Food Science Commons^™

End-Use Quality Of Historical And Modern Winter Wheats Adapted To The Great Plains Of The United States, Sujun Liu, Lan Xu, Yifan Wu, Senay Simsek, Devin J. Rose

Department of Food Science and Technology: Faculty Publications

Improving milling and baking properties is important during wheat breeding. To determine changes in milling and baking quality of hard winter wheat, 23 adapted cultivars released in the Great Plains between 1870 and 2013 were grown in triplicate in a single location (Mead, NE, USA) over two crop years (2018 and 2019). Grain yield and kernel hardness index increased by release year (p < 0.05). The observed increase in hardness index was accompanied by a decrease in percent soft kernels (p < 0.05). Diameter and weight decreased with release year in 2019 (p < 0.05), and their standard deviation increased with the release year (p < 0.05). Flour protein content decreased with release year (p < 0.05) and dough mixing quality increased (p < 0.05). No significant relationship was found for baking property variables, but bran water retention capacity (BWRC), which is correlated with whole wheat bread quality, increased with release year (p < 0.05). In conclusion, wheat kernels have become harder but more variable in shape over a century of breeding. Mixing quality showed significant improvements, and loaf volume and firmness remained constant, even in the presence of a decrease in protein concentration. Bran quality decreased across release year, which may have implications for whole grain baking quality and milling productivity.

Carbohydrate Utilization By The Gut Microbiome Determines Host Health Responsiveness To Whole Grain Type And Processing Methods, Caroline Smith, Mallory J. Suhr Van Haute, Yibo Xian, Rafael R. Segura Munoz, Sujun Liu, Robert J. Schmaltz, Amanda E. Ramer-Tait, Devin J. Rose

Department of Food Science and Technology: Faculty Publications

Little is known about how interactions among grain processing, grain type, and carbohydrate utilization (CU) by the microbiome influence the health benefits of whole grains. Therefore, two whole grains – brown rice and whole wheat – and two processing methods – boiling (porridge) and extrusion – were studied for their effects on host metabolic outcomes in mice harboring human microbiomes previously shown in vitro to have high or low CU. Mice carrying either microbiome experienced increases in body weight and glycemia when consuming Western diets supplemented with extruded grains versus porridge. However, mice with the high but not low CU …

Prebiotics Enhance Persistence Of Fermented-Food Associated Bacteria In In Vitro Cultivated Fecal Microbial Communities, Chloe M. Christensen, Car Reen Kok, Jennifer Auchtung, Robert Hutkins

Department of Food Science and Technology: Faculty Publications

It is well established that the gastrointestinal (GI) microbiota plays a major role in human health. Dietary interventions, and consumption of fermented foods that contain live microbes, in particular, are among the approaches being investigated to modulate the GI microbiota and improve health. However, the persistence of fermented food-associated bacteria (FAB) within the GI tract is typically limited by host factors that limit colonization and competition with autochthonous microbes. In this research, we examined if the addition of prebiotics, dietary substrates that are selectively metabolized by microbes to improve health, would enhance the persistence of FAB. We evaluated the persistence …

Polyploidy Events Shaped The Expansion Of Transcription Factors In Cucurbitaceae And Exploitation Of Genes For Tendril Development, Yu Zhang, Yingchao Zhang, Bing Li, Xiao Tan, Changping Zhu, Tong Wu, Shuyan Feng, Qihang Yang, Shaoqin Shen, Tong Yu, Zhuo Liu, Xiaoming Song

Department of Food Science and Technology: Faculty Publications

Cucurbitaceae is one of the most important plant families distributed worldwide. Transcription factors (TFs) regulate plant growth at the transcription level. Here, we performed a systematic analysis of 42 641 TFs from 63 families in 14 Cucurbitaceae and 10 non-cucurbit species. Whole-genome duplication (WGD) was the dominant event type in almost all Cucurbitaceae plants. The TF families were divided into 1 210 orthogroups (OGs), of which, 112 were unique to Cucurbitaceae. Although the loss of several gene families was detected in Cucurbitaceae, the gene families expanded in five species that experienced a WGD event comparing with grape. Our findings revealed …

Host Species And Captivity Distinguish The Microbiome Compositions Of A Diverse Zoo-Resident Non-Human Primate Population, Maya O. Wills, Robin R. Shields-Cutler, Emily Brunmeier, Madison Weissenborn, Tami Murphy, Dan Knights, Timothy J. Johnson, Jonathan B. Clayton

Department of Food Science and Technology: Faculty Publications

Vast numbers of microorganisms inhabit the mammalian gastrointestinal tract in a complex community referred to as the gut microbiome. An individual’s microbiome may be impacted by genetics, diet, and various environmental factors, and has been associated with many health states and diseases, though specific explanations are lacking. While these communities are well-studied in human populations, non-human primates (NHPs), in particular zoo-resident or captive NHPs, offer distinct advantages to increasing our understanding of factors that influence gut microbiome composition. Here, we characterize the gut microbiome composition of a phylogenetically diverse cohort of NHPs residing in the same urban zoo. We show …

Differential Progression Of Unhealthy Dietinduced Hepatocellular Carcinoma In Obese And Non-Obese Mice, Emma Hymel, Elizabeth M. Vlock, Kurt W. Fisher, Parashevi A. Farazi

Department of Food Science and Technology: Faculty Publications

Background

Non-alcoholic fatty liver disease (NAFLD) ranks first among liver diseases in Western countries. NAFLD is typically associated with obesity and diabetes, however it also develops in lean individuals without metabolic syndrome. The prevalence of lean NAFLD is 7 percent in the U.S. and 25–30 percent in some Asian countries. NAFLD starts with excess liver fat accumulation (NAFL), progresses to nonalcoholic steatohepatitis (NASH), cirrhosis and hepatocellular carcinoma (HCC). The pathogenesis of lean NASH-HCC and how it differs from obese NASH-HCC is not well understood.

Methods

In this work, we generated a mouse model of lean and obese NASH-HCC using a …

Updated Full Range Of Eliciting Dose Values For Cow’S Milk For Use In Food Allergen Risk Assessment, W. Marty Blom, Joost Westerhout, Joseph L. Baumert, Marie Y. Meima, Paul J. Turner, Motohiro Ebisawa, Noriyuki Yanagida, Benjamin C. Remington, Geert F. Houben

Department of Food Science and Technology: Faculty Publications

Access to Eliciting Doses (ED) for allergens enables advanced food allergen risk assessment. Previously, the full ED range for 14 allergenic foods, including milk, and recommendations for their use were provided (Houben et al., 2020). Additional food challenge studies with cow’s milk-allergic patients added 247 data points to the original dataset. Using the Stacked Model Averaging statistical method for interval-censored data on the 697 individual NOAELs and LOAELs for milk generated an updated full ED distribution. The ED01 and ED05, the doses at which 1% and 5% of the milk-allergic population would be predicted to experience any objective allergic reaction, …

Characterizing Isoform Switching Events In Esophageal Adenocarcinoma, Yu Zhang, Katherine M. Weh, Connor L. Howard, Jean-Jack Riethoven, Jennifer Clarke, Kiran H. Lagisetty, Jules Lin, Rishindra M. Reddy, Andrew C. Chang, David G. Beer, Laura A. Kresty

Department of Food Science and Technology: Faculty Publications

Isoform switching events with predicted functional consequences are common in many cancers, but characterization of switching events in esophageal adenocarcinoma (EAC) is lacking. Next-generation sequencing was used to detect levels of RNA transcripts and identify specific isoforms in treatment- naïve esophageal tissues ranging from premalignant Barrett’s esophagus (BE), BE with low- or high-grade dysplasia (BE.LGD, BE.HGD), and EAC. Samples were stratified by histopathology and TP53 mutation status, identifying significant isoform switching events with predicted functional consequences. Comparing BE.LGD with BE.HGD, a histopathology linked to cancer progression, isoform switching events were identified in 75 genes including KRAS, RNF128, and …

The Future Of Synbiotics: Rational Formulation And Design, David Fabian Gomez Gomez, Car Reen Kok, Robert Hutkins

Department of Food Science and Technology: Faculty Publications

Synbiotics, mixtures of live microbes and substrates selectively utilized by host organisms, are of considerable interest due to their ability to improve gastrointestinal health. However, formulating synbiotics remains challenging, due in part, to the absence of rational strategies to assess these products for synbiotic activities prior to clinical trials. Currently, synbiotics are formulated as either complementary or synergistic. Complementary synbiotics are made by combining probiotics and prebiotics, with each component acting independently and with the combination shown to provide a clinical health benefit. Most commercial synbiotics as well as those used in clinical trials have been of the complementary type. …

Immobilization Of A Bifidobacterial Endo-Ss-N-Acetylglucosaminidase To Generate Bioactive Compounds For Food Industry, Burcu Pekdemir, Hatice Duman, Ayşenur Arslan, Merve Kaplan, Melda Karyelioğlu, Tolgahan Özer, Hacı Mehmet Kayılı, Bekir Salih, Bethany M. Henrick, Rebbeca M. Duar, Sercan Karav

Department of Food Science and Technology: Faculty Publications

Conjugated N-glycans are considered next-generation bioactive prebiotic compounds due to their selective stimulation of beneficial microbes. These compounds are glycosidically attached to proteins through N-acetylglucosamines via specific asparagine residue (AsN-X-Ser/Thr). Certain bacteria such as Bifidobacterium longum subspecies infantis (B. infantis) have been shown to be capable of utilizing conjugated N-glycans, owing to their specialized genomic abilities. B. infantis possess a unique enzyme, Endo-ß-N-acetylglucosaminidase (EndoBI-1), which cleaves all types of conjugated N-glycans from glycoproteins. In this study, recombinantly cloned EndoBI- 1 enzyme activity was investigated using various immobilization methods: 1) adsorption, 2) entrapment-based alginate immobilization, …

Application Of Digital Twin In Evaluating Quality Changes In Tomato Value-Chain In Nigeria, Charles Nwaizu, Taofiq Olayinka Olanrewaju, Iluno Christiana

Department of Food Science and Technology: Faculty Publications

Cooling tomatoes after harvesting and keeping them refrigerated during their transportation is a key step toward preserving the quality attributes of tomatoes. This is a challenging task to accomplish in Nigeria, mainly because shipments of tomatoes from the tomato-producing states in northern Nigeria to the non-producing states in southern Nigeria were predominately not transported in a refrigerated ambient condition. To minimize postharvest losses of tomatoes during transportation, quantification of changes in quality would be extremely valuable. For this purpose, a digital tomato twin was developed based on mechanistic physics-based modeling. This digital twin simulated the actual thermal profile of tomatoes …

High-Quality Ice Plant Reference Genome Analysis Provides Insights Into Genome Evolution And Allows Exploration Of Genes Involved In The Transition From C3 To Cam Pathways, Shaoqin Shen, Nan Li, Yujie Wang, Rong Zhou, Pengchuan Sun, Hao Lin, Wei Chen, Tong Yu, Zhuo Liu, Zhiyuan Wang, Xiao Tan, Changping Zhu, Shuyan Feng, Yu Zhang, Xiaoming Song

Department of Food Science and Technology: Faculty Publications

Ice plant (Mesembryanthemum crystallinum), a member of the Aizoaceae family, is a typical halophyte crop and a model plant for studying the mechanism of transition from C3 photosynthesis to crassulacean acid metabolism (CAM). Here, we report a high-quality chromosome-level ice plant genome sequence. This 98.05% genome sequence is anchored to nine chromosomes, with a total length of 377.97 Mb and an N50 scaffold of 40.45 Mb. Almost half of the genome (48.04%) is composed of repetitive sequences, and 24 234 genes have been annotated. Subsequent to the ancient whole-genome triplication (WGT) that occurred in eudicots, there has been …

A Review Of Shiga-Toxin Producing Escherichia Coli (Stec) Contamination In The Raw Pork Production Chain, Manirul Haque, Joseph M. Bosilevac, Byron D. Chaves

Department of Food Science and Technology: Faculty Publications

Epidemiological evidence of Shiga toxin-producing Escherichia coli (STEC) infections associated with the consumption of contaminated pork highlight the need for increased awareness of STEC as an emerging pathogen in the pork supply chain. The objective of this review is to contribute to our understanding of raw pork products as potential carriers of STEC into the food supply. We summarize and critically analyze primary literature reporting the prevalence of STEC in the raw pork production chain. The reported prevalence rate of stx-positive E. coli isolates in live swine, slaughtered swine, and retail pork samples around the world ranged from 4.4 …

Nanoporous Starch Aerogels Impregnated With Phytosterols And Methods Of Preparing The Nanoporous Starch Aerogels, Ozan Nazim Ciftci

Department of Food Science and Technology: Faculty Publications

Formation of low - crystallinity phytosterol nanoparticles via cooling - controlled supercritical carbon dioxide (SC - CO₂) impregnation of phytosterols into biodegradable nanoporous starch aerogels and methods of preparing these aerogels are disclosed . The nanoporous starch aerogels increase water dissolution and bioaccessibility of the phytosterols , thereby making them available for preparation of high nutraceutical value foods .

Inflammatory Diseases And Resections Of The Digestive Tract Influence The Risk Of Circulating Food-Specific-Igg, Jacques Izard, Walker Carson, Joseph Baumert, Jennifer Clarke

Department of Food Science and Technology: Faculty Publications

Objectives: Individuals affected with inflammatory diseases of the digestive tract or have had surgical removal of sections of the digestive tract are often in need to adjust their diet. The symptomatology associated with food intake issues is often informally reported as food sensitivity. We investigated the circulating food-specific-IgG among ten conditions.

Conclusion: The risk of the having circulating food-specific IgG differed widely among the conditions investigated. The maintenance of a colonic environment might influence the risk of food sensitivity in ostomates.

A Classification System For Defining And Estimating Dietary Intake Of Live Microbes In Us Adults And Children, Maria L. Marco, Robert Hutkins, Colin Hill, Victor L. Fulgoni Iii, Christopher J. Cifelli, Jaime Gahche, Joanne L. Slavin, Daniel Merenstein, Daniel J. Tancredi, Mary E. Sanders

Department of Food Science and Technology: Faculty Publications

Background:

Consuming livemicrobes in foods may benefit human health. Live microbe estimates have not previously been associated with individual foods in dietary databases.

Objectives:

We aimed to estimate intake of live microbes in US children (aged 2–18 y) and adults (≥19 y) (n = 74,466; 51.2% female).

Methods:

Using cross-sectional data from the NHANES (2001–2018), experts assigned foods an estimated level of live microbes per gram [low (Lo), <10⁴ CFU/g; medium (Med), 10⁴–10⁷ CFU/g; or high (Hi), >10⁷ CFU/g]. Probiotic dietary supplements were also assessed. The mean intake of each live microbe …

Large-Scale Analyses Of Heat Shock Transcription Factors And Database Construction Based On Whole-Genome Genes In Horticultural And Representative Plants, Tong Yu, Yun Bai, Zhuo Liu, Zhiyuan Wang, Qihang Yang, Tong Wu, Shuyan Feng, Yu Zhang, Shaoqin Shen, Qiang Li, Liqiang Gu, Xiaoming Song

Department of Food Science and Technology: Faculty Publications

Heat shock transcription factor (Hsf) plays a critical role in regulating heat resistance. Here, 2950 Hsf family genes were identified from 111 horticultural and representative plants. More Hsf genes were detected in higher plants than in lower plants. Based on all Hsf genes, we constructed a phylogenetic tree, which indicated that Hsf genes of each branch evolved independently after species differentiation. Furthermore, we uncovered the evolutionary trajectories of Hsf genes by motif analysis. There were only six motifs (M1–M6) in lower plants, and then four novel motifs (M7–M10) appeared in higher plants. However, the motifs of some Hsf …

Great Northern Beans (Phaseolus Vulgaris L.) Lower Cholesterol In Hamsters Fed A High-Saturated-Fat Diet, An T. Nguyen, Sami A. Althwab, Haowen Qiu, Richard Zbasnik, Carlos A. Urrea, Timothy P. Carr, Vicki Schlegel

Department of Food Science and Technology: Faculty Publications

Background: Dietary interventions for high cholesterol, a primary risk factor for cardiovascular disease, are generally considered before prescribing drugs.

Objective: This study investigated the effects of whole Great Northern beans (wGNBs) and their hull (hGNB) incorporated into a high-saturated-fat (HSF) diet on cholesterol markers and hepatic/small intestinal genes involved in cholesterol regulation.

Methods: Each of the 4 groups of 11 male golden Syrian hamsters at 9 wk old were fed a normal-fat [NF; 5% (wt:wt) of soybean oil], HSF [5% (wt:wt) of soybean oil + 10% (wt:wt) of coconut oil], HSF+5% (wt:wt) wGNB, or HSF+0.5% (wt:wt) hGNB diet for 4 …

Essential Oil Yield, Composition, And Bioactivity Of Sagebrush Species In The Bighorn Mountains, Valtcho D. Zheljazkov, Charles L. Cantrell, Ekaterina A. Jeliazkova, Tess Astatkie, Vicki Schlegel

Department of Food Science and Technology: Faculty Publications

Sagebrush (Artemisia spp.) are dominant wild plants in large areas of the U.S., Canada and Mexico, and they include several species and subspecies. The aim was to determine if there are significant differences in essential oil (EO) yield, composition, and biological activity of sagebrush within the Bighorn Mountains, U.S. The EO yield in fresh herbage varied from 0.15 to 1.69% for all species, including 0.25–1.69% in A. tridentata var. vaseyana, 0.64–1.44% in A. tridentata var. tridentata, 1% in A. tridentata var. wyomingensis, 0.8–1.2% in A. longifolia, 0.8–1% in A. cana, and 0.16% in A. ludoviciana. There was …

A Farm-To-Fork Quantitative Microbial Exposure Assessment Of Β-Lactam-Resistant Escherichia Coli Among U.S. Beef Consumers, Yangjunna Zhang, John W. Schmidt, Terrance M. Arthur, Tommy L. Wheeler, Qi Zhang, Bing Wang

Department of Food Science and Technology: Faculty Publications

Integrated quantitative descriptions of the transmission of β-lactam-resistant Escherichia coli (BR-EC) from commercial beef products to consumers are not available. Here, a quantitative microbial exposure assessment model was established to simulate the fate of BR-EC in a farm-to-fork continuum and provide an estimate of BR-EC exposure among beef consumers in the U.S. The model compared the per-serving exposures from the consumption of intact beef cuts, non-intact beef cuts, and ground beef. Additionally, scenario analysis was performed to evaluate the relative contribution of antibiotic use during beef cattle production to the level of human exposure to BR-EC. The model predicted mean …

Fungi: Friend Or Foe? A Mycobiome Evaluation In Children With Autism And Gastrointestinal Symptoms, Jane Alookaran, Yuying Liu, Thomas Auchtung, Amirali Tahanan, Manouchehr Hessabi, Parisa Asgarisabet, Mohammad H. Rahbar, Nicole Y. Fatheree, Deborah A. Pearson, Rosleen Mansour, Melissa R. Van Arsdall, Fernando Navarro, J. Marc Rhoads

Department of Food Science and Technology: Faculty Publications

Gastrointestinal (GI) symptoms often affect children with autism spectrum disorders (ASD) and GI symptoms have been associated with an abnormal fecal microbiome. There is limited evidence of Candida species being more prevalent in children with ASD. We enrolled 20 children with ASD and GI symptoms (ASD + GI), 10 children with ASD but no GI symptoms (ASD - GI), and 20 from typically developing (TD) children in this pilot study. Fecal mycobiome taxa were analyzed by Internal Transcribed Spacer sequencing. GI symptoms (GI Severity Index [GSI]), behavioral symptoms (Social Responsiveness Scale -2 [SRS-2]), inflammation and fungal immunity (fecal calprotectin and …

Challenges In Gluten Analysis: A Comparison Of Four Commercial Sandwich Elisa Kits, Plaimein Amnuaycheewa, Lynn Niemann, Richard E. Goodman, Joseph L. Baumert, Steve L. Taylor

Department of Food Science and Technology: Faculty Publications

Gluten is composed of prolamin and glutelin proteins from several related grains. Because these proteins are not present in identical ratios in the various grains and because they have some differences in sequence, the ability to accurately quantify the overall amount of gluten in various food matrices to support gluten-free labeling is difficult. Four sandwich ELISAs (the R-Biopharm AG R5 RIDASCREEN®, the Neogen Veratox® R5, the Romer Labs AgraQuant® G12, and the Morinaga Wheat kits) were evaluated for their performance to quantify gluten concentrations in various foods and ingredients. The Morinaga and AgraQuant® G12 tests yielded results comparable to the …

Enhancing The Bioaccessibility Of Lycopene From Tomato Processing Byproducts Via Supercritical Carbon Dioxide Extraction, Ali Ubeyitogullari, Ozan N. Ciftci

Department of Food Science and Technology: Faculty Publications

Tomato peel and seed from tomato processing industry are treated as waste; however, they contain lycopene, a high-value bioactive compound. In this study, lycopene was extracted from tomato peel and seed using supercritical carbon dioxide (SC–CO₂) and hexane, and the bioaccessibilities of lycopene in the SC-CO₂- and hexaneextracted oleoresins were investigated for the first time. The (Z)-lycopene content of the SC-CO₂-extracted oleoresin (69%) was higher than that of hexane-extracted oleoresin (45%). Separation of the insoluble fraction from the oleoresins increased the (Z)-lycopene contents of the SC-CO₂- and hexane-extracted oil fractions to 80% …

Biogeosciences Perspectives On Integrated, Coordinated, Open, Networked (Icon) Science, D. Dwivedi, A. L. D. Santos, M. A. Barnard, T. M. Crimmins, A. Malhotra, K. A. Rod, K. S. Aho, S. M. Bell, B. Bomfim, F. Q. Brearley, H. Cadillo-Quiroz, J. Chen, C. M. Gough, E. B. Graham, C. R. Hakkenberg, L. Haygood, G. Koren, E. A. Lilleskov, L. K. Meredith, S. Naeher, Z. L. Nickerson, O. Pourret, H.-S. Song, M. Stahl, N. Taş, R. Vargas, S. Weintraub-Leff

Department of Food Science and Technology: Faculty Publications

This article is composed of three independent commentaries about the state of Integrated, Coordinated, Open, Networked (ICON) principles in the American Geophysical Union Biogeosciences section, and discussion on the opportunities and challenges of adopting them. Each commentary focuses on a different topic: (a) Global collaboration, technology transfer, and application (Section 2), (b) Community engagement, community science, education, and stakeholder involvement (Section 3), and (c) Field, experimental, remote sensing, and real-time data research and application (Section 4). We discuss needs and strategies for implementing ICON and outline short- and long-term goals. The inclusion of global data and international …

Effects Of Antimicrobial Addition On Lipid Oxidation Of Rendered Chicken Fat, Janak Dhakal, Dalton Holt, Charles G. Aldrich, Carl Knueven

Department of Food Science and Technology: Faculty Publications

This study evaluated the effects of antimicrobial acidulant addition on lipid oxidation of rendered chicken fat. Chicken fat was untreated (control) or treated with either sodium bisulfate (SBS) or lactic acid (LA) at 0.5% w/w and incubated for 6 wk at 40 °C. Peroxide value (PV), p-anisidine value (AV), and free fatty acid (FFA) levels were measured at days 0 (D0), 1(D1), 3 (D3), 5 (D5), and 7 (D7), and weeks 2 (W2), 3 (W3), 4 (W4), 5 (W5), and 6 (W6). The FFA level of untreated-control fat was ~7% and remained consistent throughout the incubation until W6 (~8.5%; P …

Production Of Bovine Colostrum For Human Consumption To Improve Health, Merve Kaplan, Ayşenur Arslan, Hatice Duman, Melda Karyelioğlu, Barış Baydemir, Bilgetekin Burak Günar, Merve Alkan, Ayşe Bayraktar, Halil İbrahim Tosun, Melih Ertürk, Günay Eskici, Rebbeca M. Duar, Bethany M. Henrick, Steven A. Frese, Sercan Karav

Department of Food Science and Technology: Faculty Publications

Colostrum contains all essential nutrients for the neonate during the first days of life, with impacts that continue far beyond these first days. Bovine colostrum has been used for human consumption due to the high concentrations of bioactive proteins, vitamins, minerals, growth factors, as well as free and conjugated oligosaccharides. Processes involved in the preparation of bovine colostrum for human consumption play a pivotal role in preserving and maintaining the activity of the bioactive molecules. As bovine colostrum is a multifunctional food that offers a myriad of benefits for human health, assessing the main processes used in preparing it with …

The Agricultural Genome To Phenome Initiative (Ag2pi): Creating A Shared Vision Across Crop And Livestock Research Communities, Christopher Tuggle, Jennifer Clarke, Jack C. M. Dekkers, David Ertl, Carolyn J. Lawrence-Dill, Eric Lyons, Brenda M. Murdoch, Nicole M. Scott, Patrick S. Schnable

Department of Food Science and Technology: Faculty Publications

Predicting phenotype from genotype is a central challenge in biology. By understanding genomic information to predict and improve traits, scientists can address the challenges and opportunities of achieving sustainable genetic improvement of complex, economically important traits in agriculturally relevant species. Converting the enormous, recent technical advances in all areas of genomics and phenomics into sustained and ecologically responsible improvements in food and fuel production is complex. It will require engaging agricultural genome to phenome (G2P) experts, drawing from a broad community, including crop and livestock scientists and essential integrative disciplines (e.g., engineers, economists, data and social scientists). To achieve this …

Phenotypic And Genomic Diversification In Complex Carbohydrate-Degrading Human Gut Bacteria, Nicholas A. Pudlo, Karthik Urs, Ryan Crawford, Ali Pirani, Todd Atherly, Roberto Jimenez, Nicolas Terrapon, Bernard Henrissat, Daniel Peterson, Cherie Ziemer, Evan Snitkin, Eric C. Martens

Department of Food Science and Technology: Faculty Publications

Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central for defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability …

Experimental Evaluation Of Ecological Principles To Understand And Modulate The Outcome Of Bacterial Strain Competition In Gut Microbiomes, Rafael R. Segura Munoz, Sara Mantz, Ines Martinez, Fuyong Li, Robert J. Schmaltz, Nicholas A. Pudlo, Karthik Urs, Eric C. Martens, Jens Walter, Amanda Ramer-Tait

Department of Food Science and Technology: Faculty Publications

It is unclear if coexistence theory can be applied to gut microbiomes to understand their characteristics and modulate their composition. Through experiments in gnotobiotic mice with complex microbiomes, we demonstrated that strains of Akkermansia muciniphila and Bacteroides vulgatus could only be established if microbiomes were devoid of these species. Strains of A. muciniphila showed strict competitive exclusion, while B. vulgatus strains coexisted but populations were still influenced by competitive interactions. These differences in competitive behavior were reflective of genomic variation within the two species, indicating considerable niche overlap for A. muciniphila strains and a broader niche space for B. vulgatus …

Large-Scale Analyses Of Heat Shock Transcription Factors And Database Construction Based On Whole-Genome Genes In Horticultural And Representative Plants, Tong Yu, Yun Bai, Zhuo Liu, Zhiyuan Wang, Qihang Yang, Tong Wu, Shuyan Feng, Yu Zhang, Shaoqin Shen, Quang Li, Liqiang Gu, Xiaoming Song

Department of Food Science and Technology: Faculty Publications

Heat shock transcription factor (Hsf) plays a critical role in regulating heat resistance. Here, 2950 Hsf family genes were identified from 111 horticultural and representative plants. More Hsf genes were detected in higher plants than in lower plants. Based on all Hsf genes, we constructed a phylogenetic tree, which indicated that Hsf genes of each branch evolved independently after species differentiation. Furthermore, we uncovered the evolutionary trajectories of Hsf genes by motif analysis. There were only six motifs (M1–M6) in lower plants, and then four novel motifs (M7–M10) appeared in higher plants. However, the motifs of some Hsf genes were …