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This study investigates the volatile compounds that contribute to the unique flavor and aroma profiles of cured meat products using alternative ingredients, specifically focusing on commercially available, conventional, and organically produced pre-converted celery ( Apium graveolens ) and Swiss chard ( Beta vulgaris subsp. maritima) juices and powders. Volatile compounds were isolated and analyzed using an optimized method involving steam distillation with liquid-liquid phase extraction coupled with gas chromatography-tandem mass spectrometry (GC-MS/MS). The key volatile compound identified in celery was 3-butylisobenzofuran-1(3H)-one, and in Swiss chard, 2-methoxy-4-vinylphenol. In both conventional and organic celery juice, senkyunolide, sedanolide, and limonene were the primary volatiles, listed in descending order of concentration. This pioneering work on volatile and aromatic compounds in alternative curing ingredients provides foundational knowledge for sensory and volatile compound studies in alternative meat curing. It also offers valuable insights for organic plant and meat producers, processors, and consumers. Practically, this research highlights volatile chemicals that could interact with other meat constituents or residues in finished products, informing and enlightening future studies on the sensory and aromatic properties of alternative cured meats. Overall, this study contributes to the development of alternative cured meats, supporting the research and innovation of organic meats.

The accurate quantification of Campylobacter jejuni in poultry samples is critical for ensuring food safety and compliance with regulatory standards. This study evaluated the performance of three enrichment media-Mueller-Hinton Broth (MHB), Bolton's Blood-Free Broth 2x (BFBB2x), and Buffered Peptone Water (BPW)-in supporting C. jejuni detection and quantification using the BAX ® Q7-RT PCR system and traditional plate count methods. Results demonstrated high reliability across all media types, with BFBB2x and MHB showing the strongest correlations (R 2 = 0.99) for the BAX ® system. BFBB2x exhibited the lowest RMSE (0.13), while MHB balanced precision (RMSE = 0.4) with sensitivity. For plate counts, MHB and BPW achieved the highest correlations (R 2 = 0.99) and precision (RMSE = 0.26), with MHB demonstrating the lowest detection limit (2.56 log 10 CFU/mL) compared to BFBB2x (2.93 log 10 CFU/mL) and BPW (3.31 log 10 CFU/mL). The findings underscore MHB's robustness as an enrichment medium, offering consistent performance across both molecular and culture-based methods. The current study supports MHB as the more effective medium for the reliable and precise quantification of C. jejuni in poultry-associated matrices, highlighting its utility in minimizing contamination risks and enhancing food safety. Future research should explore its applicability in diverse poultry products and production environments.

The standardization of the microbiome sequencing of poultry rinsates is essential for generating comparable microbial composition data among poultry processing facilities if this technology is to be adopted by the industry. Samples must first be acquired, DNA must be extracted, and libraries must be constructed. In order to proceed to library sequencing, the samples should meet quality control standards. Finally, data must be analyzed using computer bioinformatics pipelines. This data can subsequently be incorporated into more advanced computer algorithms for risk assessment. Ultimately, *a uniform sequencing pipeline will enable both the government regulatory agencies and the poultry industry to identify potential weaknesses in food safety.This chapter presents the different steps for monitoring the population dynamics of the microbiome in poultry processing using 16S rDNA sequencing., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

There is an increasing need to develop alternative antimicrobials to replace currently used antibiotics. Phytochemicals, such as essential oils, have garnered significant attention in recent years as potential antimicrobials. However, the mechanisms underlying their bactericidal activities are not yet fully understood. In this study, we investigated the bactericidal activity of eugenol oil against Salmonella enterica serovar Typhimurium ( S . Typhimurium) to elucidate its mechanism of action. We hypothesized that eugenol exerts its bactericidal effects through the production of reactive oxygen species (ROS), which ultimately leads to cell death. The result of this study demonstrated that the bactericidal activity of eugenol against S . Typhimurium was significantly ( p < 0.05) mitigated by thiourea (ROS scavenger) or iron chelator 2,2'-dipyridyl, supporting the hypothesis. This finding contributes to a better understanding of the killing mechanism by eugenol oil.

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., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

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., Importance: Researching the exposome, a summation of exposure to one's lifespan, will aid in determining the environmental factors that contribute to disease states. There is an emerging concern that microplastic-pathogen interactions in the gastrointestinal tract of broiler chickens may lead to an increase in Salmonella infection across flocks and eventually increased incidence of human salmonellosis cases. In this research article, we elucidated the effects of acute co-exposure to polyethylene microplastics and Salmonella enterica serovar Typhimurium on the ceca microbial community in vitro . Salmonella presence caused strong shifts in the cecal metabolome but not the microbiome. The inverse was true for polyethylene fiber. Polyethylene powder had almost no effect. The co-exposure had worse effects than either alone. This demonstrates that exposure effects to the gut microbial community are contaminant-specific. When combined, the interactions between exposures exacerbate changes to the gut environment, necessitating future experiments studying low-dose chronic exposure effects with in vivo model systems., Competing Interests: The authors declare no conflict of interest.

The 2021 FSIS Stabilization Guidelines for Meat and Poultry Products (Appendix B) Option 1.2 limits Phase 1 cooling from 48.8 to 26.7 °C in uncured meats to 1 h. However, this time restriction is impractical to achieve in large-diameter whole-muscle products. The objective of this study was to compare the inhibitory effect of commercial dry vinegars (DVs) and cultured sugar-vinegar blends (CSVs) on Clostridium perfringens and Bacillus cereus in uncured beef and poultry products during extended cooling. Treatments (beef: 72-73% moisture, pH 6.2-6.3, 0.85-0.95% NaCl; turkey: 76-77% moisture, pH 6.5-6.7, 1.3-1.6% NaCl) included Controls without antimicrobials, and four DV and four CSV, each tested at 0.75 and 1.25%. Batches were inoculated with 2.5-log C. perfringens or B. cereus spores, vacuum-packaged, and cooked to 73 °C. Packages were cooled from 48.8 to 27 °C (Phase 1) in 3, 4, or 5 h; Phase 2 (27-12.8 °C) and Phase 3 (12.8-4 °C) were standardized for 5-h cooling each. Pathogens were enumerated on selective agar in triplicate samples assayed at precook, postcook, and at the end of Phase 1, 2, and 3 cooling. Experiments were conducted twice. B. cereus did not grow (<0.5-log increase) in any treatment when Phase 1 cooling was extended to 5 h. C. perfringens grew rapidly (2.5 to >4.5 log) in Control treatments when Phase 1 cooling was extended to ≥3 h. All 1.25% DV ingredients limited C. perfringens growth to ≤1-log when Phase 1 cooling was extended to 3 h but supported a >1-log increase when Phase 1 cooling was extended to 5 h. All 1.25% CSV inhibited growth under 3-h Phase 1 cooling; 1.25% CSV-A and ≥0.75% CSV-D inhibited growth in turkey during 5-h Phase 1 cooling, but inhibition with 1.25% CSV-C was inconsistent in beef. This study revealed that formulating uncured meats with 1.25% DV or certain CSV can extend Phase 1 cooling to 3 h. Although all ingredients inhibited growth when used at 0.75% or greater compared to a control, greater variability of inhibition was observed among CSV than for DV., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: “Kathleen A. Glass reports financial support was provided by Foundation and Meat and Poultry Research and Education. Kathleen A. Glass reports a relationship with ConAgra Brands Inc. that includes: consulting or advisory and travel reimbursement. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper”., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Considering that certain catabolic products of anaerobic chlorophyll degradation inhibit efflux pump activity, this study was conducted to test if feeding pigs a water-soluble chlorophyllin product could affect the antibiotic resistance profiles of select wild-type populations of fecal bacteria. Trial 1 evaluated the effects of chlorophyllin supplementation (300 mg/meal) on fecal E. coli and enterococcal populations in pigs fed twice daily diets supplemented without or with ASP 250 (containing chlortetracycline, sulfamethazine and penicillin at 100, 100 and 50 g/ton, respectively). Trial 2, conducted similarly, evaluated chlorophyllin supplementation in pigs fed diets supplemented with or without 100 g tylosin/ton. Each trial lasted 12 days, and fecal samples were collected and selectively cultured at 4-day intervals to enumerate the total numbers of E. coli and enterococci as well as populations of these bacteria phenotypically capable of growing in the presence of the fed antibiotics. Performance results from both studies revealed no adverse effect ( p > 0.05) of chlorophyllin, antibiotic or their combined supplementation on average daily feed intake or average daily gain, although the daily fed intake tended to be lower ( p = 0.053) for pigs fed diets supplemented with tylosin than those fed diets without tylosin. The results from trial 1 showed that the ASP 250-medicated diets, whether without or with chlorophyllin supplementation, supported higher ( p < 0.05) fecal E. coli populations than the non-medicated diets. Enterococcal populations, however, were lower, albeit marginally and not necessarily significantly, in feces from pigs fed the ASP 250-medicated diet than those fed the non-medicated diet. Results from trial 2 likewise revealed an increase ( p < 0.05) in E. coli and, to a lesser extent, enterococcal populations in feces collected from pigs fed the tylosin-medicated diet compared with those fed the non-medicated diet. Evidence indicated that the E. coli and enterococcal populations in trial 1 were generally insensitive to penicillin or chlortetracycline, as there were no differences between populations recovered without or with antibiotic selection. Conversely, a treatment x day of treatment interaction observed in trial 2 ( p < 0.05) provided evidence, albeit slight, of an enrichment of tylosin-insensitive enterococci in feces from the pigs fed the tylosin-medicated but not the non-medicated diet. Under the conditions of the present study, it is unlikely that chlorophyllin-derived efflux pump inhibitors potentially present in the chlorophyllin-fed pigs were able to enhance the efficacy of the available antibiotics. However, further research specifically designed to optimize chlorophyll administration could potentially lead to practical applications for the swine industry.

This study investigates the impact of casein hydrolysates on the poultry ceca inoculated with Campylobacter focusing on microbial molecular preferences for different protein sources in the presence of Campylobacter jejuni. Three casein sources (intact casein (IN), casein enzyme hydrolysate (EH), and casein acid hydrolysate (AH)) were introduced to cecal contents in combination with inoculated C. jejuni in an in vitro model system incubated for 48 h at 42°C under microaerophilic conditions. Samples were collected at 0, 24, and 48 h. Genomic DNA was extracted and amplified using custom dual-indexed primers, followed by sequencing on an Illumina MiSeq platform. The obtained sequencing data were then analyzed via QIIME2-2021.11. Metabolite extracts were analyzed with ultra-high-performance liquid orbitrap chromatography-mass spectrometry (UHPLC-MS). Statistical analysis of metabolites was conducted using MetaboAnalyst 5.0, while functional analysis was performed using Mummichog 2.0 with a significance threshold set at P < 0.00001. DNA sequencing and metabolomic analyses revealed that C. jejuni was most abundant in the EH group. Microbial diversity and richness improved in casein supplemented groups, with core microbial differences observed, compared to non-supplemented groups. Vitamin B-associated metabolites significantly increased in the supplemented groups, displaying distinct patterns in vitamin B6 and B9 metabolism between EH and AH groups (P < 0.05). Faecalibacterium and Phascolarctobacterium were associated with AH and EH groups, respectively. These findings suggest microbial interactions in the presence of C. jejuni and casein supplementation are influenced by microbial community preferences for casein hydrolysates impacting B vitamin production and shaping competitive dynamics within the cecal microbial community. These findings underscore the potential of nutritional interventions to modulate the poultry GIT microbiota for improved health outcomes., Competing Interests: NO authors have competing interests., (Copyright: © 2024 Olson et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Introduction: Targeted amplicon sequencing of the 16S rRNA delineates the complex microbial interactions that occur during food spoilage, providing a tool to intensively screen microbiota response to antimicrobial processing aids and interventions. The current research determines the microbiota and spoilage indicator (total aerobes and lactic acid bacteria; LAB) response to inorganic and organic antimicrobial intervention use on the shelf-life of fresh, never-frozen, skin-on, bone-in chicken wings., Methods: Wings ( n =200) were sourced from local processor and either not treated (NT) or treated with 15-s dips of tap water (TW), organic (peracetic acid; PAA), inorganic acids (sodium bisulfate; SBS), and their combination (SBS + PAA). Wings were stored (4°C) and rinsed in neutralizing Buffered Peptone Water (BPW) for 1 min on d 0, 7, 14, and 21 post-treatment. Spoilage indicators, aerobic mesophiles and LAB, were quantified from rinsates. Genomic DNA of d 14 and 21 rinsates were extracted, and V4 of 16S rRNA gene was sequenced. Sequences were analyzed using QIIME2.2019.7. APC and LAB counts were reported as Log 10 CFU/g of chicken and analyzed in R Studio as a General Linear Model using ANOVA. Pairwise differences were determined using Tukey's HSD (P£0.05)., Results: Spoilage was indicated for all products by day 21 according to APC counts (>7 Log 10 CFU/g); however, wings treated with SBS and SBS + PAA demonstrated a 7-day extended shelf-life compared to those treated with NT, TW, or PAA. The interaction of treatment and time impacted the microbial diversity and composition ( p < 0.05), with those treated with SBS having a lower richness and evenness compared to those treated with the controls (NT and TW; p < 0.05, Q < 0.05). On d 14, those treated with SBS and SBS + PAA had lower relative abundance of typical spoilage population while having a greater relative abundance of Bacillus spp. (~70 and 50% of population; ANCOM p < 0.05). By d 21, the Bacillus spp. populations decreased below 10% of the population among those treated with SBS and SBS + PAA., Discussion: Therefore, there are differential effects on the microbial community depending on the chemical intervention used with organic and inorganic acids, impacting the microbial ecology differently., Competing Interests: CO was employed by Jones-Hamilton Co. (Walbridge, OH, United States). Jones-Hamilton Co. did provide financial support for this work. However, their financial support did not influence the design, execution, and results of the current work. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were editorial board members of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Dittoe, Feye, Ovall, Thompson and Ricke.)

Food additives are employed in the food industry to enhance the color, smell, and taste of foods, increase nutritional value, boost processing efficiency, and extend shelf life. Consumers are beginning to prioritize food ingredients that they perceive as supporting a healthy lifestyle, emphasizing ingredients they deem acceptable as alternative or "clean-label" ingredients. Ready-to-eat (RTE) meat products can be contaminated with pathogens and spoilage microorganisms after the cooking step, contributing to food spoilage losses and increasing the risk to consumers for foodborne illnesses. More recently, consumers have advocated for no artificial additives or preservatives, which has led to a search for antimicrobials that meet these demands but do not lessen the safety or quality of RTE meats. Lactates and diacetates are used almost universally to extend the shelf life of RTE meats by reducing spoilage organisms and preventing the outgrowth of the foodborne pathogen Listeria monocytogenes . These antimicrobials applied to RTE meats tend to be broad-spectrum in their activities, thus affecting overall microbial ecology. It is to the food processing industry's advantage to target spoilage organisms and pathogens specifically.

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.

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., (© The Author(s) 2023. Published by Oxford University Press on behalf of Applied Microbiology International.)

Within the realm of poultry feed mill operations, the persistent concern over microbial feed quality necessitates the establishment of a robust baseline for enhancing and sustaining the standards of commercial feeds. This dual-phase investigation, comprising Parts I, was previously published, and the current study presented here as Part II aimed to illuminate this baseline using 16S rRNA gene sequencing. In Part II, nine distinct commercial poultry feeds formulated as starters, growers, starter/growers, or supplements, the selected feeds underwent genomic DNA extraction, amplification with custom dual-indexed primers, and subsequent Illumina MiSeq sequencing. Through data analysis in QIIME2-2021.4 and R Studio, the study unveils alpha (Kruskal-Wallis) and beta (ANOSIM) diversity, taxonomic differences (ANCOM), and core microbiomes (core&#95;members), deeming main and pairwise effects statistically significant at p  < 0.05 and Q  < 0.05. Notably, the investigation identified 30% common core microbial members across the nine feed types, shedding light on potential foodborne poultry pathogens such as Helicobacter and Campylobacter . Probiotic-associated feeds exhibited distinct microbial communities, emphasizing the need to explore their impact on the early poultry gastrointestinal tract (GIT) further.

Given extensive variability in feed composition, the absence of a dedicated DNA extraction kit for poultry feed underscores the need for an optimized extraction technique for reliable downstream sequencing analyses. This study investigates the impact of five DNA extraction techniques: Qiagen QIAamp DNA Stool Mini Kit (Qiagen), modified Qiagen with Lysing Matrix B (MQ), modified Qiagen with celite purification (MQC), polyethylene glycol (PEG), and 1-Day Direct. Genomic DNA amplification and Illumina MiSeq sequencing were conducted. QIIME2-2021.4 facilitated data analysis, revealing significant diversity and compositional differences influenced by extraction methods. Qiagen exhibited lower evenness and richness compared to other methods. 1-Day Direct and PEG enhanced bacterial diversities by employing bead beating and lysozyme. Despite similar taxonomic resolution, the Qiagen kit provides a rapid, consistent method for assessing poultry feed microbiomes. Modified techniques (MQ and MQC) improve DNA purification, reducing bias in commercial poultry feed samples. PEG and 1-Day Direct methods were effective but may require standardization. Overall, this study underscores the importance of optimized extraction techniques in poultry feed analysis, with potential implications for future standardization of effective methods.

Poultry is the primary reservoir of Campylobacter , a leading cause of gastroenteritis in the United States. Currently, the selective plating methodology using selective agars, Campy Cefex and Modified Charcoal Cefoperazone Deoxycholate agar, is preferentially used for the quantification of Campylobacter spp. among poultry products. Due to the specific nature of Campylobacter , this methodology is not sensitive, which can lead to skewed detection and quantification results. Therefore, Campylobacter detection and quantification methods are urgently needed. The objective was to develop a shortened enrichment-based quantification method for Campylobacter (CampyQuant™) in post-chill poultry rinsates using the BAX ® System Real-Time PCR assay for Campylobacter . The specificity and sensitivity for the detection of C. jejuni , C. coli , and C. lari in pure culture were determined. The BAX ® System Real-Time PCR assay consistently detected and identified each species 100% of the time with an enumeration range of 4.00 to 9.00 Log 10 CFU/mL. Enrichment time parameters for low-level concentrations (0.00, 1.00, and 2.00 Log 10 CFU/mL) of Campylobacter using the BAX ® System Real-Time PCR assay were elucidated. It was determined that an enrichment time of 20 h was needed to detect at least 1.00 Log 10 CFU/mL of Campylobacter spp. Using the BAX ® System Real-Time PCR assay for Campylobacter . As a result, time of detection, detection limits, and enrichment parameters were used to develop the CampyQuant™ linear standard curve using the detected samples from the BAX ® System Real-Time PCR assay to quantify the levels in post-chill poultry rinsates. A linear fit equation was generated for each Campylobacter species using the cycle threshold from the BAX ® System Real-Time PCR assay to estimate a pre-enrichment of 1.00 to 4.00 Log 10 CFU/mL of rinsates detected. The statistical analyses of each equation yielded an R 2 of 0.93, 0.76, and 0.94 with a Log 10 RMSE of 0.64, 1.09, and 0.81 from C. jejuni , C. coli , and C. lari , respectively. The study suggests that the BAX ® System Real-Time PCR assay for Campylobacter is a more rapid, accurate, and efficient alternative method for Campylobacter enumeration.

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., Competing Interests: Author Dr. Lindsey Mehall was employed by the company Safe Foods Corporation which supplied the product peracetic acid and cetylpyridinium chloride during the onset of the study (North Little Rock, AR, USA). Safe Foods Corporation did provide financial support for this work; however, this did not influence the design, execution, and results of the current work. All other authors declare no competing interests. The commercial affiliation did not alter the adherence to PLOS ONE policies on sharing data and materials, (Copyright: © 2023 Dittoe et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The important hypothesis that organic livestock management reduces the prevalence of antimicrobial resistance is either fiercely supported or bitterly contested. Yet, empirical evidence supporting this view remains fragmentary, in part because relationships between antimicrobial use and drug resistance vary dramatically across contexts, hosts, pathogens, and country-specific regulations. Here, we synthesize global policies and definitions of 'organic' and ask if organic farming results in notable reductions in the prevalence of antimicrobial resistance when directly examined alongside conventional analogs. We synthesized the results of 72 studies, spanning 22 countries and five pathogens. Our results highlight substantial variations in country-specific policies on drug use and definitions of 'organic' that hinder broad-scale and generalizable patterns. Overall, conventional farms had slightly higher levels of antimicrobial resistance (28%) relative to organic counterparts (18%), although we found significant context-dependent variation in this pattern. Notably, environmental samples from organic and conventional farms often exhibited high levels of resistance to medically important drugs, underscoring the need for more stringent and consistent policies to control antimicrobial contaminants in the soil (particularly on organic farms, where the application of conventional manure could faciliate the spread antimicrobial resistance). Taken together, these results emphasize the challenges inherent in understanding links between drug use and drug resistance, the critical need for global standards governing organic policies, and greater investment in viable alternatives for managing disease in livestock., (© 2023. The Author(s).)

Concern exists that the continued use of antibiotics in animal feeds may lead to an increased prevalence of resistant bacteria within the host animal's gastrointestinal tract. To evaluate the effect of chlortetracycline on the persistence of Salmonella enterica serotype Typhimurium within a diverse population of porcine cecal bacteria, we cultured a mixed population of cecal bacteria without or with added chlortetracycline. When grown at a 24 h vessel turnover rate, chlortetracycline-susceptible S. Typhimurium exhibited more than 2.5 times faster ( p < 0.05) disappearance rates than theoretically expected (0.301 log 10 colony-forming unit/mL per day) but did not differ whether treated or not with 55 mg of chlortetracycline/L. Chlortetracycline-resistant S. Typhimurium was not recovered from any of these cultures. When the mixed cultures were inoculated with a chlortetracycline-resistant S. Typhimurium, rates of disappearance were nearly two times slower ( p < 0.05) than those observed earlier with chlortetracycline-susceptible S. Typhimurium, and cultures persisted at >2 log 10 colony-forming units/mL for up to 14 days of treatment with 110 mg of chlortetracycline/L. Under the conditions of this study, chlortetracycline-resistant S. Typhimurium was competitively enabled to persist longer within the mixed populations of porcine gut bacteria than chlortetracycline-susceptible S . Typhimurium, regardless of the presence or absence of added chlortetracycline.

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., Competing Interests: DISCLOSURES The authors declare that they have no conflict of interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Infection with the foodborne pathogen Campylobacter is the leading bacterial cause of human foodborne illness in the United States. The objectives of this experiment were to test the hypothesis that mixed microbial populations from the bovine rumen may be better at excluding Campylobacter than populations from freshly voided feces and to explore potential reasons as to why the rumen may be a less favorable environment for Campylobacter than feces. In an initial experiment, C. jejuni cultures inoculated without or with freshly collected bovine rumen fluid, bovine feces or their combination were cultured micro-aerobically for 48 h. Results revealed that C. jejuni grew at similar growth rates during the first 6 h of incubation regardless of whether inoculated with the rumen or fecal contents, with rates ranging from 0.178 to 0.222 h -1 . However, C. jejuni counts (log 10 colony-forming units/mL) at the end of the 48 h incubation were lowest in cultures inoculated with rumen fluid (5.73 log 10 CFUs/mL), intermediate in cultures inoculated with feces or both feces and rumen fluid (7.16 and 6.36 log 10 CFUs/mL) and highest in pure culture controls that had not been inoculated with the rumen or fecal contents (8.32 log 10 CFUs/mL). In follow-up experiments intended to examine the potential effects of hydrogen and hydrogen-consuming methanogens on C. jejuni , freshly collected bovine feces, suspended in anaerobic buffer, were incubated anaerobically under either a 100% carbon dioxide or 50:50 carbon dioxide/hydrogen gas mix. While C. jejuni viability decreased <1 log 10 CFUs/mL during incubation of the fecal suspensions, this did not differ whether under low or high hydrogen accumulations or whether the suspensions were treated without or with the mechanistically distinct methanogen inhibitors, 5 mM nitrate, 0.05 mM 2-bromosulfonate or 0.001 mM monensin. These results suggest that little if any competition between C. jejuni and hydrogen-consuming methanogens exists in the bovine intestine based on fecal incubations.

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 where there could be an interaction with Salmonella enterica Typhimurium, one of the commonly isolated serovars from processed chicken. In this study, the microbiota response to a 24-hour co-exposure to Salmonella enterica 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 to 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 model.

Introduction: Type IV secretion systems (T4SSs) are integral parts of the conjugation process in enteric bacteria. These secretion systems are encoded within the transfer ( tra ) regions of plasmids, including those that harbor antimicrobial resistance (AMR) genes. The conjugal transfer of resistance plasmids can lead to the dissemination of AMR among bacterial populations. Methods: To facilitate the analyses of the conjugation-associated genes, transfer related genes associated with key groups of AMR plasmids were identified, extracted from GenBank and used to generate a plasmid transfer gene dataset that is part of the Virulence and Plasmid Transfer Factor Database at FDA, serving as the foundation for computational tools for the comparison of the conjugal transfer genes. To assess the genetic feature of the transfer gene database, genes/proteins of the same name (e.g., traI/ TraI) or predicted function (VirD4 ATPase homologs) were compared across the different plasmid types to assess sequence diversity. Two analyses tools, the Plasmid Transfer Factor Profile Assessment and Plasmid Transfer Factor Comparison tools, were developed to evaluate the transfer genes located on plasmids and to facilitate the comparison of plasmids from multiple sequence files. To assess the database and associated tools, plasmid, and whole genome sequencing (WGS) data were extracted from GenBank and previous WGS experiments in our lab and assessed using the analysis tools. Results: Overall, the plasmid transfer database and associated tools proved to be very useful for evaluating the different plasmid types, their association with T4SSs, and increased our understanding how conjugative plasmids contribute to the dissemination of AMR genes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2023 Algarni, Foley, Tang, Zhao, Gudeta, Khajanchi, Ricke and Han.)

As demands for fresh water become more competitive between the processing plant and other consumers of water such as municipalities, interest has grown in recycling or reusing water for food processing. However, recycling the processing water from a poultry plant, for example, represents challenges due to increased organic loads and the presence of bacterial contaminants including foodborne pathogens. The objective in the current study was to evaluate the inactivation of Salmonella and E. coli O157:H7 using combinations (0.5% and 1%) of sodium bisulfate (SBS) and 1% lactic acid (LA) in water and water with organic matter in the form of horse blood serum (0.3%) with exposure times of 1 min and 5 min. Pathogen reductions after a 5 min exposure time were greater than corresponding reductions after a 1 min exposure time for all acid solutions. The Salmonella counts were significantly reduced (i.e., ≥1 log-unit) in all acid solutions after a 5 min exposure time with the combination of LA + SBS acid solutions being more effective than the corresponding 2% LA solutions. None of the acid solutions were effective in reducing the E. coli O157:H7 after a 1 min exposure time. The 1% LA + 1% SBS solution was the most effective acid solution against both pathogens and was the only acid solution effective in reducing E. coli O157:H7 by at least one log unit after 5 min of exposure.

The objective of the current study was to conduct an initial comparison of commercial yeast products in layer hen diets on egg production parameters and the corresponding impact on the cecal microbiota. A short-term feeding study was conducted with 35 laying hens receiving either a control, or 1 of 4 different yeast fermentation products, Immunowall, Hilyses (both from ICC, São Paulo, Brazil), Citristim (ADM, Decatur, IL), and Maxi-Gen Plus (CBS Bio Platforms, Calgary, Canada) with 7 hens per treatment from 40 to 46 wk of age. At the end of the trial, hens were euthanized, the ceca removed and prepared for denatured gradient gel electrophoresis (DGGE) microbial compositional analyses. Although initial shell weight and shell thickness were similar among the treatment groups, hens fed Hilyses had lower shell weight and thickness at the end of the experiment. The most predominant DGGE bands with the strongest intensity were identified as Lactobacillus species and excised double bands were identified as Bacillus, Clostridium, or Lachnospiraceae. In this short-term feeding trial, the commercial yeast products tested had little effect on egg production and shell quality, and only moderately impacted the composition of mature layer hen cecal microbiota., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Animal manure improves soil fertility and organic carbon, but long-term deposition may contribute to antibiotic resistance genes (ARGs) entering the soil-water environment. Additionally, long-term impacts of applying animal manure to soil on the soil-water microbiome, a crucial factor in soil health and fertility, are not well understood. The aim of this study is to assess: (1) impacts of long-term conservation practices on the distribution of ARGs and microbial dynamics in soil, and runoff; and (2) associations between bacterial taxa, heavy metals, soil health indicators, and ARGs in manures, soils, and surface runoff in a study following 15 years of continuous management. This management strategy consists of two conventional and three conservation systems, all receiving annual poultry litter. High throughput sequencing of the 16S ribosomal RNA was carried out on samples of cattle manure, poultry litter, soil, and runoff collected from each manureshed. In addition, four representative ARGs ( intl1 , sul1 , ermB, and bla ctx-m-32 ) were quantified from manures, soil, and runoff using quantitative PCR. Results revealed that conventional practice increased soil ARGs, and microbial diversity compared to conservation systems. Further, ARGs were strongly correlated with each other in cattle manure and soil, but not in runoff. After 15-years of conservation practices, relationships existed between heavy metals and ARGs. In the soil, Cu, Fe and Mn were positively linked to intl1 , sul1 , and ermB , but trends varied in runoff. These findings were further supported by network analyses that indicated complex co-occurrence patterns between bacteria taxa, ARGs, and physicochemical parameters. Overall, this study provides system-level linkages of microbial communities, ARGs, and physicochemical conditions based on long-term conservation practices at the soil-water-animal nexus., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Seyoum, Ashworth, Feye, Ricke, Owens, Moore and Savin.)

Listeria continues to be a persistent foodborne pathogen that is responsible for human cases of listeriosis when contaminated food products are consumed. Human subjects considered to be most susceptible include the elderly, immunocompromised, and pregnant women. Listeria is characterized as a saprophytic organism with the capability of responding and adapting to constantly changing environments because it possesses multiple stress response mechanisms to overcome varying temperatures, salt concentrations, and pH, among others. Primary foods and food products associated with listeriosis include dairy products and ready-to-eat meats such as turkey products. Historically, chicken eggs have not been identified as a primary source of Listeria, but the potential for contamination during egg production and processing does exist. Listeria species have been isolated from egg-processing plant equipment and are presumed to occur in egg-processing plant environments. Whether Listeria is consistently disseminated onto eggs beyond the egg-processing plant is a risk factor that remains to be determined. However, research has been conducted over the years to develop egg wash solutions that generate combinations of pH and other properties that would be considered inhibitory to Listeria . Even less is known regarding the association of Listeria with alternative egg production systems, but Listeria has been isolated from pasture flock broilers, so it is conceivable, given the nature of the outdoor environments, that layer birds under these conditions would also be exposed to Listeria and their eggs become contaminated. This review focuses on the possibility of Listeria occurring in conventional and alternative egg-laying production and processing systems.

Listeria monocytogenes , an intra-cellular, Gram-positive, pathogenic bacterium, is one of the leading agents of foodborne illnesses. The morbidity of human listeriosis is low, but it has a high mortality rate of approximately 20% to 30%. L. monocytogenes is a psychotropic organism, making it a significant threat to ready-to-eat (RTE) meat product food safety. Listeria contamination is associated with the food processing environment or post-cooking cross-contamination events. The potential use of antimicrobials in packaging can reduce foodborne disease risk and spoilage. Novel antimicrobials can be advantageous for limiting Listeria and improving the shelf life of RTE meat. This review will discuss the Listeria occurrence in RTE meat products and potential natural antimicrobial additives for controlling Listeria .

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.

Introduction: The antimicrobial resistance (AMR) mobilome plays a key role in the dissemination of resistance genes encoded by mobile genetics elements (MGEs) including plasmids, transposons (Tns), and insertion sequences (ISs). These MGEs contribute to the dissemination of multidrug resistance (MDR) in enteric bacterial pathogens which have been considered as a global public health risk., Methods: To further understand the diversity and distribution of AMR genes and MGEs across different plasmid types, we utilized multiple sequence-based computational approaches to evaluate AMR-associated plasmid genetics. A collection of 1,309 complete plasmid sequences from Gammaproteobacterial species, including 100 plasmids from each of the following 14 incompatibility (Inc) types: A/C, BO, FIA, FIB, FIC, FIIA, HI1, HI2, I1, K, M, N, P except W, where only 9 sequences were available, was extracted from the National Center for Biotechnology Information (NCBI) GenBank database using BLAST tools. The extracted FASTA files were analyzed using the AMRFinderPlus web-based tools to detect antimicrobial, disinfectant, biocide, and heavy metal resistance genes and ISFinder to identify IS/Tn MGEs within the plasmid sequences., Results and Discussion: In silico prediction based on plasmid replicon types showed that the resistance genes were diverse among plasmids, yet multiple genes were widely distributed across the plasmids from enteric bacterial species. These findings provide insights into the diversity of resistance genes and that MGEs mediate potential transmission of these genes across multiple plasmid replicon types. This notion was supported by the observation that many IS/Tn MGEs and resistance genes known to be associated with them were common across multiple different plasmid types. Our results provide critical insights about how the diverse population of resistance genes that are carried by the different plasmid types can allow for the dissemination of AMR across enteric bacteria. The results also highlight the value of computational-based approaches and in silico analyses for the assessment of AMR and MGEs, which are important elements of molecular epidemiology and public health outcomes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Algarni, Han, Gudeta, Khajanchi, Ricke, Kwon, Rhoads and Foley.)

Foodborne pathogen Campylobacter jejuni has been associated with ruminants. The objectives of this experiment were to determine C. jejuni survivability in mixed in vitro rumen microbial populations and the impact on methane production with or without methane inhibitors 2-bromosulfonate (BES) and/or sodium nitrate. When inoculated into rumen microbial populations without or with 0.5 mM BES, 5.0 mM nitrate or their combination, C. jejuni viability decreased from 4.7 ± 0.1 log 10 colony forming units (CFU)/mL after 24 h. Loss of C. jejuni viability was greater ( P  < 0.05) when incubated under 100% CO 2 compared to 50% H 2 :50% CO 2 , decreasing 1.46 versus 1.15 log units, respectively. C. jejuni viability was also decreased ( P  < 0.05) by more than 0.43 log units by the anti-methanogen treatments. Rumen microbial populations produced less methane ( P  = 0.05) when incubated with than without C. jejuni regardless of whether under 100% CO 2 or 50% H 2 :50% CO 2 . For either gas phase, nitrate was decreased (13.2 versus 37.9%) by the anti-methanogen treatments versus controls although not always significant. C. jejuni -inoculated populations metabolized 16.4% more ( P  < 0.05) nitrate under H 2 :CO 2 versus 100% CO 2 . Apparently, C. jejuni can compete for H 2 with methanogens but has limited survivability under rumen conditions.

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.

Poultry nutrition and feed manufacturing are interrelated for a variety of reasons. Diet formulation is essential for optimizing bird growth and feed conversion, but compositional differences and the presence of certain feed additives can alter the gastrointestinal microbial composition and functionality. Not only does dietary composition and digestibility influence poultry performance, but specific physical characteristics such as feed particle size and thermal treatments can impact the avian gastrointestinal tract (GIT) microbiota. Poultry feeds also have a characteristic microbial ecology consisting of pathogenic and nonpathogenic microorganisms. Some feed-borne pathogens such as Salmonella are well studied and linked with the colonization of birds consuming the feed. However, much less is known about the nonpathogenic feed microbiome and what impact that might have on the bird's GIT. This review discusses the potential interaction between poultry feed and the GIT microbiome, microbial ecology of feed, application of microbiome analyses to feed, and approaches for communicating these complex data sets to the poultry industry., Competing Interests: Disclosures Joshua Jendza was employed by BASF Corporation during the execution of the current project. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022. Published by Elsevier Inc.)

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., Competing Interests: DISCLOSURES There are no conflict of interests with any of the authors., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

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., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

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., Competing Interests: Disclosures There is no conflict of interest with any of the authors., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

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., Competing Interests: DISCLOSURES There is no conflict of interest for any of the authors., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

The foodborne pathogen Salmonella enterica is considered a global public health risk. Salmonella enterica isolates can develop resistance to several antimicrobial drugs due to the rapid spread of antimicrobial resistance (AMR) genes, thus increasing the impact on hospitalization and treatment costs, as well as the healthcare system. Mobile genetic elements (MGEs) play key roles in the dissemination of AMR genes in S. enterica isolates. Multiple phenotypic and molecular techniques have been utilized to better understand the biology and epidemiology of plasmids including DNA sequence analyses, whole genome sequencing (WGS), incompatibility typing, and conjugation studies of plasmids from S. enterica and related species. Focusing on the dynamics of AMR genes is critical for identification and verification of emerging multidrug resistance. The aim of this review is to highlight the updated knowledge of AMR genes in the mobilome of Salmonella and related enteric bacteria. The mobilome is a term defined as all MGEs, including plasmids, transposons, insertion sequences (ISs), gene cassettes, integrons, and resistance islands, that contribute to the potential spread of genes in an organism, including S. enterica isolates and related species, which are the focus of this review., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Algarni, Ricke, Foley and Han.)

In 2016, the United States Department of Agriculture (USDA) Food Safety and Inspection Service (FSIS) established guidelines which modified the Buffered Peptone Water (BPW) rinsate material to include additional compounds that would better neutralize residual processing aids and allow for better recovery of sublethal injured Salmonella spp. cells. While the added compounds improved the recovery of Salmonella spp., specific data to understand how the new rinse agent, neutralizing Buffered Peptone Water (nBPW), impacts the recovery of other microorganisms such as Campylobacter spp. and indicator microorganisms are lacking. Therefore, this study evaluated the impact of rinse solutions (BPW or nBPW) used in Whole Bird Carcass rinsate (WBCR) collections on the subsequent microbiome and downstream culturing methodologies. Carcasses exiting a finishing chiller were rinsed in 400 ml of BPW or nBPW. Resulting rinsates were analyzed for Enterobacteriaceae (EB), Salmonella , and Campylobacter spp. prevalence and total aerobic bacteria (APC) and EB load. The 16S rDNA of the rinsates and the matrices collected from applied microbiological analyses were sequenced on an Illumina MiSeq ® . Log 10 -transformed counts were analyzed in JMP 15 using ANOVA with means separated using Tukey's HSD, and prevalence data were analyzed using Pearson's χ 2 ( P ≤ 0.05). Diversity and microbiota compositions (ANCOM) were analyzed in QIIME 2.2019.7 ( P ≤ 0.05; Q ≤ 0.05). There was an effect of rinsate type on the APC load and Campylobacter spp. prevalence ( P < 0.05), but not the quantity or prevalence of EB or Salmonella spp. prevalence. There were differences between the microbial diversity of the two rinsate types and downstream analyses ( P < 0.05). Additionally, several taxa, including Streptococcus , Lactobacillus , Aeromonas , Acinetobacter , Clostridium , Enterococcaceae, Burkholderiaceae, and Staphylococcaceae, were differentially abundant in paired populations. Therefore, the rinse buffer used in a WBCR collection causes proportional shifts in the microbiota, which can lead to differences in results obtained from cultured microbial populations., Competing Interests: JW is employed by the company Tyson Foods (Springdale, AR, United States). The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Wages, Dittoe, Feye and Ricke.)

Salmonella Infantis has been the etiological agent of numerous foodborne outbreaks of nontyphoidal Salmonella. Consequently, there is an emergent need to mitigate Salmonella Infantis among poultry. Thus, this study evaluated the efficacy of cetylpyridinium chloride (CPC) versus peroxyacetic acid (PAA), on bone-in, skin-on chicken thighs for the reduction of Salmonella and changes in the microbiota. Exactly 100 skin-on, bone-in chicken thighs (2 trials, 0 and 24 h, k = 5, n = 5, N = 50) were inoculated with 10 8 CFU/mL of a nalidixic acid resistant strain of S. Infantis for an attachment of 10 6 CFU/g. Thighs were treated with 20 s part dips (350 mL): a no inoculum, no treatment control (NINTC); no treatment control (NTC); tap water (TW); TW+CPC; TW+PAA. Following treatment, thighs were rinsed in 150 mL of nBPW, and rinsates were collected. Rinsates were spot plated for Salmonella and aerobic bacteria (APC). Log 10 transformed counts were analyzed using a mixed-effects model (random effect = trial) with means separated using Tukey's HSD (P ≤ 0.05). The genomic DNA of rinsates was extracted, and the 16S rDNA was sequenced on an Illumina MiSeq. Microbiota data were analyzed using QIIME2, with data considered significant at P ≤ 0.05 (main effects) and Q≤0.05 (pairwise differences). Treatment × time interactions were observed for both Salmonella and APC (P < 0.05). The treatment of thighs with PAA and CPC reduced Salmonella and APC in respect to the controls. Numerically, thighs treated with CPC had less Salmonella (4.29 log 10 CFU/g) and less APC (4.56 log 10 CFU/g) at 24 h than all other treatments (P > 0.05). Differences in diversity metrics were not consistently observed between treatments; however, in trial 2, the NTC treated thighs were different than those treated with CPC (P < 0.05; Q < 0.05). In both trials, ANCOM, the analysis of microbiome compositional profiles, revealed shifts at both the phylum and order levels with thighs being different in the relative abundances of Proteobacteria (P < 0.05). In conclusion, treatment of skin-on poultry parts with CPC may reduce the risk of foodborne outbreaks caused by Salmonella Infantis., (Copyright © 2021. Published by Elsevier Inc.)

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., (© The Author(s) 2022. Published by Oxford University Press on behalf of the American Society of Animal Science.)