Food Science Commons^™

Procuring Produce In A Rural, Appalachian County: A Thematic Analysis Of Community Member Experiences, Caroline Blincoe

Theses and Dissertations--Nutrition and Food Systems

Rates of obesity and other health disparities are exceptionally high in rural Appalachian counties compared to the nation as a whole. One causal factor of these health disparities in Appalachian counties is the inequitable allocation of healthy food. Food insecurity and the local food environment are large drivers for obesity experienced by Martin County, Kentucky residents. Successful socioecological model (SEM) and policy, systems, and environmental (PSE) interventions have shown promising results in reducing obesity and enhancing food security in this population. Through the transcription of semi-structured focus group interviews, thematic analysis aimed to obtain perspectives on the local food system. …

Developing Whey Protein Encapsulated Probiotics And Evaluating Environmental Listeria Using Whole-Genome Sequencing, Shayanti Minj

Electronic Theses and Dissertations

In this study, a novel value-added dairy-based health formulation was developed using whey protein hydrolysate and probiotic organisms. In the first part of the study, different forms of whey proteins, concentrate WPC80, isolate WPI90, and hydrolysates WPH10, WPH15 and WPH20 were screened for bioactivities (antimicrobial, antioxidant, and antihypertensive activity). Hydrolysate WPH10, exhibiting the highest bioactivities was conjugated with maltodextrin. A batch of 2L conjugated solution was spray dried in a Niro drier with an inlet and outlet temperature of 200⁰C and 90⁰C, and alternatively, freeze dried at −80 °C under 50 mTorr vacuum. The bioactivities of the conjugated samples were …

Protein Extraction Protocols For Optimal Proteome Measurement And Arginine Kinase Quantitation From Cricket Acheta Domesticus For Food Safety Assessment, Utpal Bose, James A. Broadbent, Angéla Juhász, Shaymaviswanathan Karnaneedi, Elecia B. Johnston, Sally Stockwell, Keren Byrne, Vachiranee Limviphuvadh, Sebastian Maurer-Stroh, Andreas L. Lopata, Michelle L. Colgrave

Research outputs 2014 to 2021

© 2021 Elsevier Ltd Insects have been consumed by people for millennia and have recently been proposed as a complementary, sustainable source of protein to feed the world's growing population. Insects and crustaceans both belong to the arthropod family. Crustacean (shellfish) allergies are common and potentially severe; hence, the cross-reactivity of the immune system with insect proteins is a potential health concern. Herein, LC-MS/MS was used to explore the proteome of whole, roasted whole and roasted powdered cricket products. Eight protein extraction protocols were compared using the total number of protein and distinct peptide identifications. Within these data, 20 putative …

Upstream Regulator Analysis Of Wooden Breast Myopathy Proteomics In Commercial Broilers And Comparison To Feed Efficiency Proteomics In Pedigree Male Broilers, Walter G. Bottje, Kentu R. Lassiter, Vivek A. Kuttappan, Nicholas J. Hudson, Casey M. Owens, Benham Abasht, Sami Dridi, Byungwhi C. Kong

Poultry Science Faculty Publications and Presentations

In an effort to understand the apparent trade-off between the continual push for growth performance and the recent emergence of muscle pathologies, shotgun proteomics was conducted on breast muscle obtained at similar to 8 weeks from commercial broilers with wooden breast (WB) myopathy and compared with that in pedigree male (PedM) broilers exhibiting high feed efficiency (FE). Comparison of the two proteomic datasets was facilitated using the overlay function of Ingenuity Pathway Analysis (IPA) (Qiagen, CA, USA). We focused on upstream regulator analysis and disease-function analysis that provides predictions of activation or inhibition of molecules based on (a) expression of …

การผลิตโปรตีนไฮโดรไลเสตจากกุ้งฝอย Macrobrachium Lanchesteri โดยการทำแห้งแบบพ่นฝอยและเสถียรภาพระหว่างการเก็บรักษา, ฉัตรชนก ไพศาลศักดิ์

Chulalongkorn University Theses and Dissertations (Chula ETD)

กุ้งฝอย (Macrobranchium lanchesteri) เป็นสัตว์น้ำจืดที่มีโปรตีนเป็นองค์ประกอบซึ่งประกอบด้วยกรดอะมิโนและเปปไทด์ที่เป็นสารตั้งต้นสำคัญในการสร้างกลิ่นรสและรสชาติในระหว่างกระบวนการแปรรูปอาหาร งานวิจัยนี้มีวัตถุประสงค์เพื่อศึกษาสภาวะที่เหมาะสมสำหรับกระบวนการไฮโดรลิซิสของโปรตีนจากกุ้งฝอยด้วยฟลาโวไซม์ ศึกษาสภาวะการทำแห้งด้วยกระบวนการทำแห้งแบบพ่นฝอย และศึกษาเสถียรภาพของผงโปรตีนไฮโดรไลเสตในระหว่างการเก็บรักษา โดยใช้ response surface methodology (RSM) และออกแบบการทดลองแบบ central composite design (CCD) กำหนดตัวแปรต้น 3 ปัจจัย ได้แก่ อัตราส่วนความเข้มข้นของเอนไซม์ต่อสารตั้งต้น (E/S; 5-15 LAPU/g protein) อุณหภูมิ (45-55 °C) และ pH (6-8) กำหนดให้ค่าระดับการย่อยของโปรตีน (degree of hydrolysis; DH) เป็นตัวแปรอิสระ พบว่าการใช้ E/S ที่ 10 LAPU/g protein อุณหภูมิ 50°C และ pH 7 เป็นสภาวะที่เหมาะสม มีค่าระดับการย่อยของโปรตีนสูงที่สุด (20.97±0.86%) โปรตีนไฮโดรไลเสตมีน้ำหนักโมเลกุลเฉลี่ยเป็น 48.3 kDa มีปริมาณกรดอะมิโนอิสระสูงกว่าตัวอย่างควบคุม และมีคะแนนความโดยรวม ความชอบด้านกลิ่นรสและด้านรสชาติเพิ่มขึ้น เมื่อนำโปรตีนไฮโดรไลเสตไปทำแห้งแบบพ่นฝอยโดยศึกษาสภาวะที่เหมาะสมสำหรับการทำแห้งแบบพ่นฝอยของโปรตีนไฮโดรไลเสต กำหนดปัจจัยอุณหภูมิขาเข้าของกระบวนการทำแห้งแบบพ่นฝอย (120, 150 และ 180°C), อุณหภูมิขาออก 95 °C และอัตราการป้อน 10 mL/min พบว่าเมื่อใช้อุณหภูมิขาเข้า 150°C ได้ปริมาณร้อยละผลผลิตสูงสุด (72.41±0.53%) นอกจากนี้ ค่ากิจกรรมของน้ำ ค่าความชื้น และค่าความขาว เท่ากับ 0.159±0.02, 4.29±0.36 %, และ 69.83±0.50 ตามลำดับ และเมื่อศึกษาการเปลี่ยนแปลงในระหว่างการเก็บรักษาของผงโปรตีนไฮโดรไลเสตโดยบรรจุในถุงอลูมิเนียมลามิเนตชนิด aluminum/LLDPE ทึบแสงปิดสนิทแบบสุญญากาศเป็นเวลา 12 สัปดาห์ ที่อุณหภูมิ 25 ºC ติดตามผลการเปลี่ยนแปลงทุก 2 สัปดาห์ พบว่า เมื่ออายุการเก็บรักษาเพิ่มขึ้น ค่าความชื้นเพิ่มขึ้นเล็กน้อย แต่ค่ากิจกรรมของน้ำไม่เปลี่ยนแปลง …

Preparation Of Encapsulated Konjac Glucomannan-Based Fish Oil And Its Use In High Pressure Processed Goat Milk, Siriwan Suknicom

Chulalongkorn University Theses and Dissertations (Chula ETD)

This study was divided into 3 parts. The objective of first part aims to investigate the effect of konjac glucomannan (KGM) solution (0.02-0.5%, w/w) at different pH (3, 5 and 9) on the stability between 5% fish oil- skim milk with and without casein emulsion. The second part aims to study the effects of konjac glucomannan (KGM) solution (0.02-0.5%, w/w) at different pH (3-10) on the stability of 5%fish oil-milk emulsion. And the last part aims to study the effect of high-pressure (400, 500 and 600 MPa) on the improvement of the stability of 5%fish oil-milk emulsion. The results of …

Development Of Bio-Based Nanocomposites For Biosensor And Indicator Applications In Smart Food Packaging, Abdus Sobhan

Electronic Theses and Dissertations

Smart food packaging based on biosensors has been attracting more and more interest to the industrial community because of the concerns of food quality and safety. A food packaging with biosensor has a scope to enable real-time monitoring of microbial breakdown products of packaged foods. Furthermore, one of the biggest challenges in implementing biosensor for smart packaging materials is the development of bio-sensing active materials that can leverage their electrical, thermal, biodegradable and other functional properties. In this regard, nanocellulose-based activated carbon (NAC) nanocomposite was developed using the activated carbon and nanocellulose gel using the casting method with their different …

A Genetic Investigation Of Anticoagulant Rodenticide Resistance In Mus Musculus Of Western Australia: Implications For Conservation And Biosecurity, Bridget Judith Maria Lucrezia Duncan

Theses : Honours

Human-wildlife interactions have developed since the agricultural revolution that occurred 10,000 years ago, and the expansion of commensal species’ geographical distribution led to conflicts that prompted humans to adopt a wide range of control methods for pest species (Horvitz, Wang, Wan, & Nathan, 2017; Riyahi et al., 2013; Saraswat, Sinha, & Radhakrishna, 2015). The order Rodentia is characterised by a high number of successful invaders, which humans have attempted to manage with the use of anticoagulant rodenticides (ARs) since the 1940s (Capizzi, Bertolino, & Mortelliti, 2014; Ruiz-Suárez et al., 2014). The rise and spread of a genetic mutation that infers …

Investigating The Antioxidant, Immunomodulatory And Anti-Obesogenic Propertiesof Novel Bsg-Derived Extracts And Their Potential As Ingredients In Functional Foods For Older Adults, Suzanne O Brien

Theses

Brewer’s Spent Grain (BSG) represents a substantial waste product of the brewing industry, with 39 million tonnes generated globally every year. To date the primary use of BSG is as animal feed but there is significant interest in identifying alternative uses for this agro-industry by-product. BSG is rich in protein and fibre and is known to contain health-promoting bioactive compounds, thus one application would be in the area of functional foods. People are living longer and as the older adult population continues to increase globally so too is the prevalence of age-related chronic conditions. Diet plays an essential role in …

Restoration Through Regeneration: An Analysis Of Agriculture In The United States, Rebecca Norine Graham

Capstone Showcase

The industrialization of agriculture in the mid-twentieth century has revolutionized global food systems, with enough food produced annually to sustain 10 billion people on a planet of only 7.8 billion people. Such a high-yielding agricultural system comes at a great cost to the Earth’s ecosystem, as industrialized farming has taken on factory-like production methods. Particularly harmful is the livestock sector, with ruminating animals such as cattle contributing to rising global temperatures and environmental degradation. The environmental destruction caused by industrialized animal agriculture can be halted and ultimately reversed through regenerative agriculture. Regenerative agriculture is a restorative farming practice that promotes …

Investigation Of Fermentation Efficiency In Saccharomyces Cerevisiae Through Telomere Integrity And Maltase Expression, Dana Bennett

All Graduate Theses, Dissertations, and Other Capstone Projects

Many microbreweries practice serial fermentation, or serial repitching. Serial repitching is the process by which one yeast culture is reused for multiple batches of beer. Each batch of subsequent beer is called a “pitch.” This technique helps breweries limit production costs. However, fermentation is difficult to predict throughout serial fermentation. This leads to beer quality issues such as fluctuation in alcohol production, buildup of unwanted flavor compounds, and decreased carbon dioxide production, which results in reduced profit. To combat this issue, many breweries will attempt to predict fermentation efficiency through viable cell counting in order to ensure a consistent number …

Characterization Of Maize Near-Isogenic Lines With Enhanced Flavonoid Expression To Be Used As Tools In Diet-Health Complexity, Binning Wu, Haotian Chang, Rich Marini, Surinder Chopra, Lavanya Reddivari

Department of Food Science Faculty Publications

Increasing incidence of chronic diseases in the 21st century has emphasized the importance of developing crops with enhanced nutritional value. Plant-based diets are associated with reduced incidence of many chronic diseases. The growing population and increased food demand have prioritized the development of high-yielding commercial crop varieties at the expense of natural flavors as well as health-benefiting compounds including polyphenols. Flavonoids are a large subfamily of polyphenols abundant in the plant kingdom with known health-promoting effects, making them a promising trait to be re-introduced into elite lines. Given the vast array of flavonoids and the complexity of plant food metabolome …

Serum Carotenoids And Pediatric Metabolic Index Predict Insulin Sensitivity In Mexican American Children, Srinivas Mummidi, Vidya S. Farook, Lavanya Reddivari, Joselin Hernandez-Ruiz, Alvaro Diaz-Badillo, Sharon P. Fowler, Roy G. Resendez, Feroz Akhtar, Donna M. Lehman, Cristopher P. Jenkinson, Rector Arya, Jane L. Lynch, Jose A. Canas, Ralph A. Defronzo, Daniel E. Hale, John Blangero, Juan Carlos Lopez-Alvarenga, Ravindranath Duggirala, Jairam K. P. Vanamala

Department of Food Science Faculty Publications

High concentrations of carotenoids are protective against cardiometabolic risk traits (CMTs) in adults and children. We recently showed in non-diabetic Mexican American (MA) children that serum α-carotene and β-carotene are inversely correlated with obesity measures and triglycerides and positively with HDL cholesterol and that they were under strong genetic influences. Additionally, we previously described a Pediatric Metabolic Index (PMI) that helps in the identification of children who are at risk for cardiometabolic diseases. Here, we quantified serum lycopene and β-cryptoxanthin concentrations in approximately 580 children from MA families using an ultraperformance liquid chromatography-photodiode array and determined their heritabilities and correlations …

Arabinoxylan Structural Profiling Of Cool-Season Pasture Grasses Via High-Performance Anion-Exchange Chromatography With Pulsed Amperometric Detection (Hpaec-Pad) Analysis Of Endoxylanase Digests, Glenna Erin Joyce

Theses and Dissertations--Animal and Food Sciences

Arabinoxylan (AX) is a major structural polysaccharide found in the cell walls of monocots such as cereal grains and pasture grasses. The variety of AX structural components and substitution patterns contribute to AX structural diversity between different monocot species as well as plant tissues.

The rumen is the first digestion site of masticated food material in cattle and provides 70% of energy to host through fermentation of forage. There are many species of pasture grasses that act as a forage source. Differences in AX structure found in these pasture grasses may impact rumen microbial fermentation. Understanding the AX structure of …

A Comprehensive Review On Bioactive Peptides Derived From Milk And Milk Products Of Minor Dairy Species, Snigdha Guha, Heena Sharma, Gaurav Kr Deshwal, Priyanka Singh Rao

Department of Food Science and Technology: Faculty Publications

Milk from different species has been exploited for the isolation of various functional ingredients for decades. Irrespective of the source, milk is considered as a complete food, as it provides essential nutrients required by the human body. Proteins and their fractions are valuable sources of bioactive peptides that might exert a health beneficial role in the human body such as immune-modulation, antioxidant activity, ACE-inhibitory activity, anti- neoplastic, anti-microbial, etc. In milk, bioactive peptides may either be present in their natural form or released from their parental proteins due to enzymatic action. The increasing interest in bioactive peptides among researchers has …

Characterization Of Two Zygnema Strains (Zygnema Circumcarinatum Sag 698-1a And Sag 698-1b) And A Rapid Method To Estimate Nuclear Genome Size Of Zygnematophycean Green Algae, Xuehuan Feng, Andreas Holzinger, Charlotte Permann, Dirk Anderson, Yanbin Yin

Department of Food Science and Technology: Faculty Publications

Zygnematophyceae green algae (ZGA) have been shown to be the closest relatives of land plants. Three nuclear genomes (Spirogloea muscicola, Mesotaenium endlicherianum, and Penium margaritaceum) of ZGA have been recently published, and more genomes are underway. Here we analyzed two Zygnema circumcarinatum strains SAG 698-1a (mating +) and SAG 698-1b (mating −) and found distinct cell sizes and other morphological differences. The molecular identities of the two strains were further investigated by sequencing their 18S rRNA, psaA and rbcL genes. These marker genes of SAG 698-1a were surprisingly much more similar to Z. cylindricum (SAG 698-2) than to SAG 698-1b. …

Metabolic Profiling Of Historical And Modern Wheat Cultivars Using Proton Nuclear Magnetic Resonance Spectroscopy, Rachana Poudel, Fatema Bhinderwala, Martha Morton, Robert Powers, Devin J. Rose

Department of Food Science and Technology: Faculty Publications

To determine changes in the grain components between historical and modern wheat (Triticum aestivum L.) cultivars, wholemeal flours from 19 wheat cultivars and 2 landraces released or introduced between 1870 and 2013 and grown over two crop years were extracted using hydroalcoholic solution and analyzed using one dimensional 1H NMR spectral profiling. Grain yield, grain volume weight (GVW), and grain protein concentration were also measured. Grain yield increased while protein concentration decreased by release year (p < 0.001). Increasing trends (p < 0.01) were observed for tryptophan, sum of the measured amino acids, chlorogenic acid, ferulic acid, vanillic acid, and sum of the measured phenolic acids. Grain yield, phenolic acids, and tryptophan were mainly associated with modern cultivars, whereas grain protein concentration and GVW were associated with historical cultivars. The findings from this study showed changes in concentration of grain components over a century of breeding that may have implications for grain quality and human health.

Genome-Wide Identification And Comparative Analysis Of Arf Family Genes In Three Apiaceae Species, Qiaoying Pei, Nan Li, Qihang Yang, Tong Wu, Shuyan Feng, Xuehuan Feng, Zange Jing, Rong Zhou, Ke Gong, Tong Yu, Zhen Wang, Xiaoming Song

Department of Food Science and Technology: Faculty Publications

The family Apiaceae includes many important vegetables and medicinal plants. Auxin response factors (ARFs) play critical roles in regulating plant growth and development. Here, we performed a comprehensive analysis of the ARF gene family in three Apiaceae species, celery, coriander, and carrot, and compared the results with the ARF gene family of lettuce, Arabidopsis, and grape. We identified 156 ARF genes in all six species and 89 genes in the three Apiaceae species, including 28, 34, and 27 in celery, coriander, and carrot, respectively. The paralogous gene number in coriander was far greater than that in carrot and celery. Our …

Temporal Dynamics Of Chronic Inflammation On The Cecal Microbiota In Il-10-/- Mice, Anne-Marie C. Overstreet, Amanda Ramer-Tait, Jan S. Suchodolski, Jesse M. Hostetter, Chong Wang, Albert E. Jergens, Gregory J. Phillips, Michael J. Wannemeuhler

Department of Food Science and Technology: Faculty Publications

The intestinal microbiota is a critical component of mucosal health as evidenced by the fact that alterations in the taxonomic composition of the gastrointestinal microbiota are associated with inflammatory bowel diseases. To better understand how the progression of inflammation impacts the composition of the gastrointestinal microbiota, we used culture independent taxonomic profiling to identify temporal changes in the cecal microbiota of C3Bir IL-10-/- mice concomitantly with the onset and progression of colitis. This analysis revealed that IL-10-/- mice displayed a biphasic progression in disease severity, as evidenced by histopathological scores and cytokine production. Beginning at 4 weeks of age, pro-inflammatory …

Impact Of Probiotic B. Infantis Evc001 Feeding In Premature Infants On The Gut Microbiome, Nosocomially Acquired Antibiotic Resistance, And Enteric Inflammation, Marielle Nguyen, Heaven Holdbrooks, Prasanthi Mishra, Maria A. Abrantes, Sherri Eskew, Mariajamiela Garma, Cyr-Geraurd Oca, Carrie Mcguckin, Cynthia B. Hein, Ryan D. Mitchell, Sufyan Kazi, Giorgio Casaburi, Heather K. Brown, Steven A. Frese, Bethany M. Henrick

Department of Food Science and Technology: Faculty Publications

Background: Preterm birth is a major determinant of neonatal survival and morbidity, but the gut microbiome and associated enteric inflammation are also key factors in neonatal development and the risk of associated morbidities. We prospectively and longitudinally followed two cohorts of preterm infants, one of which was fed activated Bifidobacterium longum subsp. infantis (B. infantis) EVC001 8 × 109 CFU daily, and the other was not fed a probiotic. Hospital feeding protocol assigned all infants born at < 1500 g and/or < 32 weeks corrected gestational age to the probiotic feeding protocol, whereas infants born at > 1500 g and/or > 32 weeks corrected gestational age were not fed a probiotic. Fecal samples were opportunistically collected from 77 infants throughout the …

Effect Of High-Pressure Processing On The Microbial Load And Functionality Of Sugar-Cookie Dough, Luis Sabillón, Jayne E. Stratton, Devin Rose, Kent M. Eskridge, Andreia Bianchini

Department of Food Science and Technology: Faculty Publications

Background and objectives: Refrigerated dough products have the potential to be a safety hazard to consumers because they could be consumed raw or undercooked. The objectives of this study were designed to evaluate the microbial and functionality changes in high pressured sugar-cookie dough as a function of a_w (0.80–0.87), pressure level (100–600 MPa), and holding time (1–6 min).

Findings: Endogenous microbial populations were marginally reduced (0.2–0.5 log CFU/g) by pressure treatments. However, treating the dough at 600 MPa for 6 min significantly reduced counts of inoculated Escherichia coli by as much as 2.0 log CFU/g. Increasing the a_{w …}

Host Identity And Geographic Location Significantly Affect Gastrointestinal Microbial Richness And Diversity In Western Lowland Gorillas (Gorilla Gorilla Gorilla) Under Human Care, Katrina Eschweiler, Jonathan B. Clayton, Anneke Moresco, Erin A. Mckenney, Larry J. Minter, Mallory J. Suhr Van Haute, William Gasper, Shivdeep Singh Hayer, Lifeng Zhu, Kathryn Cooper, Kimberly Ange-Van Heugten

Department of Food Science and Technology: Faculty Publications

The last few decades have seen an outpouring of gastrointestinal (GI) microbiome studies across diverse host species. Studies have ranged from assessments of GI microbial richness and diversity to classification of novel microbial lineages. Assessments of the “normal” state of the GI microbiome composition across multiple host species has gained increasing importance for distinguishing healthy versus diseased states. This study aimed to determine baselines and trends over time to establish “typical” patterns of GI microbial richness and diversity, as well as interindividual variation, in three populations of western lowland gorillas (Gorilla gorilla gorilla) under human care at three …

Development Of A Multiplex Real-Time Pcr Assay For Predicting Macrolide And Tetracycline Resistance Associated With Bacterial Pathogens Of Bovine Respiratory Disease, Enakshy Dutta, John Dustin Loy, Caitlyn A. Deal, Emily L. Wynn, Michael L. Clawson, Jennifer Clarke, Bing Wang

Department of Food Science and Technology: Faculty Publications

Antimicrobial resistance (AMR) in bovine respiratory disease (BRD) is an emerging concern that may threaten both animal and public health. Rapid and accurate detection of AMR is essential for prudent drug therapy selection during BRD outbreaks. This study aimed to develop a multiplex quantitative real-time polymerase chain reaction assay (qPCR) to provide culture-independent information regarding the phenotypic AMR status of BRD cases and an alternative to the gold-standard, culture-dependent test. Bovine clinical samples (297 lung and 111 nasal) collected in Nebraska were subjected to qPCR quantification of macrolide (MAC) and tetracycline (TET) resistance genes and gold-standard determinations of AMR of …

Editorial: Gluten, From Plant To Plate: Implications For People With Celiac Disease, Michelle Lisa Colgrave, Katharina Anne Scherf, Melanie Downs, Alberto Caminero

Department of Food Science and Technology: Faculty Publications

No abstract provided.

Bovine Colostrum And Its Potential For Human Health And Nutrition, Aysenur Arslan, Merve Kaplan, Hatice Duman, Ayse Bayraktar, Melih Ertürk, Bethany M. Henrick, Steven A. Frese, Sercan Karav

Department of Food Science and Technology: Faculty Publications

Colostrum is the first milk produced post-partum by mammals and is compositionally distinct from mature milk. Bovine colostrum has a long history of consumption by humans, and there have been a number of studies investigating its potential for applications in human nutrition and health. Extensive characterization of the constituent fractions has identified a wealth of potentially bioactive molecules, their potential for shaping neonatal development, and the potential for their application beyond the neonatal period. Proteins, fats, glycans, minerals, and vitamins are abundant in colostrum, and advances in dairy processing technologies have enabled the advancement of bovine colostrum from relative limitations …

Molecular Adaptation To Folivory And The Conservation Implications For Madagascar’S Lemurs, Elaine E. Guevara, Lydia K. Greene, Marina B. Blanco, Casey Farmer, Jeannin Ranaivonasy, Joelisoa Ratsirarson, Karine L. Mahefarisoa, Tsiky Rajaonarivelo, Hajanirina H. Rakotondrainibe, Randall E. Junge, Cathy V. Williams, Elodi Rambeloson, Hoby A. Rasoanaivo, Vololonirina Rahalinarivo, Laza H. Andrianandrianina, Jonathan B. Clayton, Ryan S. Rothman, Richard R. Lawler, Brenda J. Bradley, Anne D. Yoder

Department of Food Science and Technology: Faculty Publications

The lemurs of Madagascar include numerous species characterized by folivory across several families. Many extant lemuriform folivores exist in sympatry in Madagascar’s remaining forests. These species avoid feeding competition by adopting different dietary strategies within folivory, reflected in behavioral, morphological, and microbiota diversity across species. These conditions make lemurs an ideal study system for understanding adaptation to leaf-eating. Most folivorous lemurs are also highly endangered. The significance of folivory for conservation outlook is complex. Though generalist folivores may be relatively well equipped to survive habitat disturbance, specialist folivores occupying narrow dietary niches may be less resilient. Characterizing the genetic bases …

Heuristic And Hierarchical-Based Population Mining Of Salmonella Enterica Lineage I Pan-Genomes As A Platform To Enhance Food Safety, Joao Carlos Gomes-Neto, Natasha Pavlovikj, Carmen Cano, Baha Abdalhamid, Gabriel Asad Al-Ghalith, John Dustin Loy, Dan Knights, Peter C. Iwen, Byron D. Chaves, Andrew K. Benson

Department of Food Science and Technology: Faculty Publications

The recent incorporation of bacterial whole-genome sequencing (WGS) into Public Health laboratories has enhanced foodborne outbreak detection and source attribution. As a result, large volumes of publicly available datasets can be used to study the biology of foodborne pathogen populations at an unprecedented scale. To demonstrate the application of a heuristic and agnostic hierarchical population structure guided pan-genome enrichment analysis (PANGEA), we used populations of S. enterica lineage I to achieve two main objectives: (i) show how hierarchical population inquiry at different scales of resolution can enhance ecological and epidemiological inquiries; and (ii) identify population-specific inferable traits that could provide …

Prokevo: An Automated, Reproducible, And Scalable Framework For High-Throughput Bacterial Population Genomics Analyses, Natasha Pavlovikj, Joao Carlos Gomes-Neto, Jitender S. Deogun, Andrew K. Benson

Department of Food Science and Technology: Faculty Publications

Whole Genome Sequence (WGS) data from bacterial species is used for a variety of applications ranging from basic microbiological research, diagnostics, and epidemiological surveillance. The availability of WGS data from hundreds of thousands of individual isolates of individual microbial species poses a tremendous opportunity for discovery and hypothesis-generating research into ecology and evolution of these microorganisms. Flexibility, scalability, and user-friendliness of existing pipelines for population-scale inquiry, however, limit applications of systematic, population-scale approaches. Here, we present ProkEvo, an automated, scalable, reproducible, and open-source framework for bacterial population genomics analyses using WGS data. ProkEvo was specifically developed to achieve the following …

Interspecies Variation In Hominid Gut Microbiota Controls Host Gene Regulation, Amanda L. Muehlbauer, Allison L. Richards, Adnan Alazizi, Michael B. Burns, Andres Gomez, Jonathan B. Clayton, Klara Petrzelkova, Camilla Cascardo, Justyna Resztak, Xiaoquan Wen, Roger Pique-Regi, Francesca Luca, Ran Blekhman

Department of Food Science and Technology: Faculty Publications

The gut microbiome exhibits extreme compositional variation between hominid hosts. However, it is unclear how this variation impacts host physiology across species and whether this effect can be mediated through microbial regulation of host gene expression in interacting epithelial cells. Here, we characterize the transcriptional response of human colonic epithelial cells in vitro to live microbial communities extracted from humans, chimpanzees, gorillas, and orangutans. We find that most host genes exhibit a conserved response, whereby they respond similarly to the four hominid microbiomes. However, hundreds of host genes exhibit a divergent response, whereby they respond only to microbiomes from specific …

The International Scientific Association For Probiotics And Prebiotics (Isapp) Consensus Statement On Fermented Foods, Maria L. Marco, Mary Ellen Sanders, Michael Gänzle, Marie Claire Arrieta, Paul D. Cotter, Luc De Vuyst, Colin Hill, Wilhelm Holzapfel, Sarah Lebeer, Dan Merenstein, Gregor Reid, Benjamin E. Wolfe, Robert Hutkins

Department of Food Science and Technology: Faculty Publications

An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term ‘fermented’ led the panel to define fermented foods and beverages as “foods made through desired microbial growth and enzymatic conversions of food components”. This definition, encompassing the many varieties of fermented foods, is …