genomes From The Upper Amazon, Orestis Nousias, Jinfang Zheng, Tang Li, Lyndel W. Meinhardt, Bryan Bailey, Osman Gutierrez, Indrani K. Baruah, Stephen P. Cohen, Dapeng Zhang, Yanbin Yin

Department of Food Science and Technology: Faculty Publications

Theobroma cacao, the chocolate tree, is indigenous to the Amazon basin, the greatest biodiversity hotspot on earth. Recent advancement in plant genomics highlights the importance of de novo sequencing of multiple reference genomes to capture the genome diversity present in different cacao populations. In this study, three high-quality chromosome-level genomes of wild cacao were constructed, de novo assembled with HiFi long reads sequencing, and scaffolded using a reference-free strategy. These genomes represent the three most important genetic clusters of cacao trees from the Upper Amazon region. The three wild cacao genomes were compared with two reference genomes of domesticated …

Increased Dietary Trp, Thr, And Met Supplementation Improves Performance, Health, And Protein Metabolism Of Weaned Piglets Under Mixed Management And Poor Housing Conditions, Joseane Penteado Rosa Gonçalves, Antonio Diego Brandão Melo, Qinnan Yang, Marllon José Karpeggiane De Oliveira, Danilo Alves Marçal, Manoela Trevisan Ortiz, Pedro Righetti Arnaut, Ismael França, Graziela Alves Da Cunha Valini, Cleslei Alisson Silva, Nate Korth, Natasha Pavlovikj, Paulo Henrique Reis Furtado Campos, Henrique Gastmann Brand, John Kyaw Htoo, João Carlos Gomes-Neto, Andrew K. Benson, Luciano Hauschild

Department of Food Science and Technology: Faculty Publications

A sanitary challenge was carried out to induce suboptimal herd health while investigating the effect of amino acids supplementation on piglet responses. Weaned piglets of high sanitary status (6.33 ± 0.91 kg of BW) were distributed in a 2 × 2 factorial arrangement into two similar facilities with contrasting sanitary conditions and two different diets. Our results suggest that increased Trp, Thr, and Met dietary supplementation could support the immune systems of piglets under a sanitary challenge. In this manner, AA+ supplementation improved the performance and metabolism of piglets under mixed management and poor sanitary conditions. No major temporal microbiome …

Bermad: Batch Effect Removal For Single-Cell Rna-Seq Data Using A Multi-Layer Adaptation Autoencoder With Dual-Channel Framework, Xiangxin Zhan, Yanbin Yin, Han Zhang

Department of Food Science and Technology: Faculty Publications

Motivation: Removal of batch effect between multiple datasets from different experimental platforms has become an urgent problem, since single-cell RNA sequencing (scRNA-seq) techniques developed rapidly. Although there have been some methods for this problem, most of them still face the challenge of under-correction or over-correction. Specifically, handling batch effect in highly nonlinear scRNA-seq data requires a more powerful model to address under-correction. In the meantime, some previous methods focus too much on removing difference between batches, which may disturb the biological signal heterogeneity of datasets generated from different experiments, thereby leading to over-correction.

Results: In this article, we …

High-Fat Diet Feeding Exacerbates Hiv-1 Rectal Transmission, Saroj Chandra Lohani, Amanda E. Ramer-Tait, Qingsheng Li

Department of Food Science and Technology: Faculty Publications

High-fat diet (HFD) is well known to impact various aspects of gut health and has been associated with many diseases and inflammation. However, the impact of HFD feeding on HIV-1 rectal transmission has not yet been well addressed. With an increasing threat of HIV-1 infection in men who have sex with men (MSM), where the rectal route is the primary mode of infection, it is imperative to understand the impact of HFD on gut microbiota and inflammation and consequently, its effect on HIV-1 rectal transmission. Here, we utilized our double humanized bone marrow, liver, thymus (dHu-BLT) mouse model to assess …

Twenty-Eight Years Of Gm Food And Feed Without Harm: Why Not Accept Them?, Richard E. Goodman

Department of Food Science and Technology: Faculty Publications

Since the first genetically engineered or modified crops or organisms (GMO) were approved for commercial production in 1995, no new GMO has been proven to be a hazard or cause harm to human consumers. These modifications have improved crop efficiency, reduced losses to insect pests, reduced losses to viral and microbial plant pathogens and improved drought tolerance. A few have focused on nutritional improvements producing beta carotene in Golden Rice. Regulators in the United States and countries signing the CODEX Alimentarius and Cartagena Biosafety agreements have evaluated human and animal food safety considering potential risks of allergenicity, toxicity, nutritional and …

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 …

The Evaluation Of Feed Additives On Reducing Enteric Methane Production From Cattle, Reba L. Colin

Department of Animal Science: Dissertations, Theses, and Student Research

Environmental sustainability can be positively impacted by the inclusion of feed additives to reduce enteric methane production from cattle. Methane production can be affected by feed additives that either alter the rumen environment or act as methanogenesis inhibitors. A reduction in methane from cattle can contribute to meeting carbon neutrality.

A metabolism study was conducted to evaluate Alga 1.0, a product containing bromoform, fed to cattle to evaluate the effects on gas emissions. Treatments were (0, 69, or 103 g/d Alga 1.0) fed in a corn-based diet. Headbox-style indirect calorimeters were used to measure gas emissions. Feeding Alga 1.0 linearly …

Value-Added Green Processing Of Tomato Waste To Obtain A Stable Free-Flowing Powder Lycopene Formulation Using Supercritical Fluid Technology, Purlen Sezer Okur, Ozan Ciftci

Department of Food Science and Technology: Faculty Publications

The tomato processing industry generates large amounts of waste, which creates disposal problems and negatively impacts the environment. Tomato waste contains lycopene, high-value health- and wellness-promoting bioactive, and it is a potential source of natural lycopene for food and nutraceutical applications. However, isolation of lycopene from its source requires toxic solvents, and lycopene is unstable during storage. The objective of this study was to extract lycopene from tomato waste and to convert it to a shelf-stable and easy-to-use free-flowing powder form using green extraction and particle formation processes based on supercritical carbon dioxide (SC-CO2) technology. Lycopene was extracted using SC-CO2 …

Dbapis: A Database Of Anti-Prokaryotic Immune System Genes, Yuchen Yan, Jinfang Zheng, Xinpeng Zhang, Yanbin Yin

Department of Food Science and Technology: Faculty Publications

Anti-prokaryotic immune system (APIS) proteins, typically encoded b y phages, prophages, and plasmids, inhibit prokaryotic immune systems (e.g. restriction modification, to xin-antito xin, CRISPR-Cas). A growing number of APIS genes have been characterized and dispersed in the literature. Here we developed dbAPIS ( https:// bcb.unl.edu/ dbAPIS ), as the first literature curated data repository for experimentally verified APIS genes and their associated protein families. The key features of dbAPIS include: (i) experimentally verified APIS genes with their protein sequences, functional annotation, PDB or AlphaFold predicted structures, genomic context, sequence and structural homologs from different microbiome / virome databases; (ii) classification …

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.

Salmonella Enterica Induces Biogeography-Specific Changes In The Gut Microbiome Of Pigs, Joao Carlos Gomes-Neto, Natasha Pavlovikj, Samantha A. Naberhaus, Bailey Arruda, Andrew K. Benson, Amanda J. Kreuder

Department of Food Science and Technology: Faculty Publications

Swine are a major reservoir of an array of zoonotic Salmonella enterica subsp. enterica lineage I serovars including Derby, Typhimurium, and 4,[5],12:i:- (a.k.a. Monophasic Typhimurium). In this study, we assessed the gastrointestinal (GI) microbiome composition of pigs in different intestinal compartments and the feces following infection with specific zoonotic serovars of S. enterica (S. Derby, S. Monophasic, and S. Typhimurium). 16S rRNA based microbiome analysis was performed to assess for GI microbiome changes in terms of diversity (alpha and beta), community structure and volatility, and specific taxa alterations across GI biogeography (small and large intestine, feces) …

Human Alcohol-Microbiota Mice Have Increased Susceptibility To Bacterial Pneumonia, Kelly C. Cunningham, Deandra R. Smith, Daniel Villageliú, Christi M. Ellis, Amanda E. Ramer-Tait, Jeffrey D. Price, Todd A. Wyatt, Daren L. Knoell, Patricia E. Molina, David A. Welsh, Derrick R. Samuelson

Department of Food Science and Technology: Faculty Publications

Preclinical studies have shown that chronic alcohol abuse leads to alterations in the gastrointestinal microbiota that are associated with behavior changes, physiological alterations, and immunological effects. However, such studies have been limited in their ability to evaluate the direct effects of alcohol-associated dysbiosis. To address this, we developed a humanized alcoholmicrobiota mouse model to systematically evaluate the immunological effects of chronic alcohol abuse mediated by intestinal dysbiosis. Germ-free mice were colonized with human fecal microbiota from individuals with high and low Alcohol Use Disorders Identification Test (AUDIT) scores and bred to produce human alcohol-associated microbiota or human control-microbiota F1 progenies. …

Presence, Co-Occurrence, And Daily Intake Estimates Of Aflatoxins And Fumonisins In Maize Consumed In Food-Insecure Regions Of Western Honduras, Luis Sabillón, Jackeline Alvarado, Alejandra Leiva, Rodrigo Mendoza, Raúl Espinal, John F. Leslie, Andreia Bianchini

Department of Food Science and Technology: Faculty Publications

Foodborne mycotoxins are a significant food safety risk in developing countries. Our objective was to determine the occurrence of and exposure levels to aflatoxins (AFs) and fumonisins (FBs) in maize intended for human and animal consumption in food-insecure regions of western Honduras. Total AFs and FBs were quantified with a monoclonal antibody-based affinity spectrofluorimetric method. FBs were detected in 614/631 samples of maize destined for human consumption at 0.3 to 41 mg/kg (mean, 2.7 mg/kg). Of the 614 positive samples, 147 had FB levels exceeding the U.S. Food and Drug Administration (FDA) advisory threshold of 4.0 mg/kg. AFs were detected …

Protein Enriched Bread Using Spent Wine Yeast, Zachary Christman

Applied Science Program: Theses

Yeast is a common byproduct of wine production. Wine yeast may be used as a food source. It does not contain bitter and astringent compounds such as those present in spent yeast from making beer The use of nutritional yeast and yeast extract for protein enrichment of bread are presented in this article.

Mtco1-Based Population Structure And Genetic Diversity Of Pacific Oyster Crassostrea Gigas Populations Acquired From Two Farms In South Korea, Thanh T. Biet, Su-Jin Park, Hong-Keun Park, Dongjin Park, Youn-Hee Choi

Department of Food Science and Technology: Faculty Publications

Since the early 1990s in South Korea, climatic and anthropogenic factors have incurred the reduction of the wild seeds of the Pacific oyster, Crassostrea gigas, which raised concerns about losing genetic diversity and accelerating genetic deterioration. We assessed the genetic diversity of C. gigas populations from two farms (Tongyeong and Gadeokdo) on the southern coast, where about 80% of the cultivated oysters in Korea are produced. Tongyeong showed slightly higher diversity than Gadeokdo, but both populations had a similar genetic structure characterized by low nucleotide diversity. Comparative haplotype analyses provided data supporting genetic features of the populations that include …

Dry-Aged Beef Flavor Development, And The Effect Of High Levels Of Vitamin-E On Beef Color Stability, Nicolas Herrera

Department of Animal Science: Dissertations, Theses, and Student Research

Palatability and consumer purchasing are essential factors of fresh meat. To meet consumer expectations during purchasing and consumption, fresh beef must maintain desirable cherry-red color at retail and achieve desirable cooked flavor. Dry-aged beef popularity has grown, and identifying methods to ensure quality dry-aged meat is necessary to maintain demand. To understand dry-aged palatability, this dissertation addressed effects of moisture loss and aging time, fundamental factors of dry-aged beef, using bone-in and boneless strip loins. Study two investigated flavor development using cookery methods and internal temperatures in boneless and bone-in dry-aged beef. In study one, increased dry-aging time (creation effect) …

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 …

Cellulosome-Forming Modules In Gut Microbiome And Virome, Jerry Akresi

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

Cellulosomes are large multi-enzyme complexes encoded in the genomes of some microorganisms. Cellulosomes can degrade plant cell wall celluloses, commonly found in compost soils, forest floors and dietary fibers of farm animals. The hallmarks of cellulosome complexes are cohesins that form a large scaffoldin protein and dockerins that interact with cohesin to dock enzymes onto the scaffoldin. The dockerin-containing proteins often contain Carbohydrate Active Enzymes (CAZyme) domains, predominantly the cellulases (e.g., GH48 and GH9 enzymes), which enable them to break down celluloses. A fascinating question is, has Nature also evolved other similar protein complexes that target other types of complex …

Assessing The Release Of Microplastics And Nanoplastics From Plastic Containers And Reusable Food Pouches: Implications For Human Health, Kazi Albab Hussain, Svetlana Romanova, Ilhami Okur, Dong Zhang, Jesse Kuebler, Xi Huang, Bing Wang, Lucia Fernandez-Ballester, Yongfeng Lu, Mathias Schubert, Yusong Li

Department of Civil and Environmental Engineering: Faculty Publications

This study investigated the release of microplastics and nanoplastics from plastic containers and reusable food pouches under different usage scenarios, using DI water and 3% acetic acid as food simulants for aqueous foods and acidic foods. The results indicated that microwave heating caused the highest release of microplastics and nanoplastics into food compared to other usage scenarios, such as refrigeration or room-temperature storage. It was found that some containers could release as many as 4.22 million microplastic and 2.11 billion nanoplastic particles from only one square centimeter of plastic area within 3 min of microwave heating. Refrigeration and room-temperature storage …

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 …