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Xu X, Rothrock MJ, Mishra A, Kumar GD, Mishra A. Relationship of the Poultry Microbiome to Pathogen Colonization, Farm Management, Poultry Production, and Foodborne Illness Risk Assessment. J Food Prot 2023; 86:100169. [PMID: 37774838 DOI: 10.1016/j.jfp.2023.100169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/01/2023]
Abstract
Despite the continuous progress in food science and technology, the global burden of foodborne illnesses remains substantial, with pathogens in food causing millions of infections each year. Traditional microbiological culture methods are inadequate in detecting the full spectrum of these microorganisms, highlighting the need for more comprehensive detection strategies. This review paper aims to elucidate the relationship between foodborne pathogen colonization and the composition of the poultry microbiome, and how this knowledge can be used for improved food safety. Our review highlights that the relationship between pathogen colonization varies across different sections of the poultry microbiome. Further, our review suggests that the microbiome profile of poultry litter, farm soil, and farm dust may serve as potential indicators of the farm environment's food safety issues. We also agree that the microbiome of processed chicken samples may reveal potential pathogen contamination and food quality issues. In addition, utilizing predictive modeling techniques on the collected microbiome data, we suggest establishing correlations between particular taxonomic groups and the colonization of pathogens, thus providing insights into food safety, and offering a comprehensive overview of the microbial community. In conclusion, this review underscores the potential of microbiome analysis as a powerful tool in food safety, pathogen detection, and risk assessment.
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Affiliation(s)
- Xinran Xu
- Department of Food Science and Technology, University of Georgia, Athens, GA, USA
| | - Michael J Rothrock
- Egg Safety and Quality Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, USA
| | - Aditya Mishra
- Department of Statistics, University of Georgia, Athens, GA, USA
| | | | - Abhinav Mishra
- Department of Food Science and Technology, University of Georgia, Athens, GA, USA.
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2
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Novoa Rama E, Bailey M, Kumar S, Leone C, den Bakker HC, Thippareddi H, Singh M. Characterizing the gut microbiome of broilers raised under conventional and no antibiotics ever practices. Poult Sci 2023; 102:102832. [PMID: 37343348 PMCID: PMC10404755 DOI: 10.1016/j.psj.2023.102832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 06/23/2023] Open
Abstract
Meat from broilers raised without the use of antibiotics is becoming increasingly popular among consumers. Consequently, interest in the microbial profiling of chickens produced under nonconventional practices is growing, however, research on this topic is lacking. The current study was designed to characterize the dynamics of gut microbial populations of broilers raised under conventional and no antibiotics ever (NAE) practices. Four commercial farms (2 conventional and 2 NAE) were included in this study. On each farm, cecal (n = 224) and ileal (n = 224) contents were collected from birds at different stages during the grow out of a single flock and following transportation to the processing facility. Cecal microbiota was dominated by the genera Escherichia and Enterococcus upon hatching in both conventional and NAE flocks, shifting with time toward predominantly Faecalibacterium and Bacteroides. The composition of cecal microbial communities of NAE broilers was different than that of conventional chickens (P ≤ 0.05). Conventional broilers harbored a rich, but less diverse cecal microbiota than NAE, while the ileal microbiota was primarily populated with genera previously named Lactobacillus, which exhibited a higher abundance in NAE broilers (P ≤ 0.05). In both production systems, the microbiota followed a similar temporal succession that was more evident in the ceca. Transportation to the processing plant impacted the microbial composition of the ileum (P ≤ 0.05), characterized by an increase in the relative abundance of Psychrobacter. Finally, differential abundance analysis showed a positive correlation between Campylobacter and Enorma within the cecum microbiota, and a negative correlation with Salmonella.
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Affiliation(s)
- Estefanía Novoa Rama
- Department of Food Science and Technology, University of Georgia, Athens, GA, USA
| | - Matthew Bailey
- Department of Poultry Science, Auburn University, Auburn, AL, USA
| | - Sanjay Kumar
- Department of Poultry Science, University of Georgia, Athens, GA, USA
| | - Cortney Leone
- Department of Poultry Science, University of Georgia, Athens, GA, USA
| | - Henk C den Bakker
- Department of Food Science and Technology, University of Georgia, Athens, GA, USA; Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA, USA.
| | | | - Manpreet Singh
- Department of Food Science and Technology, University of Georgia, Athens, GA, USA
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Nielsen SS, Alvarez J, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Schmidt CG, Herskin MS, Miranda Chueca MÁ, Padalino B, Pasquali P, Roberts HC, Spoolder H, Stahl K, Velarde A, Viltrop A, Winckler C, Tiemann I, de Jong I, Gebhardt‐Henrich SG, Keeling L, Riber AB, Ashe S, Candiani D, García Matas R, Hempen M, Mosbach‐Schulz O, Rojo Gimeno C, Van der Stede Y, Vitali M, Bailly‐Caumette E, Michel V. Welfare of broilers on farm. EFSA J 2023; 21:e07788. [PMID: 36824680 PMCID: PMC9941850 DOI: 10.2903/j.efsa.2023.7788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
This Scientific Opinion considers the welfare of domestic fowl (Gallus gallus) related to the production of meat (broilers) and includes the keeping of day-old chicks, broiler breeders, and broiler chickens. Currently used husbandry systems in the EU are described. Overall, 19 highly relevant welfare consequences (WCs) were identified based on severity, duration and frequency of occurrence: 'bone lesions', 'cold stress', 'gastro-enteric disorders', 'group stress', 'handling stress', 'heat stress', 'isolation stress', 'inability to perform comfort behaviour', 'inability to perform exploratory or foraging behaviour', 'inability to avoid unwanted sexual behaviour', 'locomotory disorders', 'prolonged hunger', 'prolonged thirst', 'predation stress', 'restriction of movement', 'resting problems', 'sensory under- and overstimulation', 'soft tissue and integument damage' and 'umbilical disorders'. These WCs and their animal-based measures (ABMs) that can identify them are described in detail. A variety of hazards related to the different husbandry systems were identified as well as ABMs for assessing the different WCs. Measures to prevent or correct the hazards and/or mitigate each of the WCs are listed. Recommendations are provided on quantitative or qualitative criteria to answer specific questions on the welfare of broilers and related to genetic selection, temperature, feed and water restriction, use of cages, light, air quality and mutilations in breeders such as beak trimming, de-toeing and comb dubbing. In addition, minimal requirements (e.g. stocking density, group size, nests, provision of litter, perches and platforms, drinkers and feeders, of covered veranda and outdoor range) for an enclosure for keeping broiler chickens (fast-growing, slower-growing and broiler breeders) are recommended. Finally, 'total mortality', 'wounds', 'carcass condemnation' and 'footpad dermatitis' are proposed as indicators for monitoring at slaughter the welfare of broilers on-farm.
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4
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Using E. coli population to predict foodborne pathogens in pastured poultry farms. Food Microbiol 2022; 108:104092. [DOI: 10.1016/j.fm.2022.104092] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/27/2022] [Accepted: 07/12/2022] [Indexed: 11/22/2022]
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Lee W, Matthews A, Moore D. Safety Evaluation of a Novel Algal Feed Additive for Poultry Production. Avian Dis 2022; 66:1-11. [PMID: 36214407 DOI: 10.1637/aviandiseases-d-22-00043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022]
Abstract
Feed additives are critical components for poultry health and the economic viability of antibiotic-free poultry production. The aim of the present study is to evaluate the safety of a novel algal-derived feed additive, a dried biomass powder produced from Chlamydomonas reinhardtii strain crAL082, modified to express an N-acetylmuramoyl-L-alanine amidase (EC 3.5.1.28) and a lysozyme-type enzyme (EC 3.2.1.17). A 42-day oral toxicity study showed that the crAL082 dried biomass powder was fully tolerated by broiler chicken based on the lack of detrimental effects found in performance, mortality, hematology, blood clinical chemistry, and histopathologic results compared with those of a nontreated control group, resulting in a "No Observed Adverse Effect Level" of 5000 ppm, the highest dose tested. The study demonstrates the first-ever safety result of a C. reinhardtii microalgae dried biomass powder used as a feed additive in broiler chickens. Furthermore, safety is shown for the two additional enzymes expressed within the C. reinhardtii crAL082 strain and ingested by the birds.
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Affiliation(s)
- Weiluo Lee
- Axitan Ltd., Ground Floor Offices, Whittle Way, SG1 2FS, Stevenage, United Kingdom,
| | | | - Daniel Moore
- Colorado Quality Research, Inc., Wellington, CO 80549
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Molee W, Khosinklang W, Tongduang P, Thumanu K, Yongsawatdigul J, Molee A. Biomolecules, Fatty Acids, Meat Quality, and Growth Performance of Slow-Growing Chickens in an Organic Raising System. Animals (Basel) 2022; 12:ani12050570. [PMID: 35268139 PMCID: PMC8908829 DOI: 10.3390/ani12050570] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/07/2022] [Accepted: 02/21/2022] [Indexed: 12/14/2022] Open
Abstract
This study was to determine the effect of the organic raising system (OR) on growth performance, meat quality, and physicochemical properties of slow-growing chickens. Three hundred and sixty (one-day-old) Korat chickens (KRC) were randomly assigned to control (CO) and OR groups. The groups comprised six replicates of thirty chickens each. The chickens were housed in indoor pens (5 birds/m2), wherein those in OR had free access to Ruzi pasture (1 bird/4 m2) from d 21 to d 84 of age. In the CO group, chickens were fed with a mixed feed derived from commercial feedstuffs, while those in the OR group were fed with mixed feed derived from organic feedstuffs. The results revealed a lower feed intake (p < 0.0001) and feed conversion ratio (p = 0.004) in the OR. The OR increased total collagen, protein, shear force, color of skin and meat, and decreased abdominal fat (p < 0.05). The OR improved fatty acid with increased DHA, n-3 PUFA, and decreased the ratio of n-6 to n-3 PUFA in KRC meat (p < 0.05). The synchrotron radiation-based Fourier transform infrared spectroscopy and correlation loading analyses confirmed these results. In conclusion, our results proved that OR could improve growth performance and meat quality and suggested the raising system be adopted commercially. In addition, the observed differences in biochemical molecules could also serve as markers for monitoring meat quality.
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Affiliation(s)
- Wittawat Molee
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (W.K.); (P.T.); (A.M.)
- Correspondence: ; Tel.: +66-8-9920-4970
| | - Wichuta Khosinklang
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (W.K.); (P.T.); (A.M.)
| | - Pramkamon Tongduang
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (W.K.); (P.T.); (A.M.)
| | - Kanjana Thumanu
- Research and Facility Department, Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand;
| | - Jirawat Yongsawatdigul
- School of Food Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
| | - Amonrat Molee
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (W.K.); (P.T.); (A.M.)
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Wickramasuriya SS, Park I, Lee K, Lee Y, Kim WH, Nam H, Lillehoj HS. Role of Physiology, Immunity, Microbiota, and Infectious Diseases in the Gut Health of Poultry. Vaccines (Basel) 2022; 10:vaccines10020172. [PMID: 35214631 PMCID: PMC8875638 DOI: 10.3390/vaccines10020172] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 01/10/2023] Open
Abstract
“Gut health” refers to the physical state and physiological function of the gastrointestinal tract and in the livestock system; this topic is often focused on the complex interacting components of the intestinal system that influence animal growth performance and host-microbial homeostasis. Regardless, there is an increasing need to better understand the complexity of the intestinal system and the various factors that influence gut health, since the intestine is the largest immune and neuroendocrine organ that interacts with the most complex microbiome population. As we face the post-antibiotic growth promoters (AGP) era in many countries of the world, livestock need more options to deal with food security, food safety, and antibiotic resilience to maintain agricultural sustainability to feed the increasing human population. Furthermore, developing novel antibiotic alternative strategies needs a comprehensive understanding of how this complex system maintains homeostasis as we face unpredictable changes in external factors like antibiotic-resistant microbes, farming practices, climate changes, and consumers’ preferences for food. In this review, we attempt to assemble and summarize all the relevant information on chicken gut health to provide deeper insights into various aspects of gut health. Due to the broad and complex nature of the concept of “gut health”, we have highlighted the most pertinent factors related to the field performance of broiler chickens.
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Affiliation(s)
- Samiru S. Wickramasuriya
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (S.S.W.); (I.P.); (K.L.); (Y.L.); (W.H.K.); (H.N.)
| | - Inkyung Park
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (S.S.W.); (I.P.); (K.L.); (Y.L.); (W.H.K.); (H.N.)
| | - Kyungwoo Lee
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (S.S.W.); (I.P.); (K.L.); (Y.L.); (W.H.K.); (H.N.)
- Department of Animal Science and Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Youngsub Lee
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (S.S.W.); (I.P.); (K.L.); (Y.L.); (W.H.K.); (H.N.)
| | - Woo H. Kim
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (S.S.W.); (I.P.); (K.L.); (Y.L.); (W.H.K.); (H.N.)
- College of Veterinary Medicine and Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Korea
| | - Hyoyoun Nam
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (S.S.W.); (I.P.); (K.L.); (Y.L.); (W.H.K.); (H.N.)
| | - Hyun S. Lillehoj
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (S.S.W.); (I.P.); (K.L.); (Y.L.); (W.H.K.); (H.N.)
- Correspondence: ; Tel.: +1-301-504-8771
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Aruwa CE, Pillay C, Nyaga MM, Sabiu S. Poultry gut health - microbiome functions, environmental impacts, microbiome engineering and advancements in characterization technologies. J Anim Sci Biotechnol 2021; 12:119. [PMID: 34857055 PMCID: PMC8638651 DOI: 10.1186/s40104-021-00640-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/01/2021] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal tract (GIT) health impacts animal productivity. The poultry microbiome has functions which range from protection against pathogens and nutrients production, to host immune system maturation. Fluctuations in the microbiome have also been linked to prevailing environmental conditions. Healthy poultry birds possess a natural resistance to infection. However, the exploration of environmental impacts and other relevant factors on poultry growth and health have been underplayed. Since good performance and growth rate are central to animal production, the host-microbiome relationship remains integral. Prior to the emergence of metagenomic techniques, conventional methods for poultry microbiome studies were used and were low-throughput and associated with insufficient genomic data and high cost of sequencing. Fortunately, the advent of high-throughput sequencing platforms have circumvented some of these shortfalls and paved the way for increased studies on the poultry gut microbiome diversity and functions. Here, we give an up-to-date review on the impact of varied environments on microbiome profile, as well as microbiome engineering and microbiome technology advancements. It is hoped that this paper will provide invaluable information that could guide and inspire further studies on the lingering pertinent questions about the poultry microbiome.
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Affiliation(s)
- Christiana Eleojo Aruwa
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Charlene Pillay
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Martin M Nyaga
- Next Generation Sequencing Unit, Division of Virology, Faculty of Heath Sciences, University of the Free State, Bloemfontein, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa.
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Xu X, Rothrock MJ, Mohan A, Kumar GD, Mishra A. Using farm management practices to predict Campylobacter prevalence in pastured poultry farms. Poult Sci 2021; 100:101122. [PMID: 33975043 PMCID: PMC8131732 DOI: 10.1016/j.psj.2021.101122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/16/2021] [Accepted: 02/26/2021] [Indexed: 01/04/2023] Open
Abstract
Contamination of poultry products by Campylobacter is often associated with farm management practices and processing plant practices. A longitudinal study was conducted on 11 pastured poultry farms in southeastern United States from 2014 to 2017. In this study, farm practices and processing variables were used as predictors for a random forest (RF) model to predict Campylobacter prevalence in pastured poultry farms and processing environments. Individual RF models were constructed for fecal, soil and whole carcass rinse after processing (WCR-P) samples. The performance of models was evaluated by the area under curve (AUC) from the receiver operating characteristics curve. The AUC values were 0.902, 0.894, and 0.864 for fecal, soil, and WCR-P models, respectively. Relative importance plots were generated to predict the most important variable in each RF model. Animal source of feces was identified as the most important variable in fecal model and the soy content of the brood feed was the most important variable for soil model. For WCR-P model, the average flock age showed the strongest impact on RF model. These RF models can help pastured poultry growers with food safety control strategies to reduce Campylobacter prevalence in pastured poultry farms.
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Affiliation(s)
- Xinran Xu
- Department of Food Science and Technology, University of Georgia, Athens, GA, USA
| | - Michael J Rothrock
- Egg Safety and Quality Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, USA
| | - Anand Mohan
- Department of Food Science and Technology, University of Georgia, Athens, GA, USA
| | | | - Abhinav Mishra
- Department of Food Science and Technology, University of Georgia, Athens, GA, USA.
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Wilson A, Chandry PS, Turner MS, Courtice JM, Fegan N. Comparison between cage and free-range egg production on microbial composition, diversity and the presence of Salmonella enterica. Food Microbiol 2021; 97:103754. [PMID: 33653527 DOI: 10.1016/j.fm.2021.103754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/21/2021] [Accepted: 01/28/2021] [Indexed: 01/04/2023]
Abstract
The microbial composition of the food production environment plays an important role in food safety and quality. This study employed both 16 S rRNA gene sequencing technology and culture-based techniques to investigate the bacterial microbiota of an egg production facility comprising of both free-range and conventional cage housing systems. The study also aimed to detect the presence of Salmonella enterica and determine whether its presence was positively or negatively associated with other taxa. Our findings revealed that microbiota profiles of free-range and cage houses differ considerably in relation to the relative abundance and diversity with a number of taxa unique to each system and to individual sampling sites within sheds. Core to each housing system were known inhabitants of the poultry gastrointestinal tracts, Romboutsia and Turicibacter, as well as common spoilage bacteria. Generally, free-range samples contained fewer taxa and were dominated by Staphylococcus equorum, differentiating them from the cage samples. Salmonella enterica was significantly associated with the presence of a taxa belonging to the Carnobacteriaceae family. The results of this study demonstrate that the diversity and composition of the microbiota is highly variable across egg layer housing systems, which could have implications for productivity, food safety and spoilage.
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Affiliation(s)
- Annaleise Wilson
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, Queensland, Australia; CSIRO Agriculture and Food, Coopers Plains, Queensland, Australia.
| | | | - Mark S Turner
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - Jodi M Courtice
- Division of Research and Innovation, University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Narelle Fegan
- CSIRO Agriculture and Food, Coopers Plains, Queensland, Australia
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