Scholarly Works, Food Science and Technology

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“The uniqueness of one apple versus another.” Exploring producer perspectives of hard cider in the Northeast and Mid-Atlantic United States
Calvert, Martha D.; Neill, Clinton L.; Stewart, Amanda C.; Chang, Elizabeth A. B.; Whitehead, Susan R.; Lahne, Jacob (Taylor & Francis, 2023-10-25)
Hard cider is growing in popularity throughout the United States (US). Though many scholars have investigated quality and trends in the expanding US cider industry, still little is known about cider producers’ opinions of the products that they make. How do American cider producers value and emplace value onto cider as the industry grows and competes with the broader alcoholic beverage market? This study explored producer perceptions of American hard cider by employing 21 semi-structured interviews with cider-makers throughout Virginia, Vermont, and New York – three leading cider producing states in the Northeast and Mid-Atlantic US. Interview sessions were subject to reflexive thematic analysis for themes related to preference, consumption, and cider-making. Results suggest that cider producers broadly prefer complex flavors and cider made with cider-specific apples. Yet, cider producers ascribe to a diverse spectrum of values related to the cider-making process, agriculture, and business goals, which influence their preferences and the experiences that they create for other consumers. This research also identifies a chasm in how American “cider” is being constructed and valued, offering broad implications for the domestic cider and apple agriculture industries as well as a template for bridging the divide between producer- and consumer-based food studies.
Appeal of the Apple: Exploring consumer perceptions of hard cider in the Northeast and Mid-Atlantic United States
Calvert, Martha D.; Neill, Clinton L.; Stewart, Amanda C.; Chang, Elizabeth A. B.; Whitehead, Susan R.; Lahne, Jacob (Taylor & Francis, 2023-10-23)
Alcoholic or “hard” cider is experiencing a resurgence in popularity, particularly throughout the Northeast and Mid-Atlantic regions of the United States. Yet, many stakeholders struggle to understand how consumers define and distinguish hard cider from the sea of options in the saturated alcoholic beverage market. This study aimed to explore consumer preferences for hard cider using a phenomenological, qualitative approach. The research comprised 14 focus groups with regular cider consumers (99 participants) throughout three leading cider-producing states in the Northeast and Mid-Atlantic United States: Virginia, Vermont, and New York. All focus group sessions were subject to reflexive thematic analysis for themes broadly related to cider product preference and the cider-drinking experience. Results of the study suggest that cider preference is motivated largely by sensory quality in addition to various other factors including perceived health effects, regionality and proximity, the drinking occasion, and product information. Results also emphasize the importance of nostalgia in cider sensory experiences, as well as the role of social norms in consumer valuation of cider products. Overall, this research highlights diverse consumer preferences for cider and serves as a framework for using qualitative research methods to explore consumer preferences in the food and beverage industries.
Campylobacter in aquatic and terrestrial mammals is driven by life traits: A systematic review and meta-analysis
Brooks, Michael R.; Medley, Sarah; Ponder, Monica A.; Alexander, Kathleen A. (Frontiers, 2023-02)
Introduction: Campylobacter spp. infections are responsible for significant diarrheal disease burden across the globe, with prevalence thought to be increasing. Although wild avian species have been studied as reservoirs of Campylobacter spp., our understanding of the role of wild mammalian species in disease transmission and persistence is limited. Host factors influencing infection dynamics in wild mammals have been neglected, particularly life traits, and the role of these factors in zoonotic spillover risk is largely unknown. Methods: Here, we conducted a systematic literature review, identifying mammalian species that had been tested for Campylobacter spp. infections (molecular and culture based). We used logistic regression to evaluate the relationship between the detection of Campylobacter spp. in feces and host life traits (urban association, trophic level, and sociality). Results: Our analysis suggest that C. jejuni transmission is associated with urban living and trophic level. The probability of carriage was highest in urban-associated species (p = 0.02793) and the most informative model included trophic level. In contrast, C. coli carriage appears to be strongly influenced by sociality (p = 0.0113) with trophic level still being important. Detection of Campylobacter organisms at the genus level, however, was only associated with trophic level (p = 0.0156), highlighting the importance of this trait in exposure dynamics across host and Campylobacter pathogen systems. Discussion: While many challenges remain in the detection and characterization of Camploybacter spp., these results suggest that host life traits may have important influence on pathogen exposure and transmission dynamics, providing a useful starting point for more directed surveillance approaches.
Perfiles de fermentación para contribuir con el mejoramiento de la calidad del cacao (Theobroma cacao L.) de la ecorregión de Lachuá, Cobán, Alta Verapaz
Ac-Pangan, Marlon; Ruiz-Cruz, Edgar (Universidad del Valle de Guatemala, 2022-08)
Dentro de la industria del cacao, la comercialización de granos a nivel global representa la segunda actividad comercial que genera mayor valor, solo después de la comercialización de chocolate y sus derivados. La experiencia guatemalteca de exportación ha tenido buena aceptación a nivel internacional, sin embargo, pocos avances se han realizado en el proceso de fermentación para el mejoramiento de la calidad. Se realizó la caracterización y una propuesta de un nuevo método para el monitoreo de la fermentación en tres masas y tres localidades diferentes. Los resultados mostraron que, en promedio, en la región de Lachuá el proceso de fermentación finaliza al sexto día de procesamiento cuando la temperatura alcanza un valor de 48.02oC y el pH de la testa y del cotiledón coinciden con un valor de pH de 4.50. Sin embargo; los resultados también mostraron que los perfiles de fermentación dependen de la localidad y masa de procesamiento. Además, se observó una moderada correlación linear positiva (0.547) entre temperatura de fermentación y pH de la testa y alta correlación linear negativa (-0.826) entre temperatura de fermentación y pH del cotiledón. Los protocolos utilizados actualmente en la ecorregión de Lachuá pueden ser mejorados y ajustados de acuerdo con la masa de cacao en fermentación y la localidad de procesamiento, basados en los perfiles de temperatura y pH de la testa y del cotiledón. Además, los resultados sugieren que es posible utilizar la temperatura de la masa de fermentación como un indicador para el monitoreo de los perfiles de pH durante la fermentación.
Caracterización socioeconómica, de la producción y de la comercialización de cacao (Theobroma cacao L.) en la ecorregión de Lachuá, Alta Verapaz
Ac-Pangan, Marlon; Ruiz-Cruz, Edgar (Universidad del Valle de Guatemala, 2022-08)
El cacao es parte de los planes de desarrollo de la mayoría de los países centroamericanos. Sin embargo, el cacao de Guatemala ha cobrado importancia en los últimos años debido a los pequeños modelos de producción privada y comunitaria que actualmente se encuentran exportando producto hacia Estados Unidos y países de Europa, en los cuales ha tenido gran aceptación por sus características organolépticas diferenciadas de otros cacaos del mundo y ha sido clasificado por empresas extranjeras como cacao fino. En la ecorregión de Lachuá, las familias locales viven en condiciones de pobreza y basan su economía principalmente en la producción agrícola de subsistencia y comercialización de productos agrícolas, entre los que se encuentra el cacao. El presente estudio tuvo como objetivo realizar una caracterización socioeconómica de los productores de cacao de la ecorregión de Lachuá, además de establecer las características actuales de los sistemas de producción de esta región. La edad promedio de los productores fue de 44.38 años, el ingreso promedio general fue de Q1,452.38 por mes, con un ingreso mensual Q659.09 para mujeres, y Q1,733.87 reportado por los hombres. El área promedio de producción de cacao fue de 2.17 Ha/persona, la producción promedio fue de 231.04 Kg de cacao seco/Ha. El 88.1% no fertiliza sus plantaciones, el 74.4% prefiere la comercialización de cacao fresco no drenado, el 63.9% dijo no estar conforme con el precio actual de cacao. El 55% no está interesado en expandir el cultivo; pero la mayoría (97.6%) tiene interés de explorar opciones de procesamiento para agregar valor y mejorar los ingresos económicos.
Consumer responses and willingness-to-pay for hibiscus products: A preliminary study
Ndiaye, Oumoule; Hedrick, Valisa E.; Neill, Clinton L.; Carneiro, Renata C. V.; Huang, Haibo; Fernandez-Fraguas, Cristina; Guiro, Amadou Tidiane; O'Keefe, Sean F. (Frontiers, 2023-04)
The rise in diseases like obesity and diabetes is a worldwide challenge. The consumption of functional products such as hibiscus, which has been proven to be high in bioactive compounds and dietary fiber, providing it with anticancer, antiaging, anti-inflammatory and satiety properties, should be promoted. In the U.S., promoting the consumption of hibiscus products can be a good approach to increase fiber consumption and to reduce risk of obesity, diabetes, and hypertension. However, information about knowledge of this functional product among consumers is still sparse and increasing consumption requires designing and marketing desired products made from hibiscus. Therefore in this preliminary study, we assessed consumer response to hibiscus products and investigated whether providing information about potential health benefits could impact consumer willingness-to-pay (WTP) for three types of non-alcoholic hibiscus beverages: ready-made tea, bottled juice, and kombucha. Our web-based survey was distributed through Qualtrics(XM) and a convenience sampling method was chosen. Most participants identified themselves as female, 18-34 years old, with a graduate degree. Most participants (81%) had consumed hibiscus products before and 57% had a weekly food budget lower than $60. Overall, tea and juices were the most liked hibiscus beverages, respectively. Although taste and health benefits were ranked as the main reasons to consume hibiscus beverages, additional information about hibiscus health benefits did not significantly affect WTP for these products. Without additional health benefit information, consumer WTP for non-alcoholic hibiscus beverages ranged from $2.9 to $3.60 for kombucha and $4.08-4.97 for Ready-made-tea. This study provides valuable insights that can support future research on hibiscus products and promote the development of novel hibiscus-based foods and beverages that are appealing to the U.S. market.
An evaluation and shortening of the Cooking and Food Provisioning Action Scale (CAFPAS) using item response theory
Karlsson, Simon; Harris, Kathryn L.; Melin, Jeanette; Lahne, Jacob; Wolfson, Julia A.; Collier, Elizabeth S. (Elsevier, 2023-05)
The Cooking and Food Provisioning Action Scale (CAFPAS) is a 28-item validated tool for measuring food agency, a latent construct representing an individual's ability to make and achieve food-preparation and -pro-visioning goals. Here, key measurement parameters (targeting, threshold ordering, item fit, unidimensionality, differential item functioning, local dependency, and person reliability) of the CAFPAS are evaluated using a specific case of item response theory, Rasch analysis, on data from a development sample (N = 1853; 910 from Sweden; 943 from the US). Winsteps (v.5.1.7) is used for this analysis. The similarity of the Swedish version of the CAFPAS to the original is also assessed. Based on an iterative assessment of the measurement properties with different combinations of items in the development sample, ways to shorten the CAFPAS without jeopardizing construct validity or person reliability are examined. After removing items that do not fit the Rasch model, or that appear redundant in relation to other items, an 11-item version (CAFPAS-short) is suggested and tested using further Rasch analysis on both the development sample and an additional US-based validation sample (N = 1457). Scores of cooking confidence and attitudes are then modelled with measures from the CAFPAS and CAFPAS-short using frequentist and Bayesian analysis. Results suggest that the CAFPAS-short performs similarly to the full-length version, and potential future improvements to the CAFPAS are discussed. This study represents a successful application of item response theory to investigate and shorten a psychometric scale, reducing cognitive load on participants in studies using the CAFPAS whilst minimizing loss of data reliability.
Can Xylose Be Fermented to Biofuel Butanol in Continuous Long-Term Reactors: If Not, What Options Are There?
Qureshi, Nasib; Lin, Xiaoqing; Tao, Shunhui; Liu, Siqing; Huang, Haibo; Nichols, Nancy N. (MDPI, 2023-06-26)
This study applied concentrated xylose (60–250 g/L) medium to produce butanol (acetone butanol ethanol, or ABE). A control batch fermentation of 61 g/L initial glucose using Clostridium beijerinckii P260 resulted in a productivity and yield of 0.33 g/L·h and 0.43 g/g, respectively. Use of 60 g/L xylose in a batch system resulted in productivity and yield of 0.26 g/L·h, and 0.40 g/g, respectively. In these two experiments, the culture fermented 89.3% glucose and 83.6% of xylose, respectively. When ABE recovery was coupled with fermentation for continuous solvent removal, the culture fermented all the added xylose (60 g/L). This system resulted in a productivity and yield of 0.66 g/L·h and 0.44 g/g, respectively. When the sugar concentration was further increased above 100 g/L, only a small fraction of the sugar was fermented in batch cultures without product removal. However, with simultaneous product removal, all the xylose (150 g/L) was fermented provided the culture was fed with nutrients intermittently. In this system, 66.32 g/L ABE was produced from 150 g/L xylose with a productivity of 0.44 g/L·h and yield of 0.44 g/g. Using the integrated culture system allowed sugar consumption to be increased by 300% (150 g/L). The continuous system using xylose as a feed did not sustain and after 36 days (864 h) of fermentation, it produced only 2–3 g/L ABE. Rather, the culture became acidogenic and produced 4–5 g/L acids (acetic and butyric). This study suggested that xylose be fermented in batch reactors coupled with simultaneous product recovery rather than in continuous reactors.
Exploring cider website descriptions using a novel text mining approach
Calvert, Martha D.; Cole, Elizabeth; Neill, Clinton L.; Stewart, Amanda C.; Whitehead, Susan R.; Lahne, Jacob (Wiley, 2023-05)
Rapid methods of text analysis are increasingly important tools for efficiently extracting and understanding communication within the food and beverage space. This study aimed to use frequency-based text mining and biterm topic modeling (BTM) as tools for analyzing how cider products are communicated and marketed on cider-producer websites for products made in Virginia, Vermont, and New York. BTM has been previously used to explore topics in small corpora of text data, and frequency-based text mining is efficient for exploring patterns of text across different documents or filters. The present dataset comprised 1115 cider products and their website descriptions extracted from 124 total cider-producer websites during 2020 and 2021. Results of the text mining analyses suggest that cider website descriptions emphasize food-pairing, production, and sensory quality information. Altogether, this research presents the text mining approaches for exploring food and beverage communication. Practical applicationsThis research will be valuable to stakeholders in the United States' cider industry by providing relevant insight as to how cider marketing and sensory communication varies based on extrinsic product factors, such as geography and packaging. This research also demonstrates the efficiency and potential of text mining tools for exploring language and communication related to foods, beverages, and sensory quality. Further, this research provides a framework for extracting sensory-specific language from a large corpus of data, which may be adopted by other researchers wishing to apply rapid descriptive methods in the sensory, quality, and consumer research fields.
Crop, Host, and Gut Microbiome Variation Influence Precision Nutrition: An Example of Blueberries
Weaver, Connie M.; Ferruzzi, Mario G.; Maiz, Maria; Cladis, Dennis P.; Nakatsu, Cindy H.; McCabe, George P.; Lila, Mary Ann (MDPI, 2023-05-22)
Epidemiological studies have shown associations between polyphenol-rich fruit intake and bone health, and preclinical studies have shown that blueberries improve bone health. To determine the genotype and dose of blueberries that are effective in ameliorating age-related bone loss, a multi-institutional team of investigators performed in vitro, preclinical, and clinical studies on blueberry varieties that differed in flavonoid profiles. Principal component analysis was used to select blueberry genotypes that varied in anthocyanin profiles. Total phenolic content did not predict the bioavailability of polyphenolic compounds in rats. A range in bioavailability was observed in individual polyphenolic compounds across genotypes. Both alpha and beta diversity analyses indicated that gut microbiome profiles varied with blueberry dose in rats. Additionally, the identification of specific taxa, such as Prevotellaceae_UCG-001 and Coriobacteriales, increasing after blueberry consumption adds to the mounting evidence of their role in polyphenol metabolism. All of the sources of variation can inform blueberry breeding practices to influence precision nutrition.
The Open Science of Deep Learning: Three Case Studies
Miller, Chreston; Lahne, Jacob; Hamilton, Leah (2022-03)
The open science movement, which prioritizes the open availability of research data and methods for public scrutiny and replication, includes practices like providing code implementing described algorithms in openly available publications. An area of research in which open-science principles may have particularly high impact is in deep learning, where researchers have developed a plethora of algorithms to solve complex and challenging problems, but where others may have difficulty in replicating results and applying these algorithms to other problems. In response, some researchers have begun to open up deep-learning research by making their code and resources available (e.g., datasets and/or pre-trained models) to the current and future research community. This presentation describes three case studies in deep learning where openly available resources differed and investigates the impact on the project and the outcome. This provides a venue for discussion on successes, lessons learned, and recommendations for future researchers facing similar situations, especially as deep learning increasingly becomes an important tool across disciplines. In the first case study, we present a workflow for text summarization, based on thousands of news articles. The outcome, generalizable to many situations, is a tool that can concisely report key facts and events from the articles. In the second case study, we describe the development of an Optical Character Recognition tool for archival research of physical typed notecards, in this case documenting an important, curated collection of thousands of items of clothing. In the last case study, we describe the workflow for applying common Natural Language Processing tools to a novel task: identifying descriptive language for whiskies from thousands of free-form text reviews. These case studies resulted in working solutions addressing their respective, challenging problems because of researchers embracing the concept of open science.
The Open Science of Deep Learning: Three Case Studies
Miller, Chreston; Hamilton, Leah; Lahne, Jacob (2023-02-15)
Objective: An area of research in which open science may have particularly high impact is in deep learning (DL), where researchers have developed many algorithms to solve challenging problems, but others may have difficulty in replicating results and applying these algorithms. In response, some researchers have begun to open up DL research by making their resources available (e.g., code, datasets and/or pre-trained models) to the research community. This article describes three case studies in DL where openly available resources are used and we investigate the impact on the projects, the outcomes, and make recommendations for what to focus on when making DL resources available. Methods: Each case study represents a single project using openly available DL resources for a research project. The process and progress of each case study is recorded along with aspects such as approaches taken, documentation of openly available resources, and researchers’ experience with the openly available resources. The case studies are in multiple-document text summarization, optical character recognition (OCR) of thousands of text documents, and identifying unique language descriptors for sensory science. Results: Each case study was a success but had its own hurdles. Some takeaways are well-structured and clear documentation, code examples and demos, and pre-trained models were at the core to the success of these case studies. Conclusions: Openly available DL resources were the core of the success of our case studies. The authors encourage DL researchers to continue to make their data, code, and pre-trained models openly available where appropriate.
Steelhead trout (Oncorhynchus mykiss) fed probiotic during the earliest developmental stages have enhanced growth rates and intestinal microbiome bacterial diversity
Hines, Ian S.; Santiago-Morales, Kevin D.; Ferguson, Clay S.; Clarington, Jireh; Thompson, Meaghan; Rauschenbach, Meghann; Levine, Uri; Drahos, David; Aylward, Frank O.; Smith, Stephen A.; Kuhn, David D.; Stevens, Ann M. (Frontiers, 2022-11)
Sustainable aquaculture practices can help meet the increasing human demand for seafood, while easing pressures on natural fish populations. Studies aimed at increasing fish production in aquaculture have included supplementary dietary probiotics that often promote general health and enhanced growth rates by altering the microbiome of the host. Steelhead trout (Oncorhynchus mykiss) is anadromous, like salmon, and it is a subspecies of rainbow trout capable of rapid growth, making it an attractive fish to the aquaculture industry. In this study, the impact of feeding a Bacillus subtilis probiotic on the bacterial microbiome of steelhead trout was examined temporally across several stages of animal development, from eggs (day -19) through 184 days after hatching, in relation to physiological measures. Diets included: commercial feed only as a control (A), continually-fed probiotic top-coated on commercial feed (B), commercial then switch to probiotic feed (C), or probiotic then switch to commercial feed (D). Validation of probiotic concentrations on feed and in fish tissues was performed using CFU/g and qPCR, respectively. Fish growth was measured and samples for intestinal microbiome analyses were collected at multiple timepoints during fish development. Fish fed diet D yielded higher weights than the other three diets, with little impact on other biometric parameters. However, bacterial microbiome analysis indicated an increasing trend of overall alpha diversity from the egg stage to day 29 for fish fed the various diets with diet D having the highest diversity. Fish fed diets A and D maintained a high alpha diversity beyond day 29 in contrast to a decreased trend for fish still being fed probiotics in diets B and C. The fish fed diets B and C harbored a significantly higher relative abundance of Bacillus sp. in their total microbiomes (feces + mucosa). Interestingly, the mucosal-only microbiome indicated little variation between the four groups of fish. Feeding the probiotic earlier in development, during the hatchery phase, to influence bacterial microbiome composition in the intestine (rather than later after the microbiome has been established) appears to be a more effective aquaculture practice by enhancing microbiome diversity while enabling higher fish yields.
Genome-Wide Association Study and Genomic Selection for Proteinogenic Methionine in Soybean Seeds
Singer, William; Shea, Zachary; Yu, Dajun; Huang, Haibo; Mian, M.A. Rouf; Shang, Chao; Rosso, Maria L.; Song, Qijan J.; Zhang, Bo (Frontiers, 2022-04-25)
Soybean [Glycine max (L.) Merr.] seeds have an amino acid profile that provides excellent viability as a food and feed protein source. However, low concentrations of an essential amino acid, methionine, limit the nutritional utility of soybean protein. The objectives of this study were to identify genomic associations and evaluate the potential for genomic selection (GS) for methionine content in soybean seeds. We performed a genome-wide association study (GWAS) that utilized 311 soybean accessions from maturity groups IV and V grown in three locations in 2018 and 2019. A total of 35,570 single nucleotide polymorphisms (SNPs) were used to identify genomic associations with proteinogenic methionine content that was quantified by high-performance liquid chromatography (HPLC). Across four environments, 23 novel SNPs were identified as being associated with methionine content. The strongest associations were found on chromosomes 3 (ss715586112, ss715586120, ss715586126, ss715586203, and ss715586204), 8 (ss715599541 and ss715599547) and 16 (ss715625009). Several gene models were recognized within proximity to these SNPs, such as a leucine-rich repeat protein kinase and a serine/threonine protein kinase. Identification of these linked SNPs should help soybean breeders to improve protein quality in soybean seeds. GS was evaluated using k-fold cross validation within each environment with two SNP sets, the complete 35,570 set and a subset of 248 SNPs determined to be associated with methionine through GWAS. Average prediction accuracy (r2) was highest using the SNP subset ranging from 0.45 to 0.62, which was a significant improvement from the complete set accuracy that ranged from 0.03 to 0.27. This indicated that GS utilizing a significant subset of SNPs may be a viable tool for soybean breeders seeking to improve methionine content.
Genome-wide association analysis of sucrose and alanine contents in edamame beans
Wang, Zhibo; Yu, Dajun; Morota, Gota; Dhakal, Kshitiz; Singer, William; Lord, Nilanka; Huang, Haibo; Chen, Pengyin; Mozzoni, Leandro; Li, Song; Zhang, Bo (Frontiers, 2023-02-03)
The sucrose and Alanine (Ala) content in edamame beans significantly impacts the sweetness flavor of edamame-derived products as an important attribute to consumers' acceptance. Unlike grain-type soybeans, edamame beans are harvested as fresh beans at the R6 to R7 growth stages when beans are filled 80-90% of the pod capacity. The genetic basis of sucrose and Ala contents in fresh edamame beans may differ from those in dry seeds. To date, there is no report on the genetic basis of sucrose and Ala contents in the edamame beans. In this study, a genome-wide association study was conducted to identify single nucleotide polymorphisms (SNPs) related to sucrose and Ala levels in edamame beans using an association mapping panel of 189 edamame accessions genotyped with a SoySNP50K BeadChip. A total of 43 and 25 SNPs was associated with sucrose content and Ala content in the edamame beans, respectively. Four genes (Glyma.10g270800, Glyma.08g137500, Glyma.10g268500, and Glyma.18g193600) with known effects on the process of sucrose biosynthesis and 37 novel sucrose-related genes were characterized. Three genes (Gm17g070500, Glyma.14g201100 and Glyma.18g269600) with likely relevant effects in regulating Ala content and 22 novel Ala-related genes were identified. In addition, by summarizing the phenotypic data of edamame beans from three locations in two years, three PI accessions (PI 532469, PI 243551, and PI 407748) were selected as the high sucrose and high Ala parental lines for the perspective breeding of sweet edamame varieties. Thus, the beneficial alleles, candidate genes, and selected PI accessions identified in this study will be fundamental to develop edamame varieties with improved consumers' acceptance, and eventually promote edamame production as a specialty crop in the United States.
Sensory descriptive analysis of hard ciders from the Northeast and Mid-Atlantic United States
Calvert, Martha D.; Neill, Clinton L.; Stewart, Amanda C.; Lahne, Jacob (Wiley, 2023-01-20)
Although alcoholic or “hard” cider is a beverage of growing popularity throughout the Northeastern and Mid-Atlantic United States (US), the industry lacks a consistent language for describing the sensory quality of its products. The main objective of this research was to explore the sensory attributes that can be used to describe a large representative sample (N = 42 samples) of ciders from Virginia, Vermont, and New York, using classical descriptive analysis (DA). The secondary objective of the research was to determine if cider samples’ sensory attributes differ based on extrinsic factors, such as style, packaging, and apple varieties. The study was conducted using a standard DA: 8 panelists were trained for 13 h to develop a lexicon of aroma, taste, and mouthfeel descriptors for 42 cider samples (15 single varietal ciders, 27 blended ciders). Then, subjects evaluated each cider in duplicate for all descriptive attributes in standard sensory-evaluation conditions. Results were analyzed to determine overall differences among the individual cider samples, geographic origins, cider styles, and packaging formats, as well as significant differences across individual attributes. Herein, we report on 29 attributes that can be used to discriminate cider samples, as well as a subset of attributes which differentiate ciders based on extrinsic product variables. These results provide a framework for describing ciders from the Northeast and Mid-Atlantic regions of the US, which may be further generalizable to other North American ciders. As well, these results highlight the potential for more descriptive, sensory-based style guidelines may inspire future research related to cider production practices and terroir.
Salmonella enterica serovar Cerro displays a phylogenetic structure and genomic features consistent with virulence attenuation and adaptation to cattle
Cohn, Alexa R.; Orsi, Renato H.; Carroll, Laura M.; Liao, Jingqiu; Wiedmann, Martin; Cheng, Rachel A. (Frontiers, 2022-11-30)
Salmonella enterica subsp. enterica (S.) serovar Cerro is rarely isolated from human clinical cases of salmonellosis but represents the most common serovar isolated from cattle without clinical signs of illness in the United States. In this study, using a large, diverse set of 316 isolates, we utilized genomic methods to further elucidate the evolutionary history of S. Cerro and to identify genomic features associated with its apparent virulence attenuation in humans. Phylogenetic analyses showed that within this polyphyletic serovar, 98.4% of isolates (311/316) represent a monophyletic clade within section Typhi and the remaining 1.6% of isolates (5/316) form a monophyletic clade within subspecies enterica Clade A1. Of the section Typhi S. Cerro isolates, 93.2% of isolates (290/311) clustered into a large clonal clade comprised of predominantly sequence type (ST) 367 cattle and environmental isolates, while the remaining 6.8% of isolates (21/311), primarily from human clinical sources, clustered outside of this clonal clade. A tip-dated phylogeny of S. Cerro ST367 identified two major clades (I and II), one of which overwhelmingly consisted of cattle isolates that share a most recent common ancestor that existed circa 1975. Gene presence/absence and rarefaction curve analyses suggested that the pangenome of section Typhi S. Cerro is open, potentially reflecting the gain/loss of prophage; human isolates contained the most open pangenome, while cattle isolates had the least open pangenome. Hypothetically disrupted coding sequences (HDCs) displayed clade-specific losses of intact speC and sopA virulence genes within the large clonal S. Cerro clade, while loss of intact vgrG, araH, and vapC occurred in all section Typhi S. Cerro isolates. Further phenotypic analysis suggested that the presence of a premature stop codon in speC does not abolish ornithine decarboxylase activity in S. Cerro, likely due to the activity of the second ornithine decarboxylase encoded by speF, which remained intact in all isolates. Overall, our study identifies specific genomic features associated with S. Cerro’s infrequent isolation from humans and its apparent adaptation to cattle, which has broader implications for informing our understanding of the evolutionary events facilitating host adaptation in Salmonella.
Spatial Versus Nonspatial Variance in Fecal Indicator Bacteria Differs Within and Between Ponds
Murphy, Claire M.; Weller, Daniel L.; Ovissipour, Reza; Boyer, Renee; Strawn, Laura K. (Elsevier, 2023-03)
Surface water environments are inherently heterogenous, and little is known about variation in microbial water quality between locations. This study sought to understand how microbial water quality differs within and between Virginia ponds. Grab samples were collected twice per week from 30 sampling sites across nine Virginia ponds (n = 600). Samples (100 mL) were enumerated for total coliform (TC) and Escherichia coli (EC) levels, and physicochemical, weather, and environmental data were collected. Bayesian models of coregionalization were used to quantify the variance in TC and EC levels attributable to spatial (e.g., site, pond) versus nonspatial (e.g., date, pH) sources. Mixed-effects Bayesian regressions and conditional inference trees were used to characterize relationships between data and TC or EC levels. Analyses were performed separately for each pond with ≥3 sampling sites (5 intrapond) while one interpond model was developed using data from all sampling sites and all ponds. More variance in TC levels were attributable to spatial opposed to nonspatial sources for the interpond model (variance ratio [VR] = 1.55) while intrapond models were pond dependent (VR: 0.65–18.89). For EC levels, more variance was attributable to spatial sources in the interpond model (VR = 1.62), compared to all intrapond models (VR < 1.0) suggesting that more variance is attributable to nonspatial factors within individual ponds and spatial factors when multiple ponds are considered. Within each pond, TC and EC levels were spatially independent for sites 56–87 m apart, indicating that different sites within the same pond represent different water quality for risk management. Rainfall was positively and pH negatively associated with TC and EC levels in both inter- and intrapond models. For all other factors, the direction and strength of associations varied. Factors driving microbial dynamics in ponds appear to be pond-specific and differ depending on the spatial scale considered.
Whole-Genome Sequencing-Based Characterization of Listeria Isolates from Produce Packinghouses and Fresh-Cut Facilities Suggests Both Persistence and Reintroduction of Fully Virulent L. monocytogenes
Sullivan, Genevieve; Orsi, Renato H.; Estrada, Erika; Strawn, Laura K.; Wiedmann, Martin (American Society for Microbiology, 2022-11-01)
The contamination of ready-to-eat produce with Listeria monocytogenes (LM) can often be traced back to environmental sources in processing facilities and packinghouses. To provide an improved understanding of Listeria sources and transmission in produce operations, we performed whole-genome sequencing (WGS) of LM (n = 169) and other Listeria spp. (n = 107) obtained from 13 produce packinghouses and three fresh-cut produce facilities. Overall, a low proportion of LM isolates (9/169) had inlA premature stop codons, and a large proportion (83/169) had either or both of the LIPI-3 or LIPI-4 operons, which have been associated with hypervirulence. The further analysis of the WGS data by operation showed a reisolation (at least 2 months apart) of highly related isolates (,10 hqSNP differences) in 7/16 operations. Two operations had highly related strains reisolated from samples that were collected at least 1 year apart. The identification of isolates collected during preproduction (i.e., following sanitation but before the start of production) that were highly related to isolates collected during production (i.e., after people or products have entered and begun moving through the operation) provided evidence that some strains were able to survive standard sanitation practices. The identification of closely related isolates (,20 hqSNPs differences) in different operations suggests that cross-contamination between facilities or introductions from common suppliers may also contribute to Listeria transmission. Overall, our data suggest that the majority of LM isolates collected from produce operations are fully virulent and that both persistence and reintroduction may lead to the repeat isolation of closely related Listeria in produce operations. IMPORTANCE Listeria monocytogenes is of particular concern to the produce industry due to its frequent presence in natural environments as well as its ability to survive in packinghouses and fresh-cut processing facilities over time. The use of whole-genome sequencing, which provides high discriminatory power for the characterization of Listeria isolates, along with detailed source data (isolation date and sample location) shows that the presence of Listeria in produce operations appears to be due to random and continued reintroduction as well as to the persistence of highly related strains in both packinghouses and fresh-cut facilities. These findings indicate the importance of using high-resolution characterization approaches for root cause analyses of Listeria contamination issues. In cases of repeat isolation of closely related Listeria in a given facility, both persistence and reintroduction need to be considered as possible root causes.
Salmonella Prevalence Is Strongly Associated with Spatial Factors while Listeria monocytogenes Prevalence Is Strongly Associated with Temporal Factors on Virginia Produce Farms
Murphy, Claire M.; Weller, Daniel L.; Strawn, Laura K. (American Society for Microbiology, 2023-02-02)
The heterogeneity of produce production environments complicates the development of universal strategies for managing preharvest produce safety risks. Understanding pathogen ecology in different produce-growing regions is important for developing targeted mitigation strategies. This study aimed to identify environmental and spatiotemporal factors associated with isolating Salmonella and Listeria from environmental samples collected from 10 Virginia produce farms. Soil (n = 400), drag swab (n = 400), and irrigation water (n = 120) samples were tested for Salmonella and Listeria, and results were confirmed by PCR. Salmonella serovar and Listeria species were identified by the Kauffmann-White-Le Minor scheme and partial sigB sequencing, respectively. Conditional forest analysis and Bayesian mixed models were used to characterize associations between environmental factors and the likelihood of isolating Salmonella, Listeria monocytogenes (LM), and other targets (e.g., Listeria spp. and Salmonella enterica serovar Newport). Surrogate trees were used to visualize hierarchical associations identified by the forest analyses. Salmonella and LM prevalence was 5.3% (49/920) and 2.3% (21/920), respectively. The likelihood of isolating Salmonella was highest in water samples collected from the Eastern Shore of Virginia with a dew point of >9.4°C. The likelihood of isolating LM was highest in water samples collected in winter from sites where <36% of the land use within 122 m was forest wetland cover. Conditional forest results were consistent with the mixed models, which also found that the likelihood of detecting Salmonella and LM differed between sample type, region, and season. These findings identified factors that increased the likelihood of isolating Salmonella- and LM-positive samples in produce production environments and support preharvest mitigation strategies on a regional scale. IMPORTANCE This study sought to examine different growing regions across the state of Virginia and to determine how factors associated with pathogen prevalence may differ between regions. Spatial and temporal data were modeled to identify factors associated with an increased pathogen likelihood in various on-farm sources. The findings of the study show that prevalence of Salmonella and L. monocytogenes is low overall in the produce preharvest environment but does vary by space (e.g., region in Virginia) and time (e.g., season), and the likelihood of pathogen-positive samples is influenced by different spatial and temporal factors. Therefore, the results support regional or scale-dependent food safety standards and guidance documents for controlling hazards to minimize risk. This study also suggests that water source assessments are important tools for developing monitoring programs and mitigation measures, as spatiotemporal factors differ on a regional scale.

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