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  • Food Waste from Campus Dining Hall as a Potential Feedstock for 2,3-Butanediol Production via Non-Sterilized Fermentation
    Caldwell, Alicia; Su, Xueqian; Jin, Qing; Hemphill, Phyllicia; Jaha, Doaa; Nard, Sonecia; Tiriveedhi, Venkataswarup; Huang, Haibo; OHair, Joshua (MDPI, 2024-01-31)
    Food waste is a major issue that is increasingly affecting our environment. More than one-third of food is wasted, resulting in over $400 billion in losses to the U.S. economy. While composting and other small recycling practices are encouraged from person-to-person, it is not enough to balance the net loss of 80 million tons per year. Currently, one of the most promising routes for reducing food waste is through microbial fermentation, which can convert the waste into valuable bioproducts. Among the compounds produced from fermentation, 2,3-butanediol (2,3-BDO) has gained interest recently due to its molecular structure as a building block for many other derivatives used in perfumes, synthetic rubber, fumigants, antifreeze agents, fuel additives, and pharmaceuticals. Waste feedstocks, such as food waste, are a potential source of renewable energy due to their lack of cost and availability. Food waste also possesses microbial requirements for growth such as carbohydrates, proteins, fats, and more. However, food waste is highly inconsistent and the variability in composition may hinder its ability to be a stable source for bioproducts such as 2,3-BDO. This current study focuses specifically on post-consumer food waste and how 2,3-BDO can be produced through a non-model organism, Bacillus licheniformis YNP5-TSU during non-sterile fermentation. From the dining hall at Tennessee State University, 13 food waste samples were collected over a 6-month period and the compositional analysis was performed. On average, these samples consisted of fat (19.7%), protein (18.7%), ash (4.8%), fiber (3.4%), starch (27.1%), and soluble sugars (20.9%) on a dry basis with an average moisture content of 34.7%. Food waste samples were also assessed for their potential production of 2,3-BDO during non-sterile thermophilic fermentation, resulting in a max titer of 12.12 g/L and a 33% g/g yield of 2,3-BDO/carbohydrates. These findings are promising and can lead to the better understanding of food waste as a defined feedstock for 2,3-BDO and other fermentation end-products.
  • Systematic literature review identifying bacterial constituents in the core intestinal microbiome of rainbow trout (Oncorhynchus mykiss)
    Hines, Ian S.; Marshall, Maggie A.; Smith, Stephen A.; Kuhn, David D.; Stevens, Ann M. (Wiley, 2023-08-11)
    Fish aquaculture has become the fastest growing sector in global food production. Thus, ensuring the sustainability of aquaculture practices is of the utmost importance. Studies in higher vertebrates (i.e. mammals) have demonstrated the role of the host microbiome in physiological processes from nutrient acquisition to pathogen protection. Therefore, analysis of fish microbiomes is an important factor to consider with regard to overall animal health and welfare. Rainbow trout (Oncorhynchus mykiss) are an economically valued fish cultured worldwide. Several studies have identified microbial constituents inhabiting the intestinal tract of rainbow trout. To better elucidate some of the core constituents of the rainbow trout intestinal microbiome, this systematic literature review analysed the relative abundance results from 25 articles published on the rainbow trout intestinal microbiome from 2017 to 2021. Bacteria classified within the phyla Firmicutes and Proteobacteria were observed in every study. At the family level, Lactobacillaceae was consistently observed. Additionally, bacteria in the Actinobacteria, Bacteroides, and Tenericutes phyla were identified in at least 50% of the studies. Interestingly, Mycoplasma spp. were occasionally the most dominant organisms present in the microbiome. Overall, the results here identify bacteria that are commonly found members of the rainbow trout intestinal microbiome.
  • Revitalizing the Future of Food Safety Extension
    Arnold, Nicole L.; Schonberger, H. Lester; Ferelli, Angela; Murphy, Sarah I.; Yang, Lily L. (International Association for Food Protection, 2022-05-02)
    Originally established to address agricultural needs by applying research and education in U.S. communities, the Cooperative Extension System (CES) has become increasingly involved in food safety through the supply chain. CES plays an integral role in food safety through consumer education, food employee training, regulatory guidance, and agricultural education for youth and students. CES food safety efforts have evolved to respond to current events and evolving public needs; subsequently, CES personnel communicated a myriad of challenges, including overextension within their roles, dwindling financial support, and pedagogical shifts. As a result, CES personnel have opted for creative, innovative, and timely solutions that can be harnessed by others with ties to CES. This article is based on a roundtable with Extension experts on “Revitalizing the Future of Food Safety Extension,” held at the 2019 International Association for Food Protection Annual Meeting detailing this imperative. This article serves as (i) a consolidated framework resource for educational purposes, (ii) an invitation to collaborate with food safety CES personnel, and (iii) a call for support and advocacy for CES and those within it. It also highlights the value and impact CES has, and will continue to have, in making food safer and more equitable.
  • The Impact of Marine Resource-Free Diets on Quality Attributes of Atlantic Salmon
    McLean, Ewen; Campbell, Kelly B.; Kuhn, David D.; Tlusty, Michael F.; Barrows, Frederick T. (MDPI, 2024-01-17)
    The influence of feeding Atlantic salmon for 90 days on diets that excluded fishmeal (FM) and fish oil (FO) was examined for influence on various quality traits. In addition, the effect of adding krill meal (KM; 0%, 2.5%, and 5%), as a putative feed palatant was also examined. Total replacement of FM/FO had a limited effect on production characteristics, affecting percentage yields of headed and gutted control fish and their standard length (p < 0.05). Variances between dietary groups were observed for pigmentation, and plant protein-based KM-free-fed fish returned deeper hues across their belly, NQC (Norwegian Quality Cut), and back portions (p < 0.03). No differences were measured for relative fin condition. δ13C and δ15N concentrations were lower and higher, respectively (p < 0.05) for fish fed the FM/FO-based diet. δ13C:δ15N likewise differed between treatments with FM/FO-fed salmon expressing higher ratios. Fillet mechanical characteristics varied with fish fed on animal protein-based diets, without KM expressing higher springiness and resilience (p < 0.05). Fish fed plant-based diets were generally preferred by younger taste testers. The results from this trial illustrate that FM/FO can be completely removed from salmon diets without problematic effects on quality and palatability attributes.
  • Quantitative texture analysis comparison of three legumes
    Miller, Rebekah; Duncan, Susan; Yin, Yun; Zhang, Bo; Lahne, Jacob (Frontiers, 2023-06-19)
    A validated texture-analysis method to evaluate product quality in frozen or cooked legumes is needed to support high-quality vegetable production but is not currently established in the literature. Peas, lima beans, and edamame were investigated in this study due to similar market use as well as growth in plant-based protein consumption in the United States. These three legumes were evaluated after three different processing treatments (blanch/freeze/thaw (BFT); BFT+microwave heat (BFT+M); BF+stove-top cooking (BF+C)), using both compression and puncture analysis following an American Society of Agricultural and Biological Engineers (ASABE) texture analysis method and moisture testing following an American Society for Testing and Materials (ASTM) standard method. Texture analysis results showed differences between legumes and processing methods. Compression analysis identified more differences between treatments within product type than puncture for both edamame and lima beans indicating compression might be more sensitive to texture changes in these products. Implementation of a standard texture method for legume vegetables for growers and producers would provide a consistent quality check to support efficient production of high-quality legumes. Due to the sensitivity obtained from the compression texture method in this work, compression should be considered for future research into a robust method to evaluate edamame and lima bean textures throughout the growing and production processes.
  • Analyzing larger sample sets with rapid methods: Incomplete-block designs with free-sorting and free-linking tasks
    Ac-Pangan, Marlon; Tejedor-Romero, Marino; Swatko, Kyra; Orden, David; Lahne, Jacob (Elsevier, 2024-04)
    As rapid, holistic methods for similarity and description—such as sorting and projective mapping—have grown in popularity, a limiting factor is the number of samples that can be presented to subjects: more than 25 food samples decreases the quality and stability of results. While incomplete-block designs could address this, their use has not been developed for these holistic methods. In this paper we present an empirical investigation into the use of incomplete-block designs with free sorting and the newer free linking. We compare these two methods because while their results are comparable, the cognitive tasks are different, and thus their suitability for incomplete-block designs may differ. We evaluated the effects of incomplete-block designs in two studies. In Study 1, 20 subjects evaluated 6/10 chocolate bars by free linking in an incomplete-block design, with each subject completing 2 blocks; results were compared to a complete-block evaluation of the 10 bars by free sorting and free linking. In Study 2, a total of 90 subjects evaluated 62 terms from a chocolate flavor-wheel in 3 conditions (between subjects): free sorting with complete blocks (N = 30, all 62 terms) and free sorting (N = 30) or free linking (N = 30) with 3 incomplete blocks of 16/62 terms. We introduce a novel method to evaluate stability for the incomplete-block designs that we call “pairwise simulation.” From Study 1, we find that pairwise simulation provides adequate stability estimates and that, with sufficient pairwise cooccurrences, free linking with incomplete blocks produces results that are comparable to free sorting or linking with complete blocks. From Study 2, we demonstrate that free linking with incomplete blocks can produce high quality results from a large sample set, maintaining the increased discrimination capacity that marks free linking in general, and that with incomplete blocks, free linking is likely to be more stable than free sorting. This research demonstrates that incomplete-block designs can be used with free linking, and also provides a new, effective method through pairwise simulation for evaluating stability with incomplete-block designs, which cannot be resampled using standard bootstrapping approaches.
  • “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.