Publications by authors named "Steven C Ricke"

173 Publications

Prebiotics and alternative poultry production.

Authors:
Steven C Ricke

Poult Sci 2021 Jul 27;100(7):101174. Epub 2021 Mar 27.

Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI. Electronic address:

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.
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http://dx.doi.org/10.1016/j.psj.2021.101174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8187256PMC
July 2021

Probiotics and potential applications for alternative poultry production systems.

Poult Sci 2021 Jul 26;100(7):101156. Epub 2021 Mar 26.

Faculty of Bioengineering of Animal Resources, Banat University of Animal Sciences and Veterinary Medicine - King Michael I of Romania, Timisoara, Romania. Electronic address:

Concerns over animal welfare continue to be a critical component of law and policies associated with commercial food animal production. Social and market pressures are the driving forces behind the legislation and result in the change of poultry production management systems. As a result, the movement toward cage-free and aviary-based egg production systems has become standard practices. Cage-based systems being replaced by alternative methods that offer a suitable housing environment to meet or exceed poultry welfare needs and require different management, including the ban of antibiotics in poultry diets. For broiler production, pasture- raised and free-range management systems have become more popular. However, challenges remain from exposure to disease-causing organisms and foodborne pathogens in these environments. Consequently, probiotics can be supplemented in poultry diets as commercial feed additives. The present review discusses the impacts of these probiotics on the performance of alternative poultry production systems for improving food safety and poultry health by mitigating pathogenic organisms and improving egg and meat quality and production.
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http://dx.doi.org/10.1016/j.psj.2021.101156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8181177PMC
July 2021

An overview of health challenges in alternative poultry production systems.

Poult Sci 2021 Jul 27;100(7):101173. Epub 2021 Mar 27.

Department of Animal and Dairy Science, University of Georgia, Athens, GA. Electronic address:

Due to consumer demand and changing welfare standards on health, ecology, equity, and safety concepts, poultry production has changed markedly over the past 20 y. One of the greatest changes to poultry production standards is now offering poultry limited access to the outdoors in alternative and organic poultry production operations. Although operations allowing access to the outdoors are still only a small portion of commercial poultry production, it may impact the gastrointestinal (GIT) health of the bird in different ways than birds raised under conventional management systems. The present review describes current research results in alternative systems by identifying how different poultry production operations (diet, environmental disruptive factors, diseases) impact the ecology and health of the GIT. Various research efforts will be discussed that illustrate the nutritional value of free-range forages and how forages could be beneficial to animal health and production of both meat and eggs. The review also highlights the need for potential interventions to limit diseases without using antibiotics. These alternatives could enhance both economics and sustainability in organic and free-range poultry production.
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http://dx.doi.org/10.1016/j.psj.2021.101173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8170424PMC
July 2021

Microbial ecology of alfalfa, radish, and rapeseed sprouts based on culture methods and 16S rRNA microbiome sequencing.

Food Res Int 2021 06 22;144:110316. Epub 2021 Mar 22.

Department of Food Science and Engineering, Ewha Womans University, Seoul, South Korea. Electronic address:

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.
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http://dx.doi.org/10.1016/j.foodres.2021.110316DOI Listing
June 2021

Yeast Fermentate-Mediated Reduction of Reading and Typhimurium in an Turkey Cecal Culture Model.

Front Microbiol 2021 15;12:645301. Epub 2021 Apr 15.

Meat Science and Animal Biologics Discovery, Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States.

Reading is an ongoing public health issue in the turkey industry, leading to significant morbidity in humans in the United States. Pre-harvest intervention strategies that contribute to the reduction of foodborne pathogens in food animals, such as the yeast fermentation metabolites of Original XPC (XPC), may become the key to multi-hurdle farm to fork strategies. Therefore, we developed an anaerobic turkey cecal model to assess the effects of XPC on the ceca of commercial finisher tom turkeys fed diets void of XPC and antibiotics. Using the turkey cecal culture method, ceca were tested with and without XPC for their anti- Reading and the previously defined anti-Typhimurium (ST97) effects. Ultimately, the anti- effects were independent of serovar ( > 0.05). At 0 h post inoculation (hpi), levels were equivalent between treatments at 7.3 Log CFU/mL, and at 24 hpi, counts in XPC were reduced by 5 Log CFU/mL, which was 2.1 Log lower than the control ( < 0.05). No differences in serovar prevalence existed ( > 0.05), with a 92% reduction in positive XPC-treated ceca cultures by 48 hpi ( < 0.05). To evaluate changes to the microbiota independent of the immune response, the 16S rDNA was sequenced using the Illumina MiSeq platform. Data indicated a profound effect of time and treatment for the reduction of irrespective of serovar. XPC sustained diversity metrics compared to the control, demonstrating a reduction in diversity over time ( < 0.05).
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http://dx.doi.org/10.3389/fmicb.2021.645301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081899PMC
April 2021

Incompatibility Group I1 (IncI1) Plasmids: Their Genetics, Biology, and Public Health Relevance.

Microbiol Mol Biol Rev 2021 05 28;85(2). Epub 2021 Apr 28.

Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA.

Bacterial plasmids are extrachromosomal genetic elements that often carry antimicrobial resistance (AMR) genes and genes encoding increased virulence and can be transmissible among bacteria by conjugation. One key group of plasmids is the incompatibility group I1 (IncI1) plasmids, which have been isolated from multiple of food animal origin and clinically ill human patients. The IncI group of plasmids were initially characterized due to their sensitivity to the filamentous bacteriophage If1. Two prototypical IncI1 plasmids, R64 and pColIb-P9, have been extensively studied, and the plasmids consist of unique regions associated with plasmid replication, plasmid stability/maintenance, transfer machinery apparatus, single-stranded DNA transfer, and antimicrobial resistance. IncI1 plasmids are somewhat unique in that they encode two types of sex pili, a thick, rigid pilus necessary for mating and a thin, flexible pilus that helps stabilize bacteria for plasmid transfer in liquid environments. A key public health concern with IncI1 plasmids is their ability to carry antimicrobial resistance genes, including those associated with critically important antimicrobials used to treat severe cases of enteric infections, including the third-generation cephalosporins. Because of the potential importance of these plasmids, this review focuses on the distribution of the plasmids, their phenotypic characteristics associated with antimicrobial resistance and virulence, and their replication, maintenance, and transfer.
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http://dx.doi.org/10.1128/MMBR.00031-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8139525PMC
May 2021

Variations in bacterial community structure and antimicrobial resistance gene abundance in cattle manure and poultry litter.

Environ Res 2021 06 24;197:111011. Epub 2021 Mar 24.

Department of Agriculture, Food and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche 10, 60131, Ancona, Italy.

Cattle manure and poultry litter are widely used as fertilizers as they are excellent sources of nutrients; however, potential adverse environmental effects exist during land applications, due to the release of zoonotic bacteria and antimicrobial resistance (AMR) genes. This study was conducted to understand linkages between physiochemical composition, bacterial diversity, and AMR gene presence of cattle manure and poultry litter using quantitative polymerase chain reaction to enumerate four AMR genes (ermB, sulI, intlI, and bla), Illumina sequencing of the 16 S region, and analysis of physical and chemical properties. Principal coordinate analysis of Bray-Curtis distance revealed distinct bacterial community structures between the two manure sources. Greater alpha diversity occurred in cattle manure compared to poultry litter (P < 0.05). Redundancy analysis showed a strong relationship between manure physiochemical and composition and bacterial abundance, with positive relationships occurring among electrical conductivity and carbon/nitrogen, and negative associations for total solids and soluble fractions of heavy metals. Cattle manure exhibited greater abundance of macrolide (ermB) and sulfonamide (sulI) resistant genes. Consequently, fresh cattle manure applications may result in greater potential spread of AMR genes to the soil-water environment (relative to poultry litter) and novel best management strategies (such as composting) may reduce the release of AMR genes to the soil-water environment.
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http://dx.doi.org/10.1016/j.envres.2021.111011DOI Listing
June 2021

Current Perspectives and Potential of Probiotics to Limit Foodborne in Poultry.

Front Microbiol 2020 22;11:583429. Epub 2020 Dec 22.

Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States.

Poultry has been one of the major contributors of related human foodborne illness. Numerous interventions have been applied to limit colonization in poultry at the farm level, but other strategies are under investigation to achieve more efficient control. Probiotics are viable microbial cultures that can establish in the gastrointestinal tract (GIT) of the host animal and elicit health and nutrition benefits. In addition, the early establishment of probiotics in the GIT can serve as a barrier to foodborne pathogen colonization. Thus, probiotics are a potential feed additive for reducing and eliminating the colonization of in the GIT of poultry. Screening probiotic candidates is laborious and time-consuming, requiring several tests and validations both and . The selected probiotic candidate should possess the desired physiological characteristics and anti- effects. Probiotics that limit colonization in the GIT rely on different mechanistic strategies such as competitive exclusion, antagonism, and immunomodulation. Although numerous research efforts have been made, the application of limiting probiotics used in poultry remains somewhat elusive. This review summarizes current research progress on identifying and developing probiotics against and presenting possible directions for future research efforts.
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http://dx.doi.org/10.3389/fmicb.2020.583429DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7782433PMC
December 2020

Identification of bacterial isolates from commercial poultry feed via 16S rDNA.

J Environ Sci Health B 2021 5;56(3):272-281. Epub 2021 Jan 5.

Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA.

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.
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http://dx.doi.org/10.1080/03601234.2020.1868236DOI Listing
May 2021

Endophyte-Infected Tall Fescue Affects Rumen Microbiota in Grazing Ewes at Gestation and Lactation.

Front Vet Sci 2020 14;7:544707. Epub 2020 Oct 14.

Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, United States.

Tall fescue () is a cool-season perennial grass that is widely used as a forage for many livestock species including sheep. An endophyte ( in tall fescue produces ergot alkaloids that enhance plant survival but produce toxicosis in animals. The objective of this study was to investigate the rumen microbiota from gestation and lactation in ewes grazing tall fescue pastures with high (HA) or moderate (MA) levels of endophyte infection, and their relationship with serum parameters. Data were collected at the beginning of the study (d1), the week before initiation of lambing (d51), and at the end of the trial (d115). The rumen microbiota was evaluated using 16S rRNA gene sequencing. Ewes grazing HA had greater serum non-esterified fatty acid (NEFA) ( = 0.024) levels compared with ewes in MA pasture at d115. Both the number of observed OTUs and Shannon diversity index tended ( = 0.08, = 0.06) to be greater for HA than for MA on d115. At the genus level, relative abundance increased with time in both MA and HA (on d1, d51, and d115: 15.17, 25.59, and 24.78% in MA; 14.17, 18.10, and 19.41% in HA). Taxa unclassified at the genus level including (unclassified) , and exhibited higher abundances in HA at d51 (3.72, 2.07, and 11.22%) compared with MA (2.06, 1.28, and 7.42%). The predictor microbiota for HA and MA were identified by a random forest classification model. The HA predictors included bacteria associated with unclassified and . Other OTUs classified as and could be microbial predictors for MA. The OTUs classified as and were negatively correlated with serum concentration of prolactin. Negative correlations with NEFA were observed in the microbiota such as species affiliated to unclassified and . OTUs classified as and exhibited a positive correlation with NEFA. Our study confirmed that the rumen microbiota populations were affected by high levels of toxins in endophyte-infected tall fescue and were associated with host hormone and energy metabolism.
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http://dx.doi.org/10.3389/fvets.2020.544707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7591458PMC
October 2020

Strategies to Improve Poultry Food Safety, a Landscape Review.

Authors:
Steven C Ricke

Annu Rev Anim Biosci 2021 02 6;9:379-400. Epub 2020 Nov 6.

Meat Science & Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; email:

Food safety remains a significant public health issue for the poultry industry. Foodborne pathogens can be in contact at all phases of poultry production, from initial hatch to processing and ultimately to retail and meal preparation. and have been considered the primary foodborne pathogens associated with poultry. Both organisms are major causative agents of human foodborne illness. Limiting these pathogens in poultry production requires identifying their sources and routes of transmission. This involves the ability to isolate and precisely identify them using methodologies capable of discernment at the genome level. Interventions to reduce their occurrence in poultry production employ two basic strategies: prevention of establishment and elimination of already-established pathogens. This review provides an overview of current findings and prospects for further research on poultry food safety issues.
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http://dx.doi.org/10.1146/annurev-animal-061220-023200DOI Listing
February 2021

The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota.

BMC Microbiol 2020 11 2;20(1):332. Epub 2020 Nov 2.

DIMEVET, University of Bologna, Ozzano Emilia, Bologna, Italy.

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.
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http://dx.doi.org/10.1186/s12866-020-02001-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7607615PMC
November 2020

Formic Acid as an Antimicrobial for Poultry Production: A Review.

Front Vet Sci 2020 3;7:563. Epub 2020 Sep 3.

Anitox Corporation, Lawrenceville, GA, United States.

Organic acids continue to receive considerable attention as feed additives for animal production. Most of the emphasis to date has focused on food safety aspects, particularly on lowering the incidence of foodborne pathogens in poultry and other livestock. Several organic acids are currently either being examined or are already being implemented in commercial settings. Among the several organic acids that have been studied extensively, is formic acid. Formic acid has been added to poultry diets as a means to limit spp. and other foodborne pathogens both in the feed and potentially in the gastrointestinal tract once consumed. As more becomes known about the efficacy and impact formic acid has on both the host and foodborne pathogens, it is clear that the presence of formic acid can trigger certain pathways in spp. This response may become more complex when formic acid enters the gastrointestinal tract and interacts not only with spp. that has colonized the gastrointestinal tract but the indigenous microbial community as well. This review will cover current findings and prospects for further research on the poultry microbiome and feeds treated with formic acid.
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http://dx.doi.org/10.3389/fvets.2020.00563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7494846PMC
September 2020

Antiviral activity of a novel mixture of natural antimicrobials, in vitro, and in a chicken infection model in vivo.

Sci Rep 2020 10 6;10(1):16631. Epub 2020 Oct 6.

Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, 18a Newforge Lane, Belfast, BT9 5PX, Northern Ireland, UK.

The aim of this study was to test in vitro the ability of a mixture of citrus extract, maltodextrin, sodium chloride, lactic acid and citric acid (AuraShield L) to inhibit the virulence of infectious bronchitis, Newcastle disease, avian influenza, porcine reproductive and respiratory syndrome (PRRS) and bovine coronavirus viruses. Secondly, in vivo, we have investigated its efficacy against infectious bronchitis using a broiler infection model. In vitro, these antimicrobials had expressed antiviral activity against all five viruses through all phases of the infection process of the host cells. In vivo, the antimicrobial mixture reduced the virus load in the tracheal and lung tissue and significantly reduced the clinical signs of infection and the mortality rate in the experimental group E2 receiving AuraShield L. All these effects were accompanied by a significant reduction in the levels of pro-inflammatory cytokines and an increase in IgA levels and short chain fatty acids (SCFAs) in both trachea and lungs. Our study demonstrated that mixtures of natural antimicrobials, such AuraShield L, can prevent in vitro viral infection of cell cultures. Secondly, in vivo, the efficiency of vaccination was improved by preventing secondary viral infections through a mechanism involving significant increases in SCFA production and increased IgA levels. As a consequence the clinical signs of secondary infections were significantly reduced resulting in recovered production performance and lower mortality rates in the experimental group E2.
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http://dx.doi.org/10.1038/s41598-020-73916-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7538884PMC
October 2020

Assessment of a Potential Role of DSM 18020 as a Pectinase Producer for Utilization in Poultry Diets Based on Analyses.

Front Microbiol 2020 23;11:751. Epub 2020 Apr 23.

Department of Food Science and Center for Food Safety, University of Arkansas, Fayetteville, AR, United States.

Currently, the poultry industry has been faced with consumer pressure to utilize only vegetable feedstuffs in poultry diets, eliminate antibiotics from poultry production, and rear poultry in free range systems. To maintain current production standards, the industry must determine ways to enhance nutrient uptake and utilization further. One possible solution is the supplementation of pectinase, an enzyme that degrades pectin within the cell walls of plants, in poultry diets. Therefore, the objective of the current study was to determine the potential role of a pectinase producer, DSM 18020, as a commercially utilized pectinase producer in poultry diets against other known pectinase producers, . In the current study, whole genomes of DSM 18020 (Dd18020), 3937 (Dd3937), IPO 2222 (Ds2222), C-125 (BhC125), and subsp. str. 168 (Bs168) were compared using bioinformatic approaches to compare the chromosomal genome size, GC content, protein coding genes (CDS), total genes, average protein length (a.a.) and determine the predicted metabolic pathways, predicted pectin degrading enzymes, and pectin-degradation pathways across pectinase producers. Due to insufficient information surrounding the genome of Dd18020 (lack of annotation), the genome of Dd3937, a 99% identical genome to Dd18020, was utilized to compare pectinase-associated enzymes and pathways. The results from the current study demonstrated that Dd3937 possessed the most significant proportion of pathways presented and the highest number of pathways related to degradation, assimilation, and utilization of pectin. Also, Dd18020 exhibited a high number of pectinase-related enzymes. Both Dd3937 and Dd2222 shared the pectin degradation I pathway via the EC 3.1.1.11, EC 3.2.1.82, and EC 4.2.2.- enzymes, but did not share this pathway with either species. In conclusion, Dd18020 demonstrated the genetic potential to produce multiple pectinase enzymes that could be beneficial to the degradation of pectin in poultry diets. However, for Dd18020 to become a commercially viable enzyme producer for the poultry industry, further research quantifying the pectinase production and determining the stability of the produced pectinases during feed manufacturing are necessary.
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http://dx.doi.org/10.3389/fmicb.2020.00751DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7191031PMC
April 2020

Draft Genome Sequences of 11 Bacterial Strains Isolated from Commercial Corn-Based Poultry Feed.

Microbiol Resour Announc 2020 Apr 16;9(16). Epub 2020 Apr 16.

Department of Biology, Pittsburg State University, Pittsburg, Kansas, USA

Here, we report 11 bacterial strains isolated from commercial corn-based poultry feed to determine their potential as hygienic indicator microorganisms through a comparison of genome sizes and distribution patterns of unique genes. These isolates belonged to the genera , , , , and .
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http://dx.doi.org/10.1128/MRA.00170-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163015PMC
April 2020

Response to Anaerobic Environments.

Pathogens 2020 Mar 12;9(3). Epub 2020 Mar 12.

Cell and Molecular Biology, The University of Southern Mississippi, Hattiesburg, MS 39406, USA.

is a Gram-positive facultative anaerobic bacterium that is responsible for the disease, listeriosis. It is particularly lethal in pregnant women, the fetus, the elderly and the immunocompromised. The pathogen survives and replicates over a wide range of temperatures (4 to 42 °C), pH, salt and oxygen concentrations. Because it can withstand various environments, is a major concern in food processing industries, especially in dairy products and ready-to-eat fruits, vegetables and deli meats. The environment in which the pathogen is exposed can influence the expression of virulence genes. For instance, studies have shown that variations in oxygen availability can impact resistance to stressors. Further investigation is needed to understand the essential genes required for the growth of in anaerobic conditions. Therefore, the purpose of this review is to highlight the data on under known environmental stresses in anaerobic environments and to focus on gaps in knowledge that may be advantageous to study in order to better understand the pathogenicity of the bacterium.
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http://dx.doi.org/10.3390/pathogens9030210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7157565PMC
March 2020

The Preliminary Development of an Poultry Cecal Culture Model to Evaluate the Effects of Original XPC for the Reduction of and Its Potential Effects on the Microbiota.

Front Microbiol 2019 23;10:3062. Epub 2020 Jan 23.

Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, United States.

Poultry is a major reservoir for the pathogen . inhabits the poultry gastrointestinal tract as a part of the gut microbiota. The objective of this study was to evaluate both the survival of and the changes in the population dynamics of the cecal microbiome during an inoculation in the presence or absence of the functional metabolites of Diamond V Original XPC (XPC). Two independent trials were conducted. Broiler chickens ( = 6 per Trial 1 and = 3 per Trial 2) were raised according to standard industry guidelines and euthanized on Day 41. The ceca were collected aseptically, their contents removed independently and then used in an microaerobic model with 0.1% cecal contents + with or without 1% XPC (w/v). Before the inoculation with a chloramphenicol resistant marker strain of , the cecal contents were pre-incubated with XPC at 42°C for 24 h, in a shaking incubator (200 rpm) under microaerobic conditions, then experimentally inoculated with 10/ml of into the appropriate treatment groups. At 0 and 24 h for Trial 1, and 48 h for Trial 2, sub-samples of the culture ( = 3 ceca, two technical replicates per ceca, XPC alone or ceca culture alone) were enumerated using a Petroff-Hausser counter, and the DNA was extracted for microbiome analysis. DNA was isolated using the Qiagen QIAamp Fast Stool DNA Mini Kit and sequenced using the Illumina MiSeq platform. The reads were filtered, normalized, and assigned taxonomical identities using the QIIME2 pipeline. The relative microbiota populations were identified via ANCOM. Altogether, evidence suggests that XPC alters the microbiome, and in turn reduces survival.
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http://dx.doi.org/10.3389/fmicb.2019.03062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6990144PMC
January 2020

Prebiotics and the poultry gastrointestinal tract microbiome.

Poult Sci 2020 Feb 24;99(2):670-677. Epub 2020 Jan 24.

Center of Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR 72704.

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.
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http://dx.doi.org/10.1016/j.psj.2019.12.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7587714PMC
February 2020

Gastrointestinal microbiomes of broilers and layer hens in alternative production systems.

Poult Sci 2020 Feb 24;99(2):660-669. Epub 2020 Jan 24.

Egg Safety & Quality Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens 30605, GA.

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.
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http://dx.doi.org/10.1016/j.psj.2019.12.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7587794PMC
February 2020

Aerobic plate count, and loads of whole bird carcass rinses from pre-chillers with different water management strategies in a commercial poultry processing plant.

J Environ Sci Health B 2020 15;55(2):155-165. Epub 2019 Nov 15.

Center for Food Safety and Department of Food Science, University of Arkansas, Fayetteville, Arkansas, USA.

and 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 spp. and 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.
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http://dx.doi.org/10.1080/03601234.2019.1670522DOI Listing
May 2020

Review of Antibiotic Resistance, Ecology, Dissemination, and Mitigation in U.S. Broiler Poultry Systems.

Front Microbiol 2019 15;10:2639. Epub 2019 Nov 15.

Poultry Production and Product Safety Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Fayetteville, AR, United States.

Since the onset of land application of poultry litter, transportation of microorganisms, antibiotics, and disinfectants to new locations has occurred. While some studies provide evidence that antimicrobial resistance (AMR), an evolutionary phenomenon, could be influenced by animal production systems, other research suggests AMR originates in the environment from non-anthropogenic sources. In addition, AMR impacts the effective prevention and treatment of poultry illnesses and is increasingly a threat to global public health. Therefore, there is a need to understand the dissemination of AMR genes to the environment, particularly those directly relevant to animal health using the One Health Approach. This review focuses on the potential movement of resistance genes to the soil via land application of poultry litter. Additionally, we highlight impacts of AMR on microbial ecology and explore hypotheses explaining gene movement pathways from U.S. broiler operations to the environment. Current approaches for decreasing antibiotic use in U.S. poultry operations are also described in this review.
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http://dx.doi.org/10.3389/fmicb.2019.02639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6872647PMC
November 2019

The Reduction of Pathogen Load on Ross 708 Broilers when Using Different Sources of Commercial Peracetic Acid Sanitizers in a Pilot Processing Plant.

Microorganisms 2019 Oct 29;7(11). Epub 2019 Oct 29.

Center for Food Safety and Department of Poultry Science, University of Arkansas, Fayetteville, AR 72704, USA.

Peracetic acid (PAA) in poultry processing is not necessarily the same from company to company. Anecdotal evidence suggests that PeraClean may be more stable compared to the competition; however, it is not known what impact potential differences in chemical stability may have. In order to evaluate the antimicrobial effects of PAA, one PAA (PeraClean, P) was qualitatively compared against two competitor products (Competitors 1 and 2, C1 and C2) at the University of Arkansas Pilot Processing Plant. A total of 150 Ross 708 broilers (42 d) were used in the current study. Briefly, prior to treatment, 10 birds were sampled post-evisceration (C). Then, one of four treatment groups per PAA were applied (A1, A2, B1, and B2). The birds were dipped in either 400 ppm or 600 ppm PAA (A or B), chilled in either 25 ppm or 45 ppm PAA (1 or 2), and then manually agitated in 400 mL of nBPW for 1 min. There were 10 birds per treatment group in total. The resulting rinsates were transported to the Center for Food Safety and assessed for total microbiological load with total aerobic plate counts (Trypticase Soy Agar; APC), coliforms, (Eosin Methylene Blue Media; EMB), (Xylose Lysine Deoxycholate agar, XLD), and (modified Charcoal Cefoperazone Deoxycholate Agar, mCCDA). The microbiological plates were incubated as per manufacturer's directions. Statistical analyses were calculated in JMP 14.0, with a significance level of ≤ 0.05. Data indicate that all three sources of PAA are effective sanitizers for poultry processing applications compared within treatment. Qualitatively, there were differences in efficacy between the treatments. However, additional studies will be required to determine if those differences are quantitatively distinctive and if they are attributable to differences in product stability.
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http://dx.doi.org/10.3390/microorganisms7110503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6920778PMC
October 2019

Evaluation of Incompatibility Group I1 (IncI1) Plasmid-Containing and Assessment of the Plasmids in Bacteriocin Production and Biofilm Development.

Front Vet Sci 2019 6;6:298. Epub 2019 Sep 6.

Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, AR, United States.

Mobile genetic elements, such as plasmids, can potentially increase the ability of bacteria to infect and persist in vertebrate host cells. IncI1 plasmids are widely distributed in from food animal sources and associated with clinically important strains. These plasmids often encode antimicrobial resistance; however, little is known about their impact on the virulence of strains. To assess the potential impact of the plasmids on virulence, 43 IncI1-positive isolates from human and animal sources were subjected to whole genome sequence (WGS) analyses and evaluated for their abilities to invade and persist for 48 h in Caco-2 human intestinal epithelial cells, form biofilms and encode bacteriocins. Draft WGS data were submitted to predict the presence of virulence and antimicrobial resistance genes, plasmid replicon types present, conduct plasmid multilocus sequence typing (pMLST), and core genome MLST (cgMLST) in the isolates. Caco-2 cells were infected with strains and incubated for both one and 48 h for the invasion and persistence assays, respectively. Additionally, isolates and IncI1 plasmid carrying transconjugants ( = 12) generated in were assessed for their ability to produce biofilms and bacteriocin inhibition of growth of other bacteria. All isolates infected Caco-2 cells and persisted in the cells at 48 hrs. Persistent cell counts were observed to be significantly higher than invasion assay cell counts in 26% of the isolates. Among the IncI1 plasmids, there were 18 pMLST types. Nearly 35% ( = 15) of isolates produced biofilms; however, none of the IncI1-positive transconjugants produced increased biofilms compared to the recipient. Approximately 65% ( = 28) of isolates and 67% ( = 8) of IncI1-positive transconjugants were able to inhibit growth of at least one strain; however, none inhibited the growth of strains from species other than . The study characterized IncI1 positive isolates and provided evidence about the potential contributions of IncI1 plasmids virulence phenotypes and areas where they do not. These findings should allow for more focused efforts to assess the impact of plasmids on bacterial pathophysiology and human health.
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http://dx.doi.org/10.3389/fvets.2019.00298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6743044PMC
September 2019

Non-molecular characterization of pellicle formation by poultry Kentucky strains and other poultry-associated serovars in Luria Bertani broth.

J Environ Sci Health B 2019 9;54(12):972-978. Epub 2019 Sep 9.

Center for Food Safety and Food Science Department, University of Arkansas, Fayetteville, AR, USA.

There is limited research concerning the biofilm-forming capabilities of Kentucky, a common poultry isolate. The objective was to quantitate pellicle formation of . Kentucky versus better-characterized strains of Enteritidis and Heidelberg. In separate experiments, 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 ( ≤ 0.05). In the first experiment, there was no significant effect between strain and serovars ( > 0.05), but media type affected pellicle formation significantly with LB Miller and LB minus NaCl plus 2% glucose resulting in no pellicle formation ( < 0.001). When grown in 50 mL, Kentucky 38-0085 produced larger pellicles than Kentucky 38-0055, and Heidelberg strain 38-0127 ( < 0.0001). Serial transfers of pellicles did not significantly affect pellicle formation ( > 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.
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http://dx.doi.org/10.1080/03601234.2019.1661210DOI Listing
February 2020

A Microbiomic Analysis of a Pasture-Raised Broiler Flock Elucidates Foodborne Pathogen Ecology Along the Farm-To-Fork Continuum.

Front Vet Sci 2019 7;6:260. Epub 2019 Aug 7.

Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, United States.

While conventionally grown poultry continues to dominate the U. S. poultry industry, there is an increasing demand for locally-grown, "all natural" alternatives. The use of next generation sequencing allows for not only the gross (e.g., community structure) but also fine-scale (e.g., taxa abundances) examination of these complex microbial communities. This data provides a better understanding of how a pasture flock's microbiome changes throughout the production life cycle and how that change in microbial ecology changes foodborne pathogens in alternative poultry production systems. In order to understand this ecology better, pooled broiler samples were taken during the entire flock life cycle, from pre-hatch gastrointestinal samples ( = 12) to fecal samples from the brood ( = 5), and pasture ( = 10) periods. Additional samples were taken during processing, including skin and feather rinsates ( = 12), ceca ( = 12), and whole carcass rinses ( = 12), and finally whole carcasss rinsates of final products ( = 3). Genomic DNA was extracted, 16S rDNA microbiome sequencing was conducted (Illumina MiSeq), and microbiomes were analyzed and compared using QIIME 1.9.1 to determine how microbiomes shifted throughout production continuum, as well as what environmental factors may be influencing these shifts. Significant microbiome shifts occurred during the life cycle of the pasture broiler flock, with the brood and pasture fecal samples and cecal samples being very distinct from the other pre-hatch, processing, and final product samples. Throughout these varied microbiomes, there was a stable core microbiome containing 13 taxa. Within this core microbiome, five taxa represented known foodborne pathogens () or potential/emerging pathogens () whose relative abundances varied throughout the farm-to-fork continuum, although all were more prevalent in the fecal samples. Additionally, of the 25 physiochemical and nutrient variables measured from the fecal samples, the carbon to nitrogen ratio was one of the most significant variables to warrant further investigations because it impacted both general fecal microbial ecology and and taxa within the core fecal microbiomes. These findings demonstrate the need for further longitudinal, farm-to-fork studies to understand the ecology of the microbial ecology of pasture production flocks to improve animal, environmental, and public health.
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http://dx.doi.org/10.3389/fvets.2019.00260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6692657PMC
August 2019

A Historical Review on Antibiotic Resistance of Foodborne .

Front Microbiol 2019 26;10:1509. Epub 2019 Jul 26.

Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States.

is one of the most commonly reported foodborne human bacterial gastrointestinal pathogens. is the etiological agent of campylobacteriosis, which is generally a self-limited illness and therefore does not require treatment. However, when patients are immunocompromised or have other co-morbidities, antimicrobial treatment may be necessary for clinical treatment of campylobacteriosis, macrolides and fluoroquinolones are the drugs of choices. However, the increase in antimicrobial resistance of to clinically important antibiotics may become insurmountable. Because of the transmission between poultry and humans, the poultry industry must now allocate resources to address the problem by reducing as well as antimicrobial use, which may reduce resistance. This review will focus on the incidence of antibiotic-resistant in poultry, the clinical consequences of this resistance, and the mechanisms of antibiotic resistance associated with .
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http://dx.doi.org/10.3389/fmicb.2019.01509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6676416PMC
July 2019

Short Communication: Preliminary Differences Identified in Genes Responsible for Biofilm Formation in Poultry Isolates of Heidelberg, Enteritidis, and Kentucky.

Microorganisms 2019 Jul 9;7(7). Epub 2019 Jul 9.

Center for Food Safety and Food Science Department, University of Arkansas, Fayetteville, AR 72704, USA.

is one of the most prevalent foodborne pathogens. The large quantity of serovar types results in the colonization of a large spectrum of hosts, with different environmental conditions and hazards. The aim of this study was to evaluate the differences in gene expression ( and ) of serovars Heidelberg, Kentucky, and Enteritidis during biofilm formation using quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR). Overall, there appeared to be differences in expression between the different serovars with high variation between strains. These data are important as they demonstrate considerable variability in gene expression between serovars and strains of poultry isolates of .
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http://dx.doi.org/10.3390/microorganisms7070196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6680814PMC
July 2019

Formaldehydes in Feed and Their Potential Interaction With the Poultry Gastrointestinal Tract Microbial Community-A Review.

Front Vet Sci 2019 13;6:188. Epub 2019 Jun 13.

Department of Food Science, Center of Food Safety, University of Arkansas, Fayetteville, AR, United States.

As antibiotics continue to be phased out of livestock production, alternative feed amendments have received increased interest not only from a research standpoint but for commercial application. Most of the emphasis to date has focused on food safety aspects, particularly on lowering the incidence of foodborne pathogens in livestock. Several candidates are currently either being examined or are already being implemented in commercial settings. Among these candidates are chemical compounds such as formaldehyde. Formaldehyde has historically been used to inhibit in feeds during feed processing. Currently, there are several commercial products available for this purpose. This review will cover both the historical background, current research, and prospects for further research on the poultry gastrointestinal tract and feeds treated with formaldehyde.
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http://dx.doi.org/10.3389/fvets.2019.00188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6584747PMC
June 2019

Comparison of 16S rDNA Next Sequencing of Microbiome Communities From Post-scalder and Post-picker Stages in Three Different Commercial Poultry Plants Processing Three Classes of Broilers.

Front Microbiol 2019 4;10:972. Epub 2019 Jun 4.

Center for Food Safety and Department of Food Science, University of Arkansas, Fayetteville, AR, United States.

Poultry processing systems are a complex network of equipment and automation systems that require a proactive approach to monitoring in order to protect the food supply. Process oversight requires the use of multi-hurdle intervention systems to ensure that any undesirable microorganisms are reduced or eliminated by the time the carcasses are processed into final products. In the present study, whole bird carcass rinses (WBCR) collected at the post-scalder and post-picker locations from three different poultry processing facilities (Plant A: mid-weight broiler processing, B: large-weight broiler processing, C: young broiler (Cornish) processing) were subjected to next generation sequencing (NGS) and microbial quantification using direct plating methods to assess the microbial populations present during these stages of the poultry process. The quantification of aerobic plate counts (APC) and Enterobacteriaceae (EB) demonstrated that reductions for these microbial classes were not consistent between the two sampling locations for all facilities, but did not provide a clear picture of what microorganism(s) may be affecting those shifts. With the utilization of NGS, a more complete characterization of the microbial communities present including microorganisms that would not have been identified with the employed direct plating methodologies were identified. Although the foodborne pathogens typically associated with raw poultry, and , were not identified, sequence analysis performed by Quantitative Insights of Microbiology Ecology (QIIME) indicated shifts of , and , which are microorganisms closely related to and . Additionally, the presence of and at both sampling locations and at all three facilities provides evidence that these microorganisms could potentially be utilized to assess the performance of multi-hurdle intervention systems.
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http://dx.doi.org/10.3389/fmicb.2019.00972DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6558062PMC
June 2019
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