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Chlorine and its derivatives have been used as an antibacterial agent to reduce Salmonella contamination in poultry meat during processing. We evaluated the survival of 4 different Salmonella serotypes (Typhimurium, Enteritidis, Heidelberg, and Gaminara) in the presence of 50 ppm sodium hypochlorite (NaOCl) alone or with the addition of thiourea (radical scavenger) or Dip (iron chelator) to determine the contribution of reactive oxygen species (ROS) in the bactericidal activity of NaOCl. The result showed that for all four serotypes the addition of thiourea or Dip significantly increased the % survival as compared to the respective NaOCl treatment groups, while it was significantly higher with thiourea as compared to Dip (P < 0.05). We also evaluated the survival of 11 deletion mutants of S. Typhimurium, which were demonstrated to increase (∆atpC, ∆cyoA, ∆gnd, ∆nuoG, ∆pta, ∆sdhC, and ∆zwf) or decrease the production of ROS (∆edd, ∆fumB, ∆pykA, and ∆tktB) in Escherichia coli (E. coli), in the presence of 50 ppm. The results showed that only two (∆sdhC and ∆zwf) out of 7 ROS-increasing mutants showed reduced % survival as compared to the wild-type (P < 0.05), while all four deletion ROS-decreasing mutants showed significantly higher % survival as compared to the wild-type (P < 0.05). This work suggests that the production of ROS is a major component of the bactericidal activity of NaOCl against Salmonella serotypes and there might be a significant difference in the metabolic pathways involved in ROS production between Salmonella and E. coli. [ABSTRACT FROM AUTHOR]

Feed additives that can modulate the poultry gastrointestinal tract and provide benefit to bird performance and health have recently received more interest for commercial applications. Such feed supplements offer an economic advantage because they may directly benefit poultry producers by either decreasing mortality rates of farm animals, increasing bird growth rates, or improve feed efficieny. They can also limit foodborne pathogen establishment in bird flocks by modifying the gastrointestinal microbial population. Prebiotics are known as non-digestible carbohydrates that selectively stimulate the growth of beneficial bacteria, thus improving the overall health of the host. Once prebiotics are introduced to the host, 2 major modes of action can potentially occur. Initially, the corresponding prebiotic reaches the intestine of the chicken without being digested in the upper part of the gastrointestinal tract but are selectively utilized by certain bacteria considered beneficial to the host. Secondly, other gut activities occur due to the presence of the prebiotic, including generation of short-chain fatty acids and lactic acid as microbial fermentation products, a decreased rate of pathogen colonization, and potential bird health benefits. In the current review, the effect of prebiotics on the gastrointestinal tract microbiome will be discussed as well as future directions for further research. [ABSTRACT FROM AUTHOR]

Alternative poultry production systems consisting of free-range or pasture flock raised poultry continues to increase in popularity. Based on the perceived benefits of poultry products generated from these alternative poultry production systems, they have commercial appeal to consumers. Several factors impact the health and well being of birds raised and maintained in these types of production systems. Exposure to foodborne pathogens and potential for colonization in the gastrointestinal tract has to be considered with these types of production systems. The gastrointestinal tract microbial composition and function of birds grown and maintained in alternative poultry operations may differ depending on diets, breed, and age of bird. Dietary variety and foraging behavior are potential influential factors on bird nutrition. The gastrointestinal tract microbiomes of birds raised under alternative poultry production systems are now being characterized with next-generation sequencing to identify individual microbial members and assess the impact of different factors on the diversity of microbial populations. In this review, the gastrointestinal tract microbiota contributions to free-range or pasture-raised broiler and egg layer production systems, subsequent applications, and potential future directions will be discussed. [ABSTRACT FROM AUTHOR]

Cross-contamination can be broadly defined as the transfer, direct or indirect, of microorganisms from a contaminated product to a non-contaminated product. Events that may result in cross-contamination include inadequate hygiene practices, contaminated equipment surfaces, contamination via food handling personnel, further product processing, or storage abuse All of these niches require consistent environmental surveillance systems to monitor microbial harborage sites to prevent foodborne illnesses via cross-contamination. Environmental surveillance is achieved through routine surface sampling of the food contact surfaces and surrounding areas. To better understand cross-contamination, the role of environmental surface transmission during outbreaks due to the presence and persistence of pathogenic microorganisms on various food contact surfaces must be investigated. However, studies on environmental sampling techniques are rarely performed in an actual food processing environment but rather under controlled variables within a laboratory-setting. Moreover, results and conclusions of studies differ because of the considerable variability across surface sampling tools due to individual operator dependency, low recovery rates, and low reproducibility. Information is also often lacking on environmental sampling tools used within a processing facility, the characterization of these tools, and the optimization of recovery of microorganisms for surface sampling. Thus, this review aims to: (1) discuss and compare factors impacting the recovery of microorganisms and the standardization of surface sampling methods for optimal recovery of microorganisms and (2) examine how research strategies could focus more towards the development of standard methodologies for surface sampling. [ABSTRACT FROM AUTHOR]

Studies have shown that the production of reactive oxygen species (ROS) is triggered by bactericidal antibiotics, which contributes significantly to the killing of bacterial cells and increasing mutations in surviving cells. In this study, we hypothesized that exposure of Salmonella to sublethal concentrations of hypochlorite (NaOCl), a commonly used sanitizer in household and food industries increases mutation rates, leading to the development of antibiotic resistance. We found that a sublethal concentration (20 ppm) of NaOCl increased the mutation rates of S. typhimurium 14028s significantly (p < 0.05), which was prevented by the ROS scavenger thiourea, supporting that the increased mutation was due to NaOCl-triggered ROS production. We further found that the exposure of S. typhimurium 14028s to the same sublethal concentration of NaOCl increases resistance to kanamycin among the 3 antibiotics evaluated. The results of this study suggest that when NaOCl applied as a sanitizer fails to kill Salmonella due to diluted local concentrations or presence of organic materials, it can cause an adverse outcome of developing antibiotic resistance of the pathogen. [ABSTRACT FROM AUTHOR]

Environmental methane production continues to be an ongoing global concern and interest is growing to reduce total methane production. As a part of this collective effort mitigation of methane production in ruminants has become one of the targets for ongoing research. Several strategies have emerged including dietary manipulation, administration of unique feed additives that specifically target methanogens, and host animal modulation approaches. Most of these efforts have focused on the rumen methanogen population and understanding their ecology in relationship to the non-methanogen microbial population. However, there is potential for methane production in the hindgut of the ruminant animal, and this should be considered in any overall strategy for mitigation of methane production in ruminants. The emphasis of this presentation is to discuss the current knowledge and future prospects for understanding the contribution of hindgut methanogens to overall ruminant methane production and their potential for contribution to mitigation of ruminant methane production. [ABSTRACT FROM AUTHOR]

Cookie dough is recognized as a potential vehicle of Salmonella due to common use of raw eggs as an ingredient. As seen in the E . coli O157:H7 outbreak in 2009, which was associated with commercial pre-packaged cookie dough, this product also can serve as a novel vehicle for transmission of pathogens. Additionally, many ingredients of cookie dough including flour, eggs, chocolate and peanut butter have also been associated with foodborne illness outbreaks, and therefore the potential of cookie dough carrying microbiological hazards is relatively high. Government agencies and food manufacturers warn against the consumption of cookie dough due to the potential hazards associated with it, but it was reported that young adults in the United States frequently consume cookie dough. In this review, an updated overview of food safety risks associated with each ingredient of cookie dough with main focus on microbiological hazards is provided. Additionally, intrinsic characteristics of cookie dough and their effect on food safety are also addressed in this review. [ABSTRACT FROM AUTHOR]

Eggs contaminated with Salmonella have been internationally significant sources of human illness for several decades. Most egg-associated illness has been attributed to Salmonella serovar Enteritidis, but a few other serovars (notably S. Heidelberg and S. Typhimurium) are also sometimes implicated. The edible interior contents of eggs typically become contaminated with S. Enteritidis because the pathogen's unique virulence attributes enable it to colonize reproductive tissues in systemically infected laying hens. Other serovars are more commonly associated with surface contamination of eggshells. Both research and field experience have demonstrated that the most effective overall Salmonella control strategy in commercial laying flocks is the application of multiple interventions throughout the egg production cycle. At the preharvest (egg production) level, intervention options of demonstrated efficacy include vaccination and gastrointestinal colonization control via treatments such as prebiotics, probiotics, and bacteriophages, Effective environmental management of housing systems used for commercial laying flocks is also essential for minimizing opportunities for the introduction, transmission, and persistence of Salmonella in laying flocks. At the postharvest (egg processing and handling) level, careful regulation of egg storage temperatures is critical for limiting Salmonella multiplication inside the interior contents. [ABSTRACT FROM AUTHOR]

Campylobacter growth kinetic parameters can be used to refine the sensitivity and efficiency of microbial growth-based methods. Therefore, the aim of this study was to construct growth curves for C. jejuni, C. coli, and C. lari in pure culture and calculate growth kinetics for each Campylobacter species in the same environmental conditions. Campylobacter jejuni, C. coli and C. lari were grown over 48 h and inoculated into 15 mL Hungate tubes (N = 3 trials per species; 5 biological replicates per trial; 3 species; 1 strain per species). Absorbance measurements were taken in 45 min intervals over 24 h. Optical density readings were plotted versus time to calculate growth kinetic parameters. C. jejuni exhibited the longest lag phase (p < 0.001) at 15 h 20 min ± 30 min, versus C. coli at 11 h 15 min ± 17 min, and C. lari at 9 h 27 min ± 15 min. The exponential phase duration was no longer than 5 h for all species, and doubling times were all less than 1h 30 min. The variation in growth kinetics for the three species of Campylobacter illustrates the importance of determining individual Campylobacter spp. growth responses for optimizing detection based on low bacterial levels. This study provides kinetics and estimates to define enrichment times necessary for low concentration Campylobacter detection. [ABSTRACT FROM AUTHOR]

In this review, the molecular techniques used in animal-based-methanogen studies will be discussed along with how methanogens interact not only with other microorganisms but with their animal hosts as well. These methods not only indicate the diversity and levels of methanogens, but also provide insight on their ecological functions. Most molecular techniques have been based on either 16S rRNA genes or methyl-coenzyme M reductase, a ubiquitous enzyme in methanogens. The most predominant methanogens in animals belong to the genus Methanobrevibacter. Besides methanogens contributing to overall H2 balance, methanogens also have mutual interactions with other bacteria. In addition to shared metabolic synergism, the host animal retrieves additional energy from the diet when methanogens are co-colonized with other normal flora. By comparing genes in methanogens with other bacteria, possible gene transfer between methanogens and other bacteria in the same environments appears to occur. Finally, diets in conjunction with the genetics of methanogens and hosts may represent the biological framework that dictate the extent of methanogen prevalence in these ecosystems. In addition, host evolution including the immune system could serve as an additional selective pressure for methanogen colonization. [ABSTRACT FROM AUTHOR]

Salmonellosis in the United States is one of the most costly foodborne diseases. Given that Sal-monella can originate from a wide variety of environ-ments, reduction of this organism at all stages of poultry production is critical. Salmonella species can encounter various environmental stress conditions that can dra-matically influence their survival and virulence. Previ-ous knowledge of Salmonella species genomic regulation of metabolism and physiology in relation to poultry is based on limited information of a few well-character-ized genes. Consequently, although there is some infor-mation about environmental signals that control Sal-monella growth and pathogenesis, much still remains unknown. Advancements in DNA sequencing technolo-gies revolutionized the way bacteria were studied and molecular tools such as microarrays have subsequently been used for comprehensive transcriptomic analysis of Salmonella. With microarray analysis, the expression levels of each single gene in the Salmonella genome can be directly assessed and previously unknown genetic systems that are required for Salmonella growth and survival in the poultry production cycle can be eluci-dated. This represents an opportunity for development of novel approaches for limiting Salmonella establish-ment in all phases of poultry production. In this review, recent advances in transcriptome-microarray technolo-gies that are facilitating a better understanding of Sal-monella biology in poultry production and processing are discussed. [ABSTRACT FROM AUTHOR]

Abstract: During the most recent decades increased interest in fuel from biomass in the United States and worldwide has emerged each time petroleum derived gasoline registered well publicized spikes in price. The willingness of the U.S. government to face the issues of more heavily high-priced foreign oil and climate change has led to more investment on plant-derived sustainable biofuel sources. Biomass derived from corn has become one of the primary feedstocks for bioethanol production for the past several years in the U.S. However, the argument of whether to use food as biofuel has led to a search for alternative non-food sources. Consequently, industrial research efforts have become more focused on low-cost large-scale processes for lignocellulosic feedstocks originating mainly from agricultural and forest residues along with herbaceous materials and municipal wastes. Although cellulosic-derived biofuel is a promising technology, there are some obstacles that interfere with bioconversion processes reaching optimal performance associated with minimal capital investment. This review summarizes current approaches on lignocellulosic-derived biofuel bioconversion and provides an overview on the major steps involved in cellulosic-based bioethanol processes and potential issues challenging these operations. Possible solutions and recoveries that could improve bioprocessing are also addressed. This includes the development of genetically engineered strains and emerging pretreatment technologies that might be more efficient and economically feasible. Future prospects toward achieving better biofuel operational performance via systems approaches such as risk and life cycle assessment modeling are also discussed. [Copyright &y& Elsevier]

Abstract: In recent years bioethanol has encompassed worldwide interest as a non-conventional bioenergy source. This fact has driven several bioethanol industries to produce more ethanol on a large scale via cost effective methods. However in the process of scaling up ethanol production bacterial contamination is becoming one of the more challenging problems facing the bioethanol industry. There are several traditional microbiological methods available to detect and subsequently limit these bacterial contaminants. These methods are time consuming, laborious and can be less sensitive. Consequently, it is necessary to find novel sensitive and economic detection methods to eradicate the contaminants long before they disrupt ethanol production. Molecular methods that can detect the contaminants even at very low numbers at any given stage would help in the design of more cost effective eradication strategies and better targeted antimicrobial treatments. Application of rapid molecular detection approaches have the potential to provide much more sensitive and rapid means to not only detect but quantitate microbial contaminants long before they become problematic to overall bioethanol formation. [Copyright &y& Elsevier]

The use of "omics" has become widespread across poultry production, from breeding to management to bird health to food safety and everywhere in between. While the conventional poultry industry has become more exposed to the power and utility of "omic" technologies, smaller poultry flock producers typically do not have this same level of experience. Because smaller, nonconventional poultry production is a growing portion of the overall poultry market, it is important that they also have educational access to these research tools and the resultant data. While small flock producers are dedicated and knowledgeable farmers, their knowledge of these newer technologies may be limited at best, and it is the task of academic researchers to communicate the importance of these "omic" tools and how the omic data can improve a variety of different aspects of their operations. This review discusses ways to effectively communicate complex microbiota and microbial genome sequence data to small flock producers and transforming this data into meaningful and applicable information that they can utilize to inform beneficial management decisions. [ABSTRACT FROM AUTHOR]

Poultry processing is undergoing changes both in operations as well as microbial methodologies. Traditionally, microbial data has been gathered through a series of culturing methods using liquid media and plating for isolation and enumeration. Both foodborne pathogens and nonpathogenic bacterial populations are estimated to assess food safety risks as well as the potential for spoilage. Bacterial loads from carcasses are important for estimating processing control and the effectiveness of antimicrobial applications. However, these culture-based approaches may only provide part of the microbial ecology landscape associated with chicken carcasses and the subsequent changes that occur in these populations during processing. Newer molecular-based approaches, such as 16S sequencing of the microbiota, offer a means to retrieve a more comprehensive microbial compositional profile. However, such approaches also result in large data sets which must be analyzed and interpreted. As more data is generated, this will require not only bioinformatic programs to process the data but appropriate educational forums to present the processed data to a broad audience. [ABSTRACT FROM AUTHOR]

Management of laying hens has undergone considerable changes in the commercial egg industry. Shifting commercial production from cage-based systems to cage-free has impacted the housing environment and created issues not previously encountered. Sources of microorganisms that become established in the early stages of layer chick development may originate from the hen and depend on the microbial ecology of the reproductive tract. Development of the layer hen GIT microbiota appears to occur in stages as the bird matures. Several factors can impact the development of the layer hen GIT, including pathogens, environment, and feed additives such as antibiotics. In this review, the current status of the laying hen GIT microbial consortia and factors that impact the development and function of these respective microbial populations will be discussed, as well as future research directions. [ABSTRACT FROM AUTHOR]

Global population increases, coupled with intensive animal and livestock production practices, have resulted in the generation, accumulation, and disposal of large amounts of wastes around the world. Aerosolization of microbial pathogens, endotoxins, odors, and dust particles is an inevitable consequence of the generation and handling of waste material. Bioaerosols can be a source of microbial pathogens, endotoxins, and other allergens. Given the close proximity of population centers to concentrated animal-rearing operations and municipal treatment facilities in many parts of the world, there is concern regarding the occupational and public health impacts associated with the exposure to bioaerosols from municipal and animal wastes. Major advances have been made in our understanding of bioaerosol characteristics, identifying the hazards, and identifying possible human and animal health links with aerosolized pathogens and allergens. However, significant knowledge and technology gaps still exist. These include a lack of clear understanding of the fate and transport of bioaerosols, especially within the open environment, an inability to accurately predict the health risks associated with bioaerosolized pathogens, and a lack of standardized bioaerosol sampling protocols, and efficient samplers. This review synthesizes the information related to bioaerosols and addresses the contemporary issues associated with bioaerosols from municipal and animal wastes, with a focus on pathogens.Key words: bioaerosols, pathogens, biosolids, animal wastes, health risks.Les pratiques d'élevage massif d`animaux et de bétail et l'augmentation de la population ont eu plusieurs conséquences au niveau mondial comme la production, l'accumulation et le rejet des quantités importantes de déchets. La production et la manipulation de ces rebus a des conséquences environnementales inévitables comme la formation d'aérosols microbiens et la dispersion d'endotoxines, d'odeurs et de poussière. La production de bioaérosols peut devenir une source de dissémination de microorganismes pathogènes, d'endotoxines et d'autres allergènes. En tenant compte de la proximité de la population humaine avec des élevages concentrés d'animaux et des procédés de traitement dans plusieurs régions du monde, cela suscite des inquiétudes d'ordre professionnel et de santé publique reliées à l'exposition aux bioaérosols générés par les déchets municipaux et animaux. Des progrès importants ont été accomplis dans la connaissance des propriétés des bioaérosols et cela a permis d'identifier des pathogènes et des allergènes des bioaérosols provenant des animaux et de mieux connaître les risques sur la santé humaine. Par contre nous manquons encore de connaissances significatives et nous sommes confrontés à des problèmes technologiques. Nous ne possédons pas de connaissances précises sur le destin et le transport des bioaérosols spécialement dans un environnement naturel et nous n'avons pas les moyens pour prédire les risques de santé reliés aux bioaérosols pathogènes et nous manquons de protocoles standardisés pour l'échantillonnage des bioaérosols pour obtenir des échantillons significatifs. La présente revue constitue une synthèse de l'information reliée aux bioaérosols et présente les inquiétudes actuelles des conséquences des microorganismes pathogènes des bioaérosols générés par les déchets municipaux et animaux. Mots clés : bioaérosols, pathogènes, biosolides, déchets animaux, risques pour la santé.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

Non typhoidal Salmonella spp. are among the leading causes of foodborne illness in the U.S. Some 20% of foodborne illnesses attributed to Salmonella can be associated with poultry and poultry products. Industry efforts to lower the incidence of Salmonella have been successful, but the number of illnesses from contaminated poultry has not seen a concomitant drop. In this review, the historical background of Salmonella assessment in poultry at the processing plant will be presented along with the problems inherent with current methods. In addition, opportunities for improvement via the availability of emerging detection and identification technologies as well as other food safety measures that can be taken such as consumer education. • Non typhoidal Salmonella spp. are a leading cause of foodborne illness in the U.S. • 20% of foodborne illnesses from Salmonella are from poultry and poultry products. • In this review we highlight problems inherent with current methods of detection. • We discuss emerging technologies as well as other food safety measures. [ABSTRACT FROM AUTHOR]

Alternative poultry production systems continue to expand as markets for organic and naturally produced poultry meat and egg products increase. However, these production systems represent challenges associated with variable environmental conditions and exposure to foodborne pathogens. Consequently, there is a need to introduce feed additives that can support bird health and performance. There are several candidate feed additives with potential applications in alternative poultry production systems. Prebiotic compounds selectively stimulate the growth of beneficial gastrointestinal microorganisms leading to improved health of the host and limiting the establishment of foodborne pathogens. The shift in the gastrointestinal microbiota and modulation of fermentation can inhibit the establishment of foodborne pathogens such as Campylobacter and Salmonella. Both current and potential applications of prebiotics in alternative poultry production systems will be discussed in this review. Different sources and types of prebiotics that could be developed for alternative poultry production will also be explored. [ABSTRACT FROM AUTHOR]

Humans and animals encounter a summation of exposures during their lifetime (the exposome). In recent years, the scope of the exposome has begun to include microplastics. Microplastics (MPs) have increasingly been found in locations, including in animal gastrointestinal tracts, where there could be an interaction with Salmonella enterica serovar Typhimurium, one of the commonly isolated serovars from processed chicken. However, there is limited knowledge on how gut microbiomes are affected by microplastics and if an effect would be exacerbated by the presence of a pathogen. In this study, we aimed to determine if acute exposure to microplastics in vitro altered the gut microbiome membership and activity. The microbiota response to a 24 h co-exposure to Salmonella enterica serovar Typhimurium and/or low-density polyethylene (PE) microplastics in an in vitro broiler cecal model was determined using 16S rRNA amplicon sequencing (Illumina) and untargeted metabolomics. Community sequencing results indicated that PE fiber with and without S. Typhimurium yielded a lower Firmicutes/Bacteroides ratio compared with other treatment groups, which is associated with poor gut health, and overall had greater changes to the cecal microbial community composition. However, changes in the total metabolome were primarily driven by the presence of S. Typhimurium. Additionally, the co-exposure to PE fiber and S. Typhimurium caused greater cecal microbial community and metabolome changes than either exposure alone. Our results indicate that polymer shape is an important factor in effects resulting from exposure. It also demonstrates that microplastic-pathogen interactions cause metabolic alterations to the chicken cecal microbiome in an in vitro chicken cecal mesocosm. [ABSTRACT FROM AUTHOR]

There is limited research concerning the biofilm-forming capabilities of Salmonella Kentucky, a common poultry isolate. The objective was to quantitate pellicle formation of S. Kentucky versus better-characterized Salmonella strains of Enteritidis and Heidelberg. In separate experiments, Salmonella strains and serovars were tested for their biofilm-forming abilities in different Luria-Bertani (LB) broths (1); pellicle formation in different volumes of LB without salt (2); and the potential priming effects on formation after pellicles were transferred three consecutive times (3). Data were analyzed using One-Way ANOVA with means separated using Tukey's HSD (P ≤ 0.05). In the first experiment, there was no significant effect between strain and serovars (P > 0.05), but media type affected pellicle formation significantly with LB Miller and LB minus NaCl plus 2% glucose resulting in no pellicle formation (P < 0.001). When grown in 50 mL, Kentucky 38-0085 produced larger pellicles than Kentucky 38-0055, and Heidelberg strain 38-0127 (P < 0.0001). Serial transfers of pellicles did not significantly affect pellicle formation (P > 0.05); however, Kentucky 38-0084, 38-0085 and 38-0086 produced larger pellicles than Kentucky 38-0055 and 38-0056 and Heidelberg 38-0126, 38-0127 and 38-0152. The current study demonstrates the consistent biofilm forming capabilities of Kentucky and may explain why Kentucky is frequently isolated in poultry processing facilities. [ABSTRACT FROM AUTHOR]

Aim This study aimed to assess the suitability of two media types, Bolton enrichment broth (BEB) and anaerobic dilution solution (ADS), in replicating the poultry cecal environment to investigate metabolic interactions and Campylobacter presence within poultry ceca. Methods Using an anaerobic in vitro poultry cecal model, cecal contents (free of culturable Campylobacter) were diluted in BEB and ADS, inoculated with 105 CFU of Campylobacter jejuni , and incubated for 48 h at 42°C under microaerophilic conditions. Samples were collected at 0, 24, and 48 h. Genomic DNA was extracted, amplified, and sequenced on Illumina MiSeq platform. Data underwent analysis within QIIME2-2021.11, including alpha and beta diversity assessments, ANOVA, ADONIS, ANCOM, and Bradford assay for protein concentration. Results ADS supported a more diverse microbial population than BEB, influencing C. jejuni presence. ANCOM highlighted dominant genera in BEB (Lactobacillus and Campylobacter) and affirmed C. jejuni growth in ADS. Core microbiota analysis revealed unique associations with each media type, while the Bradford assay indicated ADS consistently yielded more uniform microbial growth. Conclusions ADS was identified as a preferred diluent for faithfully replicating cecal microbial changes in the presence of Campylobacter. [ABSTRACT FROM AUTHOR]

To provide the poultry industry with effective mitigation strategies, the effects of cetylpyridinium chloride (CPC) on the reduction of Salmonella Infantis, hilA expression, and chicken skin microbiota were evaluated. Chicken breast skins (4×4 cm; N = 100, n = 10, k = 5) were inoculated with Salmonella (Typhimurium or Infantis) at 4°C (30min) to obtain 108 CFU/g attachment. Skins were shaken (30s), with remaining bacteria being considered firmly attached. Treatments were applied as 30s dips in 50 mL: no inocula-no-treatment control (NINTC), no treatment control (NTC), tap water (TW), TW+600 ppm PAA (PAA), or TW+0.5% CPC (CPC). Excess fluid was shaken off (30s). Samples were homogenized in nBPW (1 min). Samples were discarded. Salmonella was enumerated and Log10 transformed. Reverse transcriptase-qPCR (rt-qPCR) was performed targeting hilA gene and normalized using the 2-ΔΔCt method. Data were analyzed using one-way ANOVA in RStudio with means separated by Tukey's HSD (P≤0.05). Genomic DNA of rinsates was extracted, 16S rRNA gene (V4) was sequenced (MiSeq), and data analyzed in QIIME2 (P≤0.05 and Q≤0.05). CPC and PAA affected Salmonella levels differently with CPC being effective against S. Infantis compared to TW (P<0.05). Treatment with CPC on S. Infantis-infected skin altered the hilA expression compared to TW (P<0.05). When inoculated with S. Typhimurium, there was no difference between the microbiota diversity of skins treated with PAA and CPC; however, when inoculated with S. Infantis, there was a difference in the Shannon's Entropy and Jaccard Dissimilarity between the two treatments (P<0.05). Using ANCOM at the genus level, Brochothrix was significant (W = 118) among skin inoculated with S. Typhimurium. Among S. Infantis inoculated, Yersiniaceae, Enterobacterales, Lachnospiraceae CHKCI001, Clostridia vadinBB60 group, Leuconostoc, Campylobacter, and bacteria were significant (408). CPC and PAA-treated skins had lowest relative abundance of the genera. In conclusion, CPC mitigated Salmonella Infantis, altered hilA expression, and influenced the chicken skin microbiota. [ABSTRACT FROM AUTHOR]

One of the leading causes of foodborne illness in poultry products isSalmonella enterica.Salmonellahazards in poultry may be estimated and possible control methods modeled and evaluated through the use of quantitative microbiological risk assessment (QMRA) models and tools. From farm to table, there are many possible routes ofSalmonelladissemination and contamination in poultry. From the time chicks are hatched through growth, transportation, processing, storage, preparation, and finally consumption, the product could be contaminated through exposure to different materials and sources. Examination of each step of the process is necessary as well as an examination of the overall picture to create effective countermeasures against contamination and prevent disease. QMRA simulation models can use either point estimates or probability distributions to examine variables such asSalmonellaconcentrations at retail or at any given point of processing to gain insight on the chance of illness due toSalmonellaingestion. For modelingSalmonellarisk in poultry, it is important to look at variables such asSalmonellatransfer and cross contamination during processing. QMRA results may be useful for the identification and control of critical sources ofSalmonellacontamination. [ABSTRACT FROM AUTHOR]

Simple Summary: Necrotic enteritis, a secondary gastrointestinal (GIT) infection in poultry, is a costly burden to the commercialized poultry industry, impacting the welfare of broiler chickens as well as production gains. Many feed supplements have been proposed to alleviate the burden of necrotic enteritis in poultry with varied success. A promising supplement, a microencapsulated blend of organic acids and botanicals, has been demonstrated to modulate the immune system and the gastrointestinal microbial ecology in healthy birds. Therefore, we aimed to test this supplement in the feed of broiler breeder chickens infected with necrotic enteritis. To determine if the supplement improved the microbial ecology of the GIT, where necrotic enteritis resides, the GIT microbiota were elucidated using microbiome sequencing. There were minimal differences in the microbiota diversity; however, the core microorganisms of birds fed the supplement consisted of Lactobacillus and Clostridiaceae. The supplemented-fed birds also had a higher abundance of normal microbiome inhabitants, namely, Actinobacteriota, Bacteroidota, and Verrucomicrobiota, than those not fed the supplement. Therefore, the supplementation of a microencapsulated blend supported beneficial and core microorganisms, potentially improving the bird's response to NE. Previously, the supplementation of a microencapsulated blend of organic acids and botanicals improved the health and performance of broiler breeders under non-challenged conditions. This study aimed to determine if the microencapsulated blend impacted dysbiosis and necrotic enteritis (NE) in broiler breeders. Day-of-hatch chicks were assigned to non-challenge and challenge groups, provided a basal diet supplemented with 0 or 500 g/MT of the blend, and subjected to a laboratory model for NE. On d 20–21, jejunum/ileum content were collected for microbiome sequencing (n = 10; V4 region of 16S rRNA gene). The experiment was repeated (n = 3), and data were analyzed in QIIME2 and R. Alpha and beta diversity, core microbiome, and compositional differences were determined (significance at p ≤ 0.05; Q ≤ 0.05). There was no difference between richness and evenness of those fed diets containing 0 and 500 g/MT microencapsulated blend, but differences were seen between the non-challenged and challenged groups. Beta diversity of the 0 and 500 g/MT non-challenged groups differed, but no differences existed between the NE-challenged groups. The core microbiome of those fed 500 g/MT similarly consisted of Lactobacillus and Clostridiaceae. Furthermore, challenged birds fed diets containing 500 g/MT had a higher abundance of significantly different phyla, namely, Actinobacteriota, Bacteroidota, and Verrucomicrobiota, than the 0 g/MT challenged group. Dietary supplementation of a microencapsulated blend shifted the microbiome by supporting beneficial and core taxa. [ABSTRACT FROM AUTHOR]

Listeria monocytogenes is known to be an important foodborne pathogen and is the causative agent of one of the deadliest foodborne illnesses. The organism has a wide range of environmental conditions under which it will survive and grow, and often contaminates processing plants and retail environments in which ready-to-eat foods are manufactured, prepared and served. Although L. monocytogenes is not a fastidious organism and can grow in a variety of rich media, defined and minimal media are necessary to elucidate the minimal environmental nutrients that are required for the survival and growth of this organism. In addition, many of the virulence factors required for L. monocytogenes to invade and multiply in mammalian host cells are not produced in rich media and thus induction of these factors is best studied in a minimal medium. This review covers the historical development of minimal media for Listeria spp. and explores the various factors required for survival and growth of this organism. To the best of our knowledge, this is the first time that these media have been compared side by side. In order to better compare studies using different chemical substrates such as a different carbon source, all concentrations of components in each medium have been converted to molar concentrations. [ABSTRACT FROM AUTHOR]

Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs) and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens. The purpose of this study was to evaluate the difference in microbial populations from naked neck chicken ceca fed with commercial prebiotics derived from brewer’s yeast cell wall via an Illumina MiSeq platform. A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1) C: control (no prebiotic), 2) T1: Biolex® MB40 with 0.2%, and 3) T2: Leiber® ExCel with 0.2%, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and ceca removed for DNA extraction. The Illumina Miseq platform based on V4 region of 16S rRNA gene was applied for microbiome analysis. Both treatments exhibited limited impact on the microbial populations at the phylum level, with no significant differences in the OTU number of Bacteroidetes among groups and an increase of Proteobacteria OTUs for the T1 (Biolex® MB40) group. In addition there was a significant increase of genus Faecalibacterium OTU, phylum Firmicutes. According to the development of next generation sequencing (NGS), microbiome analysis based on 16S rRNA gene proved to be informative on the prebiotic impact on poultry gut microbiota in pasture-raised naked neck birds. [ABSTRACT FROM AUTHOR]

Prebiotics are defined as nondigestible food ingredients that can stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract. The Biolex R® MB40 is a commercial prebiotic that contains mannanoligosaccharides. The aims of this study were to evaluate the effects of prebiotic Biolex R® MB40 on cecal microbiota of conventionally raised chickens using PCR-based denaturing gradient gel electrophoresis (DGGE) and assessing Salmonella prevalence. Chickens were randomly selected and distributed into three groups; a negative control (NC) and two treatment groups (T1 and T2). The NC group was fed a nonmedicated feed, while the treatment groups were fed either T1 or T2, 0.05% antibiotic (BMD50) or 0.2% Biolex R® MB40 respectively. During the study, cecal contents and bird feed were plated on selective media for Salmonella, yeast and mold prevalence analysis. Ten chickens from each group were randomly selected at 1, 2, 4 and 6 wk and ceca were extracted for DNA isolation for PCR-based DGGE. Also, short-chain fatty acids (SCFAs) were analyzed from collected cecal material by gas chromatography. Only 4.2% of the samples were Salmonella positive. Presence of class 1 integron from cecal material were analyzed by PCR and 97.5% of the cecal samples were positive for integron presence, but no class I integrons were detected in the Salmonella isolates. According to the PCR-based DGGE analysis, the T2 group exhibited a cecal microbial population pattern that was similar to the T1 group prior to wk 4 and the T2 group appeared to be almost identical with the NC group after wk 4 but T2 exhibited less Bacteroides rodentium prior to wk 4. Overall results showed that the commercial prebiotic, MB40 did not lead to a detectable reduction of Salmonella but the general frequency of Salmonella was minimal in all treatments. However, feeding an MB40 supplement did result in similar DGGE band patterns as the T1 group indicating that cecal microbiotia were potentially similar in these 2 groups. Overall, it appears that MB40 (T2) exhibited similar DGGE-cecal population patterns as BMD50 (T1) which suggests that these treatments may have influenced the populations in a comparable fashion. [ABSTRACT FROM AUTHOR]

Dried plums (prunes) have been marketed to consumers for consumption directly from the package as a convenient snack and have been reported to have broad health benefits. Only recently have fractionated, dried plum ingredients been investigated for their functionality in food and feed products. Dried plum puree, dried plum fiber, dried plum powder, dried plum concentrate, and fresh plum concentrate have been investigated to date. They have been evaluated as fat replacers in baked goods, antioxidants in meat formulations, phosphate replacers in chicken marinades, and antimicrobials in food systems. Overall, dried plum products have been shown to be effective at reducing lipid oxidation and show promise as antimicrobials. [ABSTRACT FROM AUTHOR]

Enteric pathogens such as Salmonella enterica cause significant morbidity andmortality. S. enterica serovars are a diverse group of pathogens that have evolved to survive in a wide range of environments and across multiple hosts. S. enterica serovars such as S. Typhi, S. Dublin, and S. Gallinarum have a restricted host range, in which they are typically associated with one or a few host species, while S. Enteritidis and S. Typhimurium have broad host ranges. This review examines how S. enterica has evolved through adaptation to different host environments, especially as related to the chicken host, and continues to be an important human pathogen. Several factors impact host range, and these include the acquisition of genes via horizontal gene transfer with plasmids, transposons, and phages, which can potentially expand host range, and the loss of genes or their function, which would reduce the range of hosts that the organism can infect. S. Gallinarum, with a limited host range, has a large number of pseudogenes in its genome compared to broader-host-range serovars. S. enterica serovars such as S. Kentucky and S. Heidelberg also often have plasmids that may help them colonize poultry more efficiently. The ability to colonize different hosts also involves interactions with the host's immune system and commensal organisms that are present. Thus, the factors that impact the ability of Salmonella to colonize a particular host species, such as chickens, are complex and multifactorial, involving the host, the pathogen, and extrinsic pressures. It is the interplay of these factors which leads to the differences in host ranges that we observe today. [ABSTRACT FROM AUTHOR]

Plant essential oils have previously been shown to exhibit antimicrobial activities against various microorganisms. In this study, cold pressed terpeneless Valencia orange oil (CPTVO) was examined at various temperatures (37, 10, and 4 °C) to determine its antimicrobial activity against 3 strains of E. coli O157:H7 recovered from beef products. A micro broth dilution method using 96 well microtiter plates was used with trypticase soy broth with 0.15% agar and 2,3,5 tetrazolium chloride as a growth indicator as the medium. Serial dilutions of CPTVO were made, resulting in final concentrations of oil ranging from 0.2% to 25% or 0.1% to 10%. Plates were incubated statically at 4, 10, or 37 °C, and sampled hourly. After 6 h at 37 °C, all strains were inhibited at concentrations ranging from 0.2% to 0.6%, with a mean of 0.4 ± 0.01%. At 10 °C, all strains were inhibited at concentrations ranging from 0.8% to 6.3%, with a mean of 1.1%± 0.2%, after 6 h. At 4 °C, all strains were inhibited after 6 h at concentrations ranging from 2.3% to 4.6%, with a mean of 3.5%± 2.1%. After 24 h at 4 °C the strains were inhibited at concentrations ranging from 0.7% to 1% with a mean of 0.8%± 0.3%. The ranges appear to be the result of effects from the variable nature of a complex media and an antimicrobial that presents potential multiple mechanisms for inhibition. It appears CPTVO is a viable option to inhibit E. coli O157:H7 growth at refrigeration temperatures. Practical Application: Beef products are often the source of foodborne illness from the organism E. coli O157:H7. Orange essential oils have been in the human diet for centuries, and the research reported here indicates that some of these oils may be used as surface applications during cold temperatures to inhibit the foodborne pathogen E. coli O157:H7. [ABSTRACT FROM AUTHOR]

Contamination of food contact surfaces with pathogens is considered an important vehicle for the indirect transmission of food-borne diseases. Five different cleaning cloths were assessed for the ability to remove viruses from food contact surfaces (stainless steel surface and nonporous solid surface) and to transfer viruses back to these surfaces. Cleaning cloths evaluated include two different cellulose/cotton cloths, one microfiber cloth, one nonwoven cloth, and one cotton terry bar towel. Four viral surrogates (murine norovirus [MNV], feline calicivirus [FCV], bacteriophages PRD1 and MS2) were included. Removal of FCV from stainless steel was significantly greater (P ≤ 0.05) than that from nonporous solid surface, and overall removal of MNV from both surfaces was significantly less (P ≤ 0.05) than that of FCV and PRD1. Additionally, the terry towel removed significantly fewer total viruses (P ≤ 0.05) than the microfiber and one of the cotton/cellulose cloths. The cleaning cloth experiments were repeated with human norovirus. For transfer of viruses from cloth to surface, both cellulose/cotton cloths and microfiber transferred an average of 3.4 and 8.5 total PFU, respectively, to both surfaces, and the amounts transferred were significantly different (P ≤ 0.05) from those for the nonwoven cloth and terry towel (309 and 331 total PFU, respectively). There was no statistically significant difference (P > 0.05) in the amount of virus transfer between surfaces. These data indicate that while the cleaning cloths assessed here can remove viruses from surfaces, some cloths may also transfer a significant amount of viruses back to food contact surfaces. [ABSTRACT FROM AUTHOR]

Abstract: Bioethanol continues to be offered as a viable solution for complex problems ranging from global warming and national energy security to local economic development. Fuel bioethanol burns cleaner than gasoline, is derived from renewable agricultural products, and creates local jobs and income. In December 2007, President Bush signed into law the Energy Independence and Security Act, which increased the renewable fuel standard that was mandated under energy Policy Act of 2005 to 36 billion gallons by 2022.In order to achieve this goal, ethanol production would need to be generated primarily from corn and cellulosic materials. Bioethanol producers are currently involved in variety of technological innovations to reduce energy consumption and production costs, increased efficiency and reduced emissions using the best available control technologies. However, industrial ethanol fermentation is a non-sterile process and contaminant microorganisms can lead to a decrease in industrial productivity and significant economic loss. Currently, bioethanol industries use different antimicrobials including antibiotics to control the contaminants in the fermentors. The emergence of antibiotic resistance among contaminant bacteria in bioethanol fermentors warrants the need for alternative antimicrobials to retain bioethanol production at a profitable level. In addition more and more ethanol producers are seeking to generate distillers grains that can be labeled antibiotic free to be sold in international markets where some restrictions are already in place for reducing and/or eliminating antibiotics usage in animal feed. This review examines the contamination problems, various intervention methods, emergence of antibiotic resistance in contaminant bacteria, and potential alternative options to elucidate antimicrobial products from various natural sources. In particular, emphasis has been given for natural antibacterial products from plant derived products to suggest a new research avenue for the search of new, non-conventional antimicrobial agents to control the contamination problem in the fuel bioethanol industries. [Copyright &y& Elsevier]

Background: There has been increased interest in the study of molecular survival mechanisms expressed by foodborne pathogens present on food surfaces. Determining genomic responses of these pathogens to antimicrobials is of particular interest since this helps to understand antimicrobial effects at the molecular level. Assessment of bacterial gene expression by transcriptomic analysis in response to these antimicrobials would aid prediction of the phenotypic behavior of the bacteria in the presence of antimicrobials. However, before transcriptional profiling approaches can be implemented routinely, it is important to develop an optimal method to consistently recover pathogens from the food surface and ensure optimal quality RNA so that the corresponding gene expression analysis represents the current response of the organism. Another consideration is to confirm that there is no interference from the "background" food or meat matrix that could mask the bacterial response. Findings: Our study involved developing a food model system using chicken breast meat inoculated with mid-log Salmonella cells. First, we tested the optimum number of Salmonella cells required on the poultry meat in order to extract high quality RNA. This was analyzed by inoculating 10-fold dilutions of Salmonella on the chicken samples followed by RNA extraction. Secondly, we tested the effect of two different bacterial cell recovery solutions namely 0.1% peptone water and RNAprotect (Qiagen Inc.) on the RNA yield and purity. In addition, we compared the efficiency of sonication and bead beater methods to break the cells for RNA extraction. To check chicken nucleic acid interference on downstream Salmonella microarray experiments both chicken and Salmonella cDNA labeled with different fluorescent dyes were mixed together and hybridized on a single Salmonella array. Results of this experiment did not show any cross-hybridization signal from the chicken nucleic acids. In addition, we demonstrated the application of this method in a meat model transcriptional profiling experiment by studying the transcriptomic response of Salmonella inoculated on chicken meat and exposed to d-limonene. We successfully applied our method in this experiment to recover the bacterial cells from the meat matrix and to extract the RNA. We obtained high yield and pure RNA. Subsequently, the RNA was used for downstream transcriptional profiling studies using microarrays and over 600 differentially regulated genes were identified. Conclusions: Our result showed that 8 log cfu/g of Salmonella is ideal to obtain optimal RNA amount and purity. Our results demonstrated that RNAprotect yielded higher RNA amounts (approximately 10 to 30 fold) when compared to 0.1% peptone water. The differences between the RNA-protect and 0.1% peptone samples were significant at a p-value of 0.03 for the bead beater method and 0.0005 for the sonication method, respectively. The microarray experiment demonstrated that the chicken samples do not interfere with the hybridization of Salmonella cDNA on the array slide. Hence, the background chicken RNA will not interfere with the microarray analysis when poultry meat models are used. Finally, we successfully demonstrated the application of the poultry meat model proposed in this study by conducting transcriptional profiling analysis of Salmonella inoculated on the poultry. Results of this study proved that this method has the potential to be employed in other meat model studies. [ABSTRACT FROM AUTHOR]

Post chill whole poultry carcasses from a commercial processing plant were stored in a processing combo at room temperature (70 °F/21 °C) for 54 h to mimic the scenario of temperature abuse before further processing. Temperature data were collected in 1-min intervals and averaged each hour by 9 temperature data loggers. Two linear regressions were developed for the combo and internal breast temperature and slopes were nearly identical. Microbial data was collected by performing whole bird carcass rinses that were enumerated for aerobic plate count (APC), Enterobacteriaceae, Escherichia coli, and total coliform. Samples were collected from the chiller chute at time zero for initial bacterial counts. Carcass sampling continued once the internal breast temperature achieved 45 °F (7 °C 10 h) and continued every 2 h until the final internal breast temperature was 63 °F (17 °C 54 h). Linear regressions were developed for the first 26 h, which exhibited no statistically significant growth except for Enterobacteriaceae. A 2nd linear regression (28 to 54 h) exhibited significant growth for all analyses. Overall, APC increased from a log10 colony forming unit (CFU)/mL count of 2.86 to 7.02, Enterobacteriaceae increased from 0.66 to 6.64, coliform increased from 0.72 to 4.81, and E. coli increased from 0.53 to 4.45. Denaturing gradient gel electrophoresis was performed to detect changes in the bacterial populations, which indicated 95% similarity within sampled groups, but the overall percent similarity among samples collected over 54 h was 8%. From the data, microbial growth demonstrates a period of 26 h for minimal growth; therefore, the product could be further processed rather than designated as waste. [ABSTRACT FROM AUTHOR]

Methionine is an essential amino acid for animals and is typically considered one of the first limiting amino acids in animal feed formulations. Methionine deficiency or excess in animal diets can lead to sub-optimal animal performance and increased environmental pollution, which necessitates its accurate quantification and proper dosage in animal rations. Animal bioassays are the current industry standard to quantify methionine bioavailability. However, animal-based assays are not only time consuming, but expensive and are becoming more scrutinized by governmental regulations. In addition, a variety of artifacts can hinder the variability and time efficacy of these assays. Microbiological assays, which are based on a microbial response to external supplementation of a particular nutrient such as methionine, appear to be attractive potential alternatives to the already established standards. They are rapid and inexpensive in vitro assays which are characterized with relatively accurate and consistent estimation of digestible methionine in feeds and feed ingredients. The current review discusses the potential to develop Escherichia coli-based microbial biosensors for methionine bioavailability quantification. Methionine biosynthesis and regulation pathways are overviewed in relation to genetic manipulation required for the generation of a respective methionine auxotroph that could be practical for a routine bioassay. A prospective utilization of Escherichia coli methionine biosensor would allow for inexpensive and rapid methionine quantification and ultimately enable timely assessment of nutritional profiles of feedstuffs. [ABSTRACT FROM AUTHOR]

Optimal broiler performance is dependent on several factors such as bird genetics, environment management, and nutrition. The gastrointestinal tract microbial ecology and metabolic activities have long been considered factors contributing to broiler performance responses. However, until recently, it was difficult to define the impact of the gastrointestinal microorganisms on the broiler host. With advances in microbiome sequencing technology, there has been a rapid increase in data generated using both experimental and commercial broiler operations. As the gastrointestinal microbiome data becomes more in-depth, opportunities to link microbiota composition to broiler performance metrics such as broiler growth rate and feed conversion efficiency have emerged. In parallel, with the increased understanding of the microbiota, there has been a shift to modulate the microbiome in order to alter metabolic patterns such as fermentation products. In this review, fermentation pathways and metabolites and the relationship with the microbiome will be discussed. Additionally, this review will connect these patterns and interpretations with current broiler performance data and the potential future directions these relationships could take the broiler industry. [ABSTRACT FROM AUTHOR]

Abstract: Streptococcus bovis is an indigenous resident in the gastrointestinal tracts of both humans and animals. S. bovis is one of the major causes of bacterial endocarditis and has been implicated in the incidence of human colon cancer, possibly due to chronic inflammatory response at the site of intestinal colonization. Certain feeding regimens in ruminants can lead to overgrowth of S. bovis in the rumen, resulting in the over-production of lactate and capsular polysaccharide causing acute ruminal acidosis and bloat, respectively. There are multiple strategies in controlling acute lactic acidosis and bloat. The incidence of the two diseases may be controlled by strict dietary management. Gradual introduction of grain-based diets and the feeding of coarsely chopped roughage decrease the incidence of the two disease entities. Ionophores, which have been used to enhance feed conversion and growth rate in cattle, have been shown to inhibit the growth of lactic acid bacteria in the rumen. Other methods of controlling lactic acid bacteria in the ruminal environment (dietary supplementation of long-chain fatty acids, induction of passive and active immune responses to the bacteria, and the use of lytic bacteriophages) have also been investigated. It is anticipated that through continued in-depth ecological analysis of S. bovis the characteristics responsible for human and animal pathogenesis would be sufficiently identified to a point where more effective control strategies for the control of this bacteria can be developed. [Copyright &y& Elsevier]

For more than 100 years research on food irradiation has demonstrated that radiation will make food safer and improve the shelf life of irradiated foods. Using the current food safety technology, we may have reached the point of diminishing returns even though recent figures from the CDC show a significant drop in the number of foodborne illnesses. However, too many people continue to get sick and die from eating contaminated food. New and under utilized technologies such as food irradiation need to be re-examined to achieve new levels of safety for the food supply. Effects of irradiation on the safety and quality of meat and poultry are discussed. Irradiation control of the principle microbial pathogens including viruses, the differences among at-risk sub-populations, factors affecting the diminished rate of improvement in food safety and published D values for irradiating raw meat and poultry are presented. Currently permitted levels of irradiation are probably not sufficient to control pathogenic viruses. Typical gram-negative spoilage organisms are very sensitive to irradiation. Their destruction leads to a significant increase in the acceptable shelf life. In addition, the destruction of these normal spoilage organisms did not provide a competitive growth advantage for irradiation injured food pathogens. Another of the main focuses of this review is a detailed compilation of the effects of most of the food additives that have been proposed to minimize the negative quality effect of irradiation. Most of the antimicrobials and antioxidants used singly or in combination produced an increased lethality of irradiation and a decrease in oxidation by-products. Combinations of dosage, temperature, dietary and direct additives, storage temperature and packaging atmosphere can produce meats that the average consumer will find indistinguishable from non-irradiated meats. A discussion of the production of unique radiological by-products is also included. [ABSTRACT FROM AUTHOR]

Microbiome studies in animal science using 16S rRNA gene sequencing have become increasingly common in recent years as sequencing costs continue to fall and bioinformatic tools become more powerful and user-friendly. The combination of molecular biology, microbiology, microbial ecology, computer science, and bioinformatics—in addition to the traditional considerations when conducting an animal science study—makes microbiome studies sometimes intimidating due to the intersection of different fields. The objective of this review is to serve as a jumping-off point for those animal scientists less familiar with 16S rRNA gene sequencing and analyses and to bring up common issues and concerns that arise when planning an animal microbiome study from design through analysis. This review includes an overview of 16S rRNA gene sequencing, its advantages, and its limitations; experimental design considerations such as study design, sample size, sample pooling, and sample locations; wet lab considerations such as field handing, microbial cell lysis, low biomass samples, library preparation, and sequencing controls; and computational considerations such as identification of contamination, accounting for uneven sequencing depth, constructing diversity metrics, assigning taxonomy, differential abundance testing, and, finally, data availability. In addition to general considerations, we highlight some special considerations by species and sample type. [ABSTRACT FROM AUTHOR]

Listeria monocytogenes has been implicated in several ready-to-eat (RTE) foodborne outbreaks, due in part to its ability to survive under refrigerated conditions. Thus, the objective of this study was to evaluate the effects of sodium bisulfate (SBS), sodium lactate (SL), and their combination as short-duration antimicrobial dips (10-s) on L. monocytogenes and the microbiome of inoculated organic frankfurters (8 Log10 CFU/g). Frankfurters were treated with tap water (TW), SBS0.39%, SBS0.78%, SL0.78%, SL1.56%, SBS+SL0.39%, SBS+SL0.78%. In addition, frankfurters were treated with frankfurter solution water (HDW)+SBS0.78%, HDW+SL1.56%, and HDW+SBS+SL0.78%. After treatment, frankfurters were vacuum packaged and stored at 4°C. Bacterial enumeration and 16S rDNA sequencing occurred on d 0, 7, 14, 21. Counts were Log10 transformed and calculated as growth potential from d 0 to d 7, 14, and 21. Data were analyzed in R using mixed-effects model and One-Way ANOVA (by day) with differences separated using Tukey's HSD at P ≤ 0.05. The 16S rDNA was sequenced on an Illumina MiSeq and analyzed in Qiime2-2018.8 with significance at P ≤ 0.05 and Q ≤ 0.05 for main and pairwise effects. An interaction of treatment and time was observed among the microbiological plate data with all experimental treatments reducing the growth potential of Listeria across time (P < 0.0001). Efficacy of treatments was inconsistent across time; however, on d 21, SBS0.39% treated franks had the lowest growth potential compared to the control. Among diversity metrics, time had no effect on the microbiota (P > 0.05), but treatment did (P < 0.05). Thus, the treatments potentially promoted a stable microbiota across time. Using ANCOM, Listeria was the only significantly different taxa at the genus level (P < 0.05, W = 52). Therefore, the results suggest incorporating SBS over SL as an alternative antimicrobial for the control of L. monocytogenes in organic frankfurters without negatively impacting the microbiota. However, further research using multiple L. monocytogenes strains will need to be utilized in order to determine the scope of SBS use in the production of RTE meat. [ABSTRACT FROM AUTHOR]

[Display omitted] • This study investigated the microbiome of sprouts by 16S rRNA microbiome sequencing. • Proteobacteria (phylum) and Enterobacteriaceae (family) were predominant on sprouts. • Alfalfa sprouts exhibited the highest abundance of Enterobacteriaceae. • Species richness and evenness were highest on radish sprouts and lowest on alfalfa. • Sprout microbiomes were affected by type and brand, not by distribution route. Sprouts harbor high populations of bacteria and cause numerous foodborne disease outbreaks, yet little is known about their microbial composition. The present study aimed to define the microbiological ecology of sprouts using 16S rRNA microbiome sequencing and culture-dependent methods. Different types (radish, alfalfa, and rapeseed), brands (A, B, and C), and distribution routes (online and offline) of sprouts (n = 70) were considered for microbiome analysis, as well as quantitative (aerobic plate count and coliforms) and qualitative analyses (Escherichia coli O157:H7, Listeria monocytogenes , and Salmonella Typhimurium). The aerobic plate count ranged from 7 to 8 CFU/g, and the coliforms ranged from 6 to 7 log CFU/g. Microbiome analysis revealed that Proteobacteria was the dominant phylum, accounting for 79.0% in alfalfa sprouts, 68.5% in rapeseed sprouts, and 61.9% in radish sprouts. Enterobacteriaceae was the dominant family in alfalfa sprouts (33.9%) and rapeseed sprouts (14.6%), while Moraxellaceae (11.9%) were prevalent on radish sprouts. The majority of the dominant genera were common in the environment, such as soil or water. Alfalfa sprouts yielded the lowest aerobic plate count but the highest relative abundance of Enterobacteriaceae compared to the other sprouts. These results could explain why alfalfa sprouts are a leading cause of sprout-related foodborne disease outbreaks. Alpha-diversity results (Chao1 and Shannon indices) suggested that species richness was greater on radish sprouts than the other sprout types. Beta-diversity results showed samples were clustered by types, indicating dissimilarity in microbial communities. However, the distribution route had a limited influence on microbial composition. The present study provides a comparative examination of the microbial profiles of sprouts. Microbiome analyses contribute to an in-depth understanding of the microbial ecology of sprouts, leading to potential control measures for ensuring food safety. [ABSTRACT FROM AUTHOR]

The study's objective was to identify typical aerobic isolates from commercial, corn-soybean meal poultry diets utilizing 16S rDNA, assign them their corresponding taxonomy, and compare the data with the previously published WGS analysis of these same isolates. Ten grams of a commercial corn-soybean meal poultry diet was homogenized in 100 mL of tryptic soy broth for 2 min, serially diluted, plated onto tryptic soy agar (TSA), and incubated aerobically for 24 h at 37 °C. Subsequently, 20 unique colonies were streaked for isolation on TSA and incubated aerobically for 24 h at 37 °C. This process was repeated three consecutive times for purification of isolates until only 11 morphologically distinct colonies were obtained. DNA was extracted using Qiagen's DNeasey® Blood and Tissue Kit. The 16S rRNA V4 region was targeted using an Illumina MiSeq and analyzed via QIIME2-2020.2. Alpha diversity and Beta diversity metrics were generated, and taxa were aligned using Silva in Qiime2-2020.2. Twenty-five distinct genera were identified within the 11 different colonies. Because 16S rDNA identification can provide an understanding of pathogen associations and microbial niches within an ecosystem, the information may present a potential method to establish and characterize the hygienic indicator microorganisms associated with poultry feed. [ABSTRACT FROM AUTHOR]

Background: Microencapsulated organic acids and botanicals have the potential to develop into important tools for the poultry industry. A blend of organic acids and botanicals (AviPlus®P) has previously shown to reduce Salmonella and Campylobacter in chickens; however, changes to the microbiota of the jejunum and ileum have not been evaluated. Microbiota diversity is linked to, but not correlated with, the efficacy of natural products; therefore, understanding the effects on the microbiota is necessary for evaluating their potential as an antibiotic alternative. Results: Ileal and jejunal segments from control and supplement-fed chickens (300 and 500 g/metric ton [MT]) were subjected to alpha diversity analysis including Shannon's diversity and Pielou's Evenness. In both analytics, the diversity in the ileum was significantly decreased compared to the jejunum irrespective of treatment. Similarly, beta diversity metrics including Bray-Curtis dissimilarity index and Weighted Unifrac Distance Matrix, were significant (Q < 0.05) for both tissue and treatments comparisons. Alpha and beta diversity analytics indicated compartmentalization effects between the ileum and jejunum. Additionally, analysis of communities in the microbiota (ANCOM) analysis showed Lactobacilliaceae predominated the total operational taxonomic units (OTU), with a stepwise increase from 53% in the no treatment control (NTC) to 56% in the 300 g/MT and 67% in the 500 g/MT group. Staphylococcaceae were 2% in NTC and 2 and 0% in 300 and 500 g/MT groups. Enterobacteriaceae decreased in the 500 g/MT (31%) and increased in the 300 g/MT (37%) compared to the NTC (35%). Aerococcaceae was 0% for both doses and 7% in NTC. Ruminococcaceae were 0% in NTC and 2 and 1% in the 300 and 500 g/MT. These changes in the microbial consortia were statistically (Q < 0.05) associated with treatment groups in the jejunum that were not observed in the ileum. Least discriminant analysis effect size (LEfSE) indicated different changes directly corresponding to treatment. Enterobacteriaceae demonstrated a stepwise decrease (from NTC onward) while Clostridiaceae, were significantly increased in the 500 g/MT compared to NTC and 300 g/MT (P < 0.05). Conclusion: The bioactive site for the microencapsulated blend of organic acids and botanicals was the jejunum, and dietary inclusion enhanced the GIT microbiota and may be a viable antibiotic alternative for the poultry industry. [ABSTRACT FROM AUTHOR]

Salmonella and Campylobacter are significant issues for poultry processors because of increasing regulatory standards as well as public health concerns. The goal of this study is to report the effects of two different pre-chiller systems that utilize different temperatures and water recirculation systems on whole bird carcass rinsates. Both pre-chiller tanks were contained within a single poultry processing facility and operated at different temperatures and water systems. The incidence of Campylobacter spp. and Salmonella spp., as well as the aerobic plate counts on whole bird carcass rinses are reported in this study from each pre-chiller system. The results from this study reveal that there are significant differences in how microbial populations and pathogens change over time in each pre-chiller system. Furthermore, we identify that these patterns are different per system. Such data are impactful as it indicates that measuring carcasses within a plant must consider both temperature and water recirculation as it may prevent comparability of different lines within a single processing facility. [ABSTRACT FROM AUTHOR]

Controlling Salmonella in poultry is an ongoing food safety measure and while significant progress has been made, there is a need to continue to evaluate different strategies that include understanding Salmonella -poultry interaction, Salmonella -microbiota interactions, Salmonella genetics and response to adverse conditions, and preharvest and postharvest parameters that enable persistence. The purpose of this symposium is to discuss different strategies to consider from feed milling to the farm to the processing environment. This Poultry Science Association symposium paper is divided into 5 different sections that covers 1) immunological aspects of Salmonella control, 2) application of Salmonella genetics for targeted control strategies in poultry production, 3) improving poultry feed hygienics: utilizing feed manufacture techniques and equipment to improve feed hygienics, 4) practical on farm interventions for controlling Salmonella —what works and what may not work, and 5) monitoring and mitigating Salmonella in poultry. These topics elucidate the critical need to establish control strategies that will improve poultry gut health and limit conditions that exposes Salmonella to stress causing alterations to virulence and pathogenicity both at preharvest and postharvest poultry production. This information is relevant to the poultry industry's continued efforts to ensure food safety poultry production. [ABSTRACT FROM AUTHOR]

Salmonella is one of major foodborne pathogens and the leading cause of foodborne illness-related hospitalizations and deaths. It is critical to develop a sensitive and rapid detection assay that can identify Salmonella to ensure food safety. In this study, a DNA sensor-based suspension array system of high multiplexing ability was developed to identify eight Salmonella serovars commonly associated with foodborne outbreaks to the serotype level. Each DNA sensor was prepared by activating pre-encoded microspheres with oligonucleotide probes that are targeting virulence genes and serovar-specific regions. The mixture of 12 different types of DNA sensors were loaded into a 96-well microplate and used as a 12-plex DNA sensor array platform. DNA isolated from Salmonella was amplified by multiplex polymerase chain reaction (mPCR), and the presence of Salmonella was determined by reading fluorescent signals from hybridization between probes on DNA sensors and fluorescently labeled target DNA using the Bio-Plex® system. The developed multiplex array was able to detect synthetic DNA at the concentration as low as 100 fM and various Salmonella serovars as low as 100 CFU/mL within 1 h post-PCR. Sensitivity of this assay was further improved to 1 CFU/mL with 6-h enrichment. The array system also correctly and specifically identified serotype of tested Salmonella strains without any cross-reactivity with other common foodborne pathogens. Our results indicate the developed DNA sensor suspension array can be a rapid and reliable high-throughput method for simultaneous detection and molecular identification of common Salmonella serotypes. [ABSTRACT FROM AUTHOR]

Developing novel and effective antimicrobial methods is imperative for ensuring food safety during commercial apple production. In the present study, the bactericidal effects of dipping apples into a combination of bisulfate of soda (BS) and peracetic acid (PAA) was investigated using Listeria innocua as a surrogate inoculated to whole apples. Decontamination treatments included washing with water as control, chlorine at 150 ppm, 1% BS with 60 ppm PAA, 3% BS with 60 ppm PAA, and 3% BS with 60 ppm PAA and a surfactant sticker (0.1% Tween). After dipping with antimicrobial solutions for 2 min, apples were stored over a time period of up to 2 weeks and L. innocua survivors were enumerated from apple core collected from 30 min, 1 day, 7 days, and 14 days. Washing with water showed little antimicrobial effect; only a 1.52 log 10 -cycle reduction was observed after 14 days ( L. innocua population at 0 and 14 days: 5.96 and 4.44 log CFU/g, respectively), indicating that washing was not sufficient to control L. innocua on apple. When apples were treated with chlorine, L. innocua populations were reduced to 3.58, 2.19 log CFU/g after 1 and 7 days, respectively, but afterward increased to 3.80 log CFU/g at 14 days of storage. In contrast, the combined treatment of BS and PAA resulted in marked bactericidal activities (log 10 -cycle reduction by 1% BS with 60 ppm PAA after 30 min, 1, 7, and 14 days: 2.57, 2.70, 5.45, and 4.30 log CFU/g, respectively; log 10 -cycle reduction by 3% BS with 60 ppm PAA: 3.66, 5.24, 5.50, and 5.56 log CFU/g). Adding a surfactant sticker did not result in a significant increase in antimicrobial effects thus 3% BS with 60 ppm PAA would be an optimal treatment for use in the apple industry. This combined decontamination method has important advantages including consumer and industry preference for natural compound, its potential application to industry, and cost-effectiveness. The combined treatment of BS and PAA may be a useful decontamination method for improving the microbiological safety in whole apples. [ABSTRACT FROM AUTHOR]

The soilborne pathogen Listeria monocytogenes frequently contaminates food products and food processing environments and is able to survive desiccation, high osmotic pressures, and starvation. However, little is known about how this pathogen survives starvation at 4°C. This study provides evidence that L. monocytogenes is able to survive total nutrient starvation for 4 weeks. L. monocytogenes strains EGD-e, Scott A, F2365, and HCC23 were starved individually in sterile water. Colony counts declined over 4 weeks, with Scott A declining the most rapidly. Transmission electron microscopy images revealed degradation of starving cell membranes and altered cytosols. Starving cells were subjected to the metabolic inhibitors fluoride, arsenite, 2,4-dinitrophenol, iodoacetate, and cyanide individually. Iodoacetate, which inhibits glyceraldehyde-3-phosphate dehydrogenase, completely reduced cultivable counts below the level of detection compared with the control starving cells; 2,4-dinitrophenol, which dissipates proton motive force, almost completely reduced cultivable counts. These results suggest that L. monocytogenes strains EGD-e, Scott A, F2365, and HCC23 are actively using part of the glycolysis pathway while starving. These results suggest that starving L. monocytogenes cells retain aspects of active metabolism. [ABSTRACT FROM AUTHOR]