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Publication The comparative genomics of Bifidobacterium callitrichos reflects dietary carbohydrate utilization within the common marmoset gut(2018-01-01) Albert, Korin; Rani, Asha; Sela, David A.Bifidobacterium is a diverse genus of anaerobic, saccharolytic bacteria that colonize many animals, notably humans and other mammals. The presence of these bacteria in the gastrointestinal tract represents a potential coevolution between the gut microbiome and its mammalian host mediated by diet. To study the relationship between bifidobacterial gut symbionts and host nutrition, we analyzed the genome of two bifidobacteria strains isolated from the feces of a common marmoset (Callithrix jacchus), a primate species studied for its ability to subsist on host-indigestible carbohydrates. Whole genome sequencing identified these isolates as unique strains of Bifidobacterium callitrichos. All three strains, including these isolates and the previously described type strain, contain genes that may enable utilization of marmoset dietary substrates. These include genes predicted to contribute to galactose, arabinose, and trehalose metabolic pathways. In addition, significant genomic differences between strains suggest that bifidobacteria possess distinct roles in carbohydrate metabolism within the same host. Thus, bifidobacteria utilize dietary components specific to their host, both humans and non-human primates alike. Comparative genomics suggests conservation of possible coevolutionary relationships within the primate clade.Publication The Effect of Multistage Refinement on the Bio-Physico-Chemical Properties and Gel-Forming Ability of Fish Protein Isolates from Mackerel (Rastrelliger kanagurta)(2023-01-01) Grossmann, LutzThe objective of this research was to improve the protein extraction processes of Rastrelliger kanagurta (Indian mackerel) to generate protein isolate with enhanced bio-physico-chemical properties and gel-forming ability. To achieve this, two novel approaches were designed that utilized an additional alkaline separation step and were compared to a conventional process: acid solubilization → alkaline solubilization → pI and acid solubilization → pI → alkaline solubilization. The novel extraction designs resulted in a lower lipid content, lipid oxidation, and TCA-soluble peptides, as well as improving the color and sensory features of the refined proteins, which corresponded to the lowest total heme pigments (p < 0.05). Furthermore, the protein isolate recovered with the modified processes showed significant changes in biochemical properties (decreases in Ca2+-ATPase activity/reactive sulfhydryl content and an increase in surface hydrophobicity) and dynamic rheological behavior. As a result, by altering the extraction procedure it was possible to obtain improved gel characteristics such as gel strength, color, expelled moisture, and improved gel microstructure. Moreover, this study demonstrated that the gel network was partly stabilized by disulfide bonds, according to SDS-PAGE. Overall, this study demonstrates that by optimizing protein extraction procedures a considerable improvement in quality can be achieved and that an additional alkaline extraction after isoelectric point precipitation results in the optimized gel-forming ability of mackerel proteins.Publication Surface Modified Carvacrol-rich Satureja khuzestanica Essential Oil Nanoemulsion: A Novel Paclitaxel Formulation Induced Apoptosis on Paclitaxel-Resistant Breast Cancer Cells(2024-01-01) McClements, David JulianBackground: The ability of cancer cells to develop multidrug resistance (MDR) is a major challenge in modern chemotherapy. The current generation of commercially available paclitaxel formulations have not been designed to treat resistant tumours. In this study, a nanoemulsion-based delivery system was developed to enhance the efficacy of paclitaxel against resistant breast cancer cells. Methods: The nanoemulsion was formulated using carvacrol-rich Satureja khuzestanica essential oil. Modification of nanoemulsion was performed by incorporating tocopheryl polyethylene glycol 1000 succinate (TPGS) which could inhibit drug resistance in cancer cells. Fabrication of paclitaxel nanoemulsion was performed by high speed homogenization. The cytotoxicity of prepared formulation against resistant breast cancer cells was investigated by MTT assay. Flow cytometry technique was used for cell cycle arrest analysis and examination of the apoptosis induction ability of prepared nanoemulsion. Results: The nanoemulsion had a relatively small mean droplet diameter (93.6 ± 4.2 nm) and good long-term stability. The ability of paclitaxel to inhibit P-gp function in paclitaxel-resistant breast cancer cells (MCF-7/PTX) was synergistically enhanced by administering it within the nanoemulsion. The cytotoxicity of the prepared nanoemulsion on the HUVEC normal cells was much lower than that of MCF-7/PTX cells. Cell cycle analysis utilizing flow cytometry showed that the paclitaxel-loaded nanoemulsion promoted G2-M arrest. Flow cytometry also demonstrated that this nanoemulsion induced apoptosis in MCF-7/PTX cells. Interestingly, apoptosis increased from 20.0% for the free paclitaxel treated group to 85.2 % for the paclitaxel-loaded nanoemulsion treated group. Conclusion: This novel paclitaxel nanoemulsion efficiently suppressed the drug resistance of breast cancer cells and induced effective apoptosis in very low concentrations of paclitaxel.Publication Adaptive laboratory evolution of Salmonella enterica in acid stress(2023-01-01) Ghoshal, Mrinalini; Bechtel, Tyler D.; Gibbons, John G.; McLandsborough, LynneAdaptive laboratory evolution (ALE) studies play a crucial role in understanding the adaptation and evolution of different bacterial species. In this study, we have investigated the adaptation and evolution of Salmonella enterica serovar Enteritidis to acetic acid using ALE.Publication Nutrient Density, Added Sugar, and Fiber Content of Commercially Available Fruit Snacks in the United States(2024-01-01) Fu, Hao; Lee, Chi Hyun; Nolden, Alissa A.; Kinchla, Amanda J.Fruit snacks have become a popular and convenient snacking choice and have the potential to contribute to a well-balanced diet. However, the nutritional quality of fruit snack products has not yet been studied. The objective of the present study is to provide a nutritional assessment of the fruit snack product category. This study used the Mintel Global New Product Database to collect data about fruit snack products launched in the United States from 2017 to 2022. Fruit snack products (n = 2405) are divided into nine product categories based on product characteristics. Nutrition composition was assessed using a comprehensive score, Nutrient Rich Food (NRF) model, and by examining individual components (added sugar and fiber). The results show that dried fruit has the highest nutrient density, fiber content, and the lowest added sugar content. Conversely, fruit-flavored snacks have the lowest nutrient density, fiber content, and added sugar content. Currently, fruit puree, canned fruit with juice, and dried fruit are the only fruit snacks that meet the current recommendations set by the USDA Dietary Guidelines. Future directions for the fruit snack category should consider decreasing the added sugar content, increasing the fiber content, and enhancing their sensory profile to improve the overall nutrient density.Publication Kahweol, a coffee diterpene, increases lifespan via insulin/insulin-like growth factor-1 and AMP-activated protein kinase signaling pathways in Caenorhabditis elegans(2023-01-01) Cho, Junhyo; Park, YeonhwaCoffee is one of the most widely consumed beverages and is known to have many health benefits. Our previous study reported that kahweol, a diterpene found in coffee, reduced fat accumulation by reducing food intake in Caenorhabditis elegans. Based on the widely known observation of caloric restriction and lifespan, we determined if kahweol extends lifespan in C. elegans. Kahweol significantly extended the lifespan of wild-type C. elegans. However, kahweol increased the lifespan of the eat-2 null mutant that has a reduced food intake phenotype, suggesting that kahweol extends lifespan independent of reduced food intake. Therefore, we further determine the target of kahweol on lifespan extension. Kahweol had no effects on the lifespan of both daf-2 (the homolog of insulin/insulin-like growth factor-1 receptor) and daf-16 (the homolog of Forkhead box O transcription factor and a major downstream target of daf-2) null mutants, suggesting kahweol extended lifespan via insulin/insulin-like growth factor-1 signaling pathway. In addition, kahweol failed to extend lifespan in tub-1 (the homolog of TUB bipartite transcription factor) and aak-2 (the homolog of AMP-activated protein kinase) null mutants, suggesting these roles on kahweol’s effect on lifespan. However, the treatment of kahweol increased the lifespan in sir-2.1 (the homolog of NAD-dependent deacetylase sirtuin-1) and skn-1 (the homolog of nuclear factor erythroid 2-related factor 2) null mutants over the control, suggesting independent functions of these genes on kahweol’s lifespan extension. These results indicate that the insulin/insulin-like growth factor-1 signaling and AMPK pathways may play critical roles in extending lifespan by kahweol in C. elegans.Publication Food-grade cationic antimicrobial ε-polylysine transiently alters the gut microbial community and predicted metagenome function in CD-1 mice(2017-01-01) You, Xiaomeng; Einson, Jonah E.; Lopez-Pena, Cynthia Lyliam; Song, Mingyue; Xiao, Hang; McClements, David Julian; Sela, DavidDiet is an important factor influencing the composition and function of the gut microbiome, but the effect of antimicrobial agents present within foods is currently not understood. In this study, we investigated the effect of the food-grade cationic antimicrobial ε-polylysine on the gut microbiome structure and predicted metagenomic function in a mouse model. The relative abundances of predominant phyla and genera, as well as the overall community structure, were perturbed in response to the incorporation of dietary ε-polylysine. Unexpectedly, this modification to the gut microbiome was experienced transiently and resolved to the initial basal composition at the final sampling point. In addition, a differential non-random assembly was observed in the microbiomes characterized from male and female co-housed animals, although their perturbation trajectories in response to diet remain consistent. In conclusion, antimicrobial ε-polylysine incorporated into food systems transiently alters gut microbial communities in mice, as well as their predicted function. This indicates a dynamic but resilient microbiome that adapts to microbial-active dietary components.Publication An In Vitro Comparison of the Digestibility and Gastrointestinal Fate of Scallops and Plant-Based Scallop Analogs(2023-01-01) Zhang, Zhiyun; Qin, Dingkui; Kobata, Kanon; Rao, Jiajia; Lu, Jiakai; McClements, David JulianConcerns exist regarding the negative environmental impact and health risks associated with ocean fishing and aquaculture, such as stock depletion, pollution, biodiversity loss, and toxin presence. To address these concerns, plant-based seafood analogs are being developed. Our previous study successfully created plant-based scallop analogs using pea proteins and citrus pectin, resembling real scallops in appearance and texture. This study focuses on comparing the digestive fate of these analogs to real scallops, as it can impact their nutritional properties. Using an in vitro digestion model (INFOGEST), we simulated oral, gastric, and small intestinal conditions. The analysis revealed differences in the microstructure, physicochemical properties, and protein digestibility between the plant-based scallops and real scallops. The particle size and charge followed the following similar trends for both types of scallops: the particle size decreased from the mouth to the stomach to the small intestine; the particles were negative in the mouth, positive in the stomach, and negative in the small intestine. The protein digestibility of the plant-based scallops was considerably lower than that of real scallops. For instance, around 18.8% and 61.4% of protein was digested in the stomach and small intestine phases for the real scallop (80.2% total digestion), whereas around 8.7% and 47.7% of the protein was digested for the plant-based scallop (56.4% total digestion). The lower digestibility of the plant-based scallops may have been due to differences in the protein structure, the presence of dietary fibers (pectin), or antinutritional factors in the plant proteins. These findings are crucial for developing more sustainable next-generation plant-based seafood analogs.Publication Optimizing Protein Fiber Spinning to Develop Plant-Based Meat Analogs via Rheological and Physicochemical Analyses(2023-01-01) Joshi, Kartik; Shabani, Elnaz; Fijul Kabir, S. M.; Zhou, Hualu; McClements, David Julian; Park, Jay HoonThe substitution of meat products in the human diet with plant-based analogs is growing due to environmental, ethical, and health reasons. In this study, the potential of fiber-spinning technology was explored to spin protein fiber mimicking the structural element of meat muscle for the purpose of developing plant-based meat analogs. Overall, this approach involved extruding fine fibers and then assembling them into hierarchical fibrous structures resembling those found in whole muscle meat products. Considering the nutritional facts and to help build muscle fiber, soy protein, polysaccharide (pectin, xanthan gum, or carrageenan), plasticizer (glycerol), and water were used in the formulations to spin into fibers using an extruder with circular orifice dies. Extrudability and thermal and rheological properties were assessed to characterize the properties of the spun fiber. The extrusion trials showed that the presence of the polysaccharides increased the cohesiveness of the fibers. The properties of the fibers produced also depended on the temperature used during extrusion, varying from pasty gels to elastic strands. The extrudability of the fibers was related to the rheological properties (tan δ) of the formulations. This study demonstrated that fiber-spinning technology can be used to produce fibrous materials from plant-derived ingredients. However, the formulation and operating conditions must be optimized to obtain desirable physicochemical and functional attributes in the fibers produced.Publication Ecologies, synergies, and biological systems shaping human milk composition—a report from “Breastmilk Ecology: Genesis of Infant Nutrition (BEGIN)” Working Group 2(2023-01-01) Smilowitz, Jennifer T.; Allen, Lindsay H.; Dallas, David C.; McManaman, James; Raiten, Daniel J.; Rozga, Mary; Sela, David A.; Seppo, Antti; Williams, Janet E.; Young, Bridget E.; McGuire, Michelle K.Human milk is universally recognized as the preferred food for infants during the first 6 mo of life because it provides not only essential and conditionally essential nutrients in necessary amounts but also other biologically active components that are instrumental in protecting, communicating important information to support, and promoting optimal development and growth in infants. Despite decades of research, however, the multifaceted impacts of human milk consumption on infant health are far from understood on a biological or physiological basis. Reasons for this lack of comprehensive knowledge of human milk functions are numerous, including the fact that milk components tend to be studied in isolation, although there is reason to believe that they interact. In addition, milk composition can vary greatly within an individual as well as within and among populations. The objective of this working group within the Breastmilk Ecology: Genesis of Infant Nutrition (BEGIN) Project was to provide an overview of human milk composition, factors impacting its variation, and how its components may function to coordinately nourish, protect, and communicate complex information to the recipient infant. Moreover, we discuss the ways whereby milk components might interact such that the benefits of an intact milk matrix are greater than the sum of its parts. We then apply several examples to illustrate how milk is better thought of as a biological system rather than a more simplistic “mixture” of independent components to synergistically support optimal infant health.Publication Effects of annealing temperature and time on the structural and physicochemical properties of sweet potato flour hydrogels(2023-01-01) Zhang, Ziwen; Shang, Mengshan; McClements, David Julian; Qiu, Chao; Ji, Na; Dai, Lei; Qin, Yang; Xiong, Liu; Sun, QingjieThe physicochemical properties of sweet potato flour (SPF) can be modified by annealing. Native SPF was annealed in deionized water at a flour-to-water ratio of 1:3 (w/v) and temperatures of 50, 55, 60, or 65 °C for either 12 or 24 h. Annealed SPF maintained the A-type crystalline region and displayed increased relative crystallinity, increased pasting temperature, and decreased breakdown. SPF gels showed enhanced hardness together with better springiness when SPF was annealed at low temperature/long time or high temperature/short time. Annealed SPF hydrogel sheets contained larger, more uniform, and smoother pores than native ones. Noticeably, hydrogel sheets made of SPF annealed at 50 °C for 24 h exhibited advanced fracture strain from 93% to 176%. Overall, this work showed that annealing could modulate the characteristics of SPR hydrogels, which may widen the extent of applications in food industries. However, the annealing conditions need to be optimized.Publication Exploring Washing Procedures for Produce Brush Washer(2023-01-01) Gensler, Catherine; Harper, Kelsi; Stoufer, Sloane; Moore, Matthew D.; Kinchla, Amanda J.; McLandsborough, LynnePrevious environmental monitoring projects in food production facilities have revealed inconsistencies in how produce brush washer machines are cleaned after use; thus, the study of effective sanitation procedures for these machines is needed. Four chlorine solution treatments (ranging from 25 to 200 ppm), as well as a water-only treatment, were tested for efficacy in reducing bacterial loads for a selected small brush washer machine. Results indicate that rinsing with the machine’s power and water alone, a frequent practice among some produce processors, yielded a reduction of 0.91–1.96 log CFU per brush roller in bacterial counts, which was not statistically significant (p > 0.05). However, the chlorine treatments were found to be effective in reducing bacterial loads significantly, with higher concentrations being the most effective. The 200 ppm and 100 ppm chlorine treatments yielded bacterial reductions of 4.08 and 3.95 log CFU per brush roller, respectively, leaving bacterial levels statistically similar to the levels at postprocess decontamination, meaning these are the most effective at killing bacteria of all the chlorine concentrations tested. These data suggest the use of at least 100 ppm chlorine sanitizer solution is a good method to sanitize hard-to-clean produce washing machines, yielding an approximate 4 log CFU reduction of the inoculated bacteria.Publication Sucrose Concentration and Fermentation Temperature Impact the Sensory Characteristics and Liking of Kombucha(2023-01-01) Cohen, Gil; Sela, David; Nolden, Alissa A.Kombucha is a fermented tea beverage consumed for its probiotics and functional properties. It has a unique sensory profile driven by the properties of tea polyphenols and fermentation products, including organic acids. Fermentation temperature and sucrose content affect the fermentation process and the production of organic acids; yet less is known about their impacts on the sensory profile and consumer acceptance. Thus, we aimed to examine the impact of sucrose concentration and fermentation temperature on sensory attributes and liking. For this study, kombucha tea was fermented at three different concentrations of sucrose and fermented at two temperatures for 11 days. Fermentation was monitored by pH, brix, and titratable acidity, and consumers (n = 111) evaluated the kombucha for sensory attributes and overall liking. The fermentation temperature resulted in significant differences in titratable acidity, with higher temperatures producing more organic acids, resulting in higher astringency, and suppressed sweetness. The lower fermentation was reported as significantly more liked, with no difference in liking between the 7.5% and 10% sucrose kombucha samples. Fermentation temperature had the greatest impact on the sensory profile rather than sucrose concentration, which had a greater effect on the fermentation rate and production organic acids.Publication Bifidobacterium infantis utilizes N-acetylglucosamine-containing human milk oligosaccharides as a nitrogen source(2023-01-01) Li, Shuqi; You, Xiaomeng; Rani, Asha; Özcan, Ezgi; Sela, David ABifidobacterium longum subsp. infantis (B. infantis) utilizes oligosaccharides secreted in human milk as a carbohydrate source. These human milk oligosaccharides (HMOs) integrate the nitrogenous residue N-acetylglucosamine (NAG), although HMO nitrogen utilization has not been described to date. Herein, we characterize the B. infantis nitrogen utilization phenotype on two NAG-containing HMO species, LNT and LNnT. This was characterized through in vitro growth kinetics, incorporation of isotopically labeled NAG nitrogen into the proteome, as well as modulation of intracellular 2-oxoglutarate levels while utilizing HMO nitrogen. Further support is provided by comparative transcriptomics and proteomics that identified global regulatory networks deployed during HMO nitrogen utilization. The aggregate data demonstrate that B. infantis strains utilize HMO nitrogen with the potential to significantly impact fundamental and clinical studies, as well as enable applications.Publication Comparison of a One-Step Real-Time RT-PCR and a Nested Real-Time RT-PCR for a Genogroup II Norovirus Reveals Differences in Sensitivity Depending Upon Assay Design and Visualization(2021-01-01) Manuel, Clyde S.; Suther, Cassandra; Moore, Matthew D.; Jaykus, Lee-AnnHuman norovirus (NoV) is the leading cause of acute viral gastroenteritis and a major source of foodborne illness. Detection of NoV in food and environmental samples is typically performed using molecular techniques, including real-time reverse transcription polymerase chain reaction (RT-PCR) and less frequently, nested real-time PCR. In this study, we conducted a controlled comparison of two published NoV detection assays: a broadly reactive one-step real-time RT-PCR and a two-step nested real-time PCR assay. A 20% human fecal suspension containing a genogroup II human NoV was serially diluted, genome extracted, and subjected to amplification using the two assays compared via PCR Units. Additional amplicon confirmation was performed by dot blot hybridization using digoxigenin (DIG)-labeled oligonucleotide probes. Both assays displayed similar amplification standard curves/amplification efficiencies; however, the nested assay consistently detected one log(10) lower virus. Dot blot hybridization improved the detection limit of the nested real-time PCR by one log(10) NoV genome copies but impaired the detection limit of the one-step real-time RT-PCR by one log(10) NoV genome copies. These results illustrate the complexities in designing and interpreting molecular techniques having a sufficient detection limit to detect low levels of viruses that might be anticipated in contaminated food and environmental samples.Publication Comparison of Two Aspergillus oryzae Genomes From Different Clades Reveals Independent Evolution of Alpha-Amylase Duplication, Variation in Secondary Metabolism Genes, and Differences in Primary Metabolism(2021-01-01) Chacón-Vargas, Katherine; McCarthy, Colin O.; Choi, Dasol; Wang, Long; Yu, Jae-Hyuk; Gibbons, John G.Microbes (bacteria, yeasts, molds), in addition to plants and animals, were domesticated for their roles in food preservation, nutrition and flavor. Aspergillus oryzae is a domesticated filamentous fungal species traditionally used during fermentation of Asian foods and beverage, such as sake, soy sauce, and miso. To date, little is known about the extent of genome and phenotypic variation of A. oryzae isolates from different clades. Here, we used long-read Oxford Nanopore and short-read Illumina sequencing to produce a highly accurate and contiguous genome assemble of A. oryzae 14160, an industrial strain from China. To understand the relationship of this isolate, we performed phylogenetic analysis with 90 A. oryzae isolates and 1 isolate of the A. oryzae progenitor, Aspergillus flavus. This analysis showed that A. oryzae 14160 is a member of clade A, in comparison to the RIB 40 type strain, which is a member of clade F. To explore genome variation between isolates from distinct A. oryzae clades, we compared the A. oryzae 14160 genome with the complete RIB 40 genome. Our results provide evidence of independent evolution of the alpha-amylase gene duplication, which is one of the major adaptive mutations resulting from domestication. Synteny analysis revealed that both genomes have three copies of the alpha-amylase gene, but only one copy on chromosome 2 was conserved. While the RIB 40 genome had additional copies of the alpha-amylase gene on chromosomes III, and V, 14160 had a second copy on chromosome II and an third copy on chromosome VI. Additionally, we identified hundreds of lineage specific genes, and putative high impact mutations in genes involved in secondary metabolism, including several of the core biosynthetic genes. Finally, to examine the functional effects of genome variation between strains, we measured amylase activity, proteolytic activity, and growth rate on several different substrates. RIB 40 produced significantly higher levels of amylase compared to 14160 when grown on rice and starch. Accordingly, RIB 40 grew faster on rice, while 14160 grew faster on soy. Taken together, our analyses reveal substantial genome and phenotypic variation within A. oryzae.Publication Cloning, Heterologous Expression, and Characterization of a βκ-Carrageenase From Marine Bacterium Wenyingzhuangia funcanilytica: A Specific Enzyme for the Hybrid Carrageenan–Furcellaran(2021-01-01) Cao, Siqi; Zhang, Yuying; Chen, Guangning; Shen, Jingjing; Han, Jin; Chang, Yaoguang; Xiao, Hang; Xue, ChanghuCarrageenan is a group of important food polysaccharides with high structural heterogeneity. Furcellaran is a typical hybrid carrageenan, which contains the structure consisted of alternative beta-carrageenan and kappa-carrageenan motifs. Although several furcellaran-hydrolyzing enzymes have been characterized, their specificity for the glycosidic linkage was still unclear. In this study, we cloned, expressed, and characterized a novel GH16_13 furcellaran-hydrolyzing enzyme Cgbk16A_Wf from the marine bacterium Wenyingzhuangia fucanilytica CZ1127. Cgbk16A_Wf exhibited its maximum activity at 50 degrees C and pH 6.0 and showed high thermal stability. The oligosaccharides in enzymatic products were identified by liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) and nuclear magnetic resonance (NMR) spectroscopy. It was confirmed that Cgbk16A_Wf specifically cleaves the beta-1,4 linkages between beta-carrageenan and kappa-carrageenan motifs from non-reducing end to reducing end. Considering the structural heterogeneity of carrageenan and for the unambiguous indication of the specificity, we recommended to name the furcellaran-hydrolyzing activity represented by Cgbk16A as beta kappa-carrageenase instead of furcellaranase.Publication A Human Gut Commensal Ferments Cranberry Carbohydrates to Produce Formate(2017-01-01) Özcan, Ezgi; Sun, Jiadong; Rowley, David C.; Sela, David A.Commensal bifidobacteria colonize the human gastrointestinal tract and catabolize glycans that are impervious to host digestion. Accordingly, Bifidobacterium longum typically secretes acetate and lactate as fermentative end products. This study tested the hypothesis that B. longum utilizes cranberry-derived xyloglucans in a strain-dependent manner. Interestingly, the B. longum strain that efficiently utilizes cranberry xyloglucans secretes 2.0 to 2.5 mol of acetate-lactate. The 1.5 acetate:lactate ratio theoretical yield obtained in hexose fermentations shifts during xyloglucan metabolism. Accordingly, this metabolic shift is characterized by increased acetate and formate production at the expense of lactate. α-L-Arabinofuranosidase, an arabinan endo-1,5-α-L-arabinosidase, and a β-xylosidase with a carbohydrate substrate-binding protein and carbohydrate ABC transporter membrane proteins are upregulated (>2-fold change), which suggests carbon flux through this catabolic pathway. Finally, syntrophic interactions occurred with strains that utilize carbohydrate products derived from initial degradation from heterologous bacteria.Publication Population Genomic Analysis of Listeria monocytogenes From Food Reveals Substrate-Specific Genome Variation(2021-01-01) Bechtel, Tyler D.; Gibbons, John G.Listeria monocytogenes is the major causative agent of the foodborne illness listeriosis. Listeriosis presents as flu-like symptoms in healthy individuals, and can be fatal for children, elderly, pregnant women, and immunocompromised individuals. Estimates suggest that L. monocytogenes results in similar to 1,600 illnesses and similar to 260 deaths annually in the United States. L. monocytogenes can survive and persist in a variety of harsh environments, including conditions encountered in production of fermented dairy products such as cheese. For instance, microbial growth is often limited in soft cheese fermentation because of harsh pH, water content, and salt concentrations. However, L. monocytogenes has caused a number of deadly listeriosis outbreaks through the contamination of cheese. The purpose of this study was to understand if genetically distinct populations of L. monocytogenes are associated with particular foods, including cheese and dairy. To address this goal, we analyzed the population genetic structure of 504 L. monocytogenes strains isolated from food with publicly available genome assemblies. We identified 10 genetically distinct populations spanning L. monocytogenes lineages 1, II, and III and serotypes 1/2a, 1/2b, 1/2c, 4b, and 4c. We observed an overrepresentation of isolates from specific populations with cheese (population 2), fruit/vegetable (population 2), seafood (populations 5, 8 and 9) and meat (population 10). We used the Large Scale Blast Score Ratio pipeline and Roary to identify genes unique to population 1 and population 2 in comparison with all other populations, and screened for the presence of antimicrobial resistance genes and virulence genes across all isolates. We identified > 40 genes that were present at high frequency in population 1 and population 2 and absent in most other isolates. Many of these genes encoded for transcription factors, and cell surface anchored proteins. Additionally, we found that the virulence genes aut and ami were entirely or partially deleted in population 2. These results indicate that some L. monocytogenes populations may exhibit associations with particular foods, including cheese, and that gene content may contribute to this pattern.Publication Utilization of Polysaccharide-Based High Internal Phase Emulsion for Nutraceutical Encapsulation: Enhancement of Carotenoid Loading Capacity and Stability(2021-01-01) Yan, Chi; Wu, Xiaolin; Wang, Yi; Peng, Shengfeng; Chen, Jun; Zou, Liqiang; McClements, David Julian; Liu, WeiThe main goal of the present work was to access the ability of high internal phase emulsions (HIPEs) to encapsulate fl-carotene. The carotenoid loading capacity of the HIPEs was around 20-fold higher when OSAstarch/chitosan complexes were used than when only OSA-starch was used. This impact could be mainly assigned to the capacity of the former HIPEs to trap carotenoid caystals in a stable form. The OSA-starch/chitosan complexes were shown to absorb on the oil droplets interface and form a 3D network in the aqueous phase, which helped to prevent droplet coalescence induced by fl-carotene crystal. The incorporation of fl-carotene within the oil droplets enhanced its resistance to chemical degradation when exposed to heat, ultraviolet radiation, or gastrointestinal conditions. Our results provide information that may aid the design and development of edible soft solids containing high carotenoid levels, which may be applied in food and pharmaceutical industry.