1
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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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Park JY, Jo JW, An YJ, Lee JJ, Kim BS. Alterations in sea urchin (Mesocentrotus nudus) microbiota and their potential contributions to host according to barren severity. NPJ Biofilms Microbiomes 2023; 9:83. [PMID: 37907565 PMCID: PMC10618176 DOI: 10.1038/s41522-023-00450-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023] Open
Abstract
Sea urchins are biotic factors driving the decline of kelp forests in marine ecosystems. However, few studies have analyzed the microbiota of surviving sea urchins in barren regions with scarce diet resources. Here, we analyzed the microbiota in the pharynx and gut of the sea urchin Mesocentrotus nudus located along the coast of an expanding barren region in South Korea. The ecological adaptation of genera in sea urchins was predicted using the neutral assembly model. The pharynx and gut microbiota were different, and microbes in the surrounding habitats dispersed more to the pharynx than to the gut. The gut microbiota in sea urchins is altered by barren severity and plays different roles in host energy metabolism. These findings help to understand the microbiota in sea urchins according to urchin barren and its contribution to the survival of sea urchins in severe barren regions with limited macroalgae.
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Affiliation(s)
- Joon-Young Park
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do, 24252, Republic of Korea
| | - Jae-Won Jo
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do, 24252, Republic of Korea
| | - Yu-Jeong An
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do, 24252, Republic of Korea
| | - Jin-Jae Lee
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do, 24252, Republic of Korea
| | - Bong-Soo Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do, 24252, Republic of Korea.
- The Korean Institute of Nutrition, Hallym University, Chuncheon, Gangwon-do, Republic of Korea.
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3
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Jin S, Liu X, Wang J, Pan L, Zhang Y, Zhou G, Tang C. Hyperspectral imaging combined with fluorescence for the prediction of microbial growth in chicken breasts under different packaging conditions. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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4
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Gichure JN, Coorey R, Njage PMK, Dykes GA, Muema EK, Buys EM. The Microbial Genetic Diversity and Succession Associated with Processing Waters at Different Broiler Processing Stages in an Abattoir in Australia. Pathogens 2023; 12:pathogens12030488. [PMID: 36986410 PMCID: PMC10053010 DOI: 10.3390/pathogens12030488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
The high organic content of abattoir-associated process water provides an alternative for low-cost and non-invasive sample collection. This study investigated the association of microbial diversity from an abattoir processing environment with that of chicken meat. Water samples from scalders, defeathering, evisceration, carcass-washer, chillers, and post-chill carcass rinsate were collected from a large-scale abattoir in Australia. DNA was extracted using the Wizard® Genomic DNA Purification Kit, and the 16S rRNA v3-v4 gene region was sequenced using Illumina MiSeq. The results revealed that the Firmicutes decreased from scalding to evisceration (72.55%) and increased with chilling (23.47%), with the Proteobacteria and Bacteroidota changing inversely. A diverse bacterial community with 24 phyla and 392 genera was recovered from the post-chill chicken, with Anoxybacillus (71.84%), Megamonas (4.18%), Gallibacterium (2.14%), Unclassified Lachnospiraceae (1.87%), and Lactobacillus (1.80%) being the abundant genera. The alpha diversity increased from scalding to chilling, while the beta diversity revealed a significant separation of clusters at different processing points (p = 0.01). The alpha- and beta-diversity revealed significant contamination during the defeathering, with a redistribution of the bacteria during the chilling. This study concluded that the genetic diversity during the defeathering is strongly associated with the extent of the post-chill contamination, and may be used to indicate the microbial quality of the chicken meat.
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Affiliation(s)
- Josphat Njenga Gichure
- Department of Consumer and Food Sciences, University of Pretoria, Hatfield 0028, South Africa
- Department of Food Science, Nutrition and Technology, South Eastern Kenya University, Kitui P.O. Box 170-90200, Kenya
| | - Ranil Coorey
- School of Molecular and Life Sciences, Faculty of Science and Engineering, Curtin University, Perth 6845, Australia
| | - Patrick Murigu Kamau Njage
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gary A Dykes
- School of Agriculture and Food Sciences, University of Queensland, St. Lucia 4067, Australia
| | - Esther K Muema
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield 0028, South Africa
| | - Elna M Buys
- Department of Consumer and Food Sciences, University of Pretoria, Hatfield 0028, South Africa
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5
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Min H, An F, Wei T, Wang S, Ma P, Dai Y. Microbial community structure and biogenic amines content variations in chilled chicken during storage. Food Sci Nutr 2023; 11:627-638. [PMID: 36789075 PMCID: PMC9922133 DOI: 10.1002/fsn3.3122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/28/2022] [Accepted: 10/25/2022] [Indexed: 01/03/2023] Open
Abstract
The aim of this study was to investigate the sensory indicators, biogenic amine contents, and bacterial community structure and diversity of chilled chicken stored at 4°C under aerobic conditions. Bacterial diversity and dominant bacteria were analyzed using high-throughput sequencing technique (HTS). The relationship between biogenic amine contents and microbial community structure was studied. The results showed that contents of putrescine and cadaverine increased significantly with storage time. Proteobacteria was absolutely dominant flora at the phylum level. The predominant spoilage bacteria found in chicken thighs were Pseudomonas, Acinetobacter, Aeromonas, Shewanella, and Yersinia, and the difference with chicken breasts was related to the presence of Myroides and absence of Yersinia. Myroides, Yersinia, and Shewanella were reported for the first time as an important contributor to the spoilage-related microflora. Bacterial diversity and richness indices showed fluctuating and decreasing trend with storage time. The redundancy analysis showed that the relative abundance of Pseudomonas, Yersinia, and Janthinobacterium was positively related to the contents of putrescine, cadaverine, and tyramine, while Shewanella and Aeromonas showed positive relationship with putrescine content. Furthermore, positive relationship of Myroides and Desulfovibrio with the contents of cadaverine and tyramine was proposed for the first time. The key findings of this study can provide experimental data for food safety monitoring during refrigerated storage and preservation for poultry meat products.
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Affiliation(s)
- Hong Min
- NMPA Key Laboratory for Testing Technology of Pharmaceutical MicrobiologyShaanxi Institute for Food and Drug ControlXi'anPeople's Republic of China
| | - Fengqiu An
- School of Environmental and Chemical EngineeringXi'an Polytechnic UniversityXi'anPeople's Republic of China
| | - Ting Wei
- School of Environmental and Chemical EngineeringXi'an Polytechnic UniversityXi'anPeople's Republic of China
| | - Song Wang
- Shaanxi Institute for Food and Drug ControlXi'anPeople's Republic of China
| | - Pengfei Ma
- Shaanxi Institute for Food and Drug ControlXi'anPeople's Republic of China
| | - Yong Dai
- Shaanxi Institute for Food and Drug ControlXi'anPeople's Republic of China
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6
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Ban GH, Kim BK, Kim SR, Rhee MS, Kim SA. Bacterial microbiota profiling of oyster mushrooms (Pleurotus ostreatus) based on cultivation methods and distribution channels using high-throughput sequencing. Int J Food Microbiol 2022; 382:109917. [PMID: 36116389 DOI: 10.1016/j.ijfoodmicro.2022.109917] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/30/2022] [Accepted: 09/04/2022] [Indexed: 11/25/2022]
Abstract
The annual consumption and production of oyster mushrooms (Pleurotus ostreatus) have continued to rise due to its nutritive and health-promoting benefits. Cultivated mushrooms are mostly grown in small to medium-scaled scale production plants that present hygienic challenges which could, in turn, increase associated foodborne pathogenic outbreaks. The present study aimed to investigate the shift in microbial ecologies of oyster mushrooms from pre-distribution (cultivation in bottles or on shelves) to post-distribution at supermarkets and open-air markets. Aerobic plate counts and coliforms were quantified using traditional microbiological techniques, and the microbiome associated with oyster mushrooms (n = 70) was analyzed using 16S rRNA amplicon sequencing for an enhanced level of bacterial microbiota profiling. Overall, coliforms recovered from pre-distribution bottle-cultivated mushrooms were 1.9 log CFU/g higher (p < 0.05) than that of shelf-cultivated mushrooms. The mean aerobic plate counts of oyster mushrooms distributed to open-air markets was 1.2 log CFU/g higher (p < 0.05) than packaged mushrooms from supermarkets while there were no significant differences in coliform counts. The pattern of bacterial composition differed by post-distribution channels, with oyster mushrooms collected from the open-air markets demonstrating the richest microbiome diversity. An increase in the relative abundance of Enterobacteriaceae (55-68 %) and Pseudomonadaceae (27-35 %) was observed in pre- and post-distribution mushrooms, respectively. However, no distinct bacterial microbiota differences were observed for the different cultivation methods or different geographical locations for each market type. The current findings add to our understanding of the effects of cultivation methods and commercial distribution channels regarding the microbiome of oyster mushrooms and may inform potential intervention strategies for future production and distribution processes. Furthermore, the tandem analyses of culture-dependent and culture-independent methods can provide more comprehensive information than that obtained when using each approach independently.
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Affiliation(s)
- Ga-Hee Ban
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul, South Korea
| | - Bo-Kyeong Kim
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul, South Korea
| | - Se-Ri Kim
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, South Korea
| | - Min Suk Rhee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Sun Ae Kim
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul, South Korea.
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7
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Li F, Zhu P, Li Z, Zhao W, Gao H, Hong Q, Song J, Yang S. Moraxella nasovis sp. nov., isolated from a sheep with respiratory disease. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, coccus-shaped bacteria, designated ZY201115T, was isolated from the nasal cavity of a sheep with respiratory disease in Yunnan Province, south-west China, and its taxonomic affiliation was studied by applying a polyphasic approach. The strain grew at 18–41 °C (optimum, 37 °C), at pH 6.0–9.0 (optimum, pH 8.0) and in 0.5–3.0% (w/v) NaCl (optimum, 1.0 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain is affiliated to the genus
Moraxella
with highest similarity to
Moraxella bovis
ATCC 10900T (96.6 %). Phylogenomic analysis based on 811 single-copy genes also indicated that the strain represents a novel species in the genus
Moraxella
and formed a deep and separated clade with
Moraxella caviae
NCTC 10293T. The highest genomic orthologous average nucleotide identity and digital DNA–DNA hybridization values between the strain and the type strains in the genus
Moraxella
were 73.7% (
M. caviae
NCTC 10293T) and 25.3% (
Moraxella osloensis
CCUG 350T), respectively. The G+C content of the complete genome sequence was 42.1 mol%. The predominant fatty acids (>5 %) were C18:1 ω9c, C17:1 ω8c, C12:03OH and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The major polar lipids were phosphatidylglycerol, cardiolipin, monolysocardiolipin, phosphatidylethanolamine and hemibismonoacylglycerophosphate. The major respiratory quinone was CoQ-8. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic characterizations, strain ZY201115T clearly represents a novel species of the genus
Moraxella
, for which the name Moraxella nasovis sp. nov. is proposed. The type strain is ZY201115T (=CCTCC AB 2021473T=CCUG 75922T).
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Affiliation(s)
- Fuxiang Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, PR China
| | - Pei Zhu
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, PR China
| | - Zhanhong Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, PR China
| | - Wenhua Zhao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, PR China
| | - Huafeng Gao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, PR China
| | - Qionghua Hong
- Yunnan Provincial Meat Caprine Engineering Research Center, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, PR China
| | - Jianling Song
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, PR China
| | - Shibiao Yang
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, PR China
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8
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Marmion M, Macori G, Ferone M, Whyte P, Scannell A. Survive and thrive: Control mechanisms that facilitate bacterial adaptation to survive manufacturing-related stress. Int J Food Microbiol 2022; 368:109612. [DOI: 10.1016/j.ijfoodmicro.2022.109612] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/21/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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9
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Seo DW, Yum SJ, Lee HR, Kim SM, Jeong HG. Microbiota Analysis and Microbiological Hazard Assessment in Chinese Chive ( Allium tuberosum Rottler) Depending on Retail Types. J Microbiol Biotechnol 2022; 32:195-204. [PMID: 34949749 PMCID: PMC9628847 DOI: 10.4014/jmb.2112.12013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022]
Abstract
Chinese chive (Allium tuberosum Rottler) has potential risks associated with pathogenic bacterial contamination as it is usually consumed raw. In this study, we investigated the microbiota of Chinese chives purchased from traditional markets and grocery stores in March (Spring) and June (Summer) 2017. Differences in bacterial diversity were observed, and the microbial composition varied across sampling times and sites. In June, potential pathogenic genera, such as Escherichia, Enterobacter, and Pantoea, accounted for a high proportion of the microbiota in samples purchased from the traditional market. A large number of pathogenic bacteria (Acinetobacter lwoffii, Bacillus cereus, Klebsiella pneumoniae, and Serratia marcescens) were detected in the June samples at a relatively high rate. In addition, the influence of the washing treatment on Chinese chive microbiota was analyzed. After storage at 26°C, the washing treatment accelerated the growth of enterohemorrhagic Escherichia coli (EHEC) because it caused dynamic shifts in Chinese chive indigenous microbiota. These results expand our knowledge of the microbiota in Chinese chives and provide data for the prediction and prevention of food-borne illnesses.
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Affiliation(s)
- Dong Woo Seo
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Su-jin Yum
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Heoun Reoul Lee
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Seung Min Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Hee Gon Jeong
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Republic of Korea,Corresponding author Phone: +82-42-821-6726 E-mail:
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10
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Bajagai YS, Trotter M, Williams TM, Costa DFA, Whitton MM, Ren X, Wilson CS, Stanley D. The role of microbiota in animal health and productivity: misinterpretations and limitations. ANIMAL PRODUCTION SCIENCE 2022. [DOI: 10.1071/an21515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Kim HE, Kim J, Maeng S, Oh B, Hwang KT, Kim BS. Microbiota of Breast Tissue and Its Potential Association with Regional Recurrence of Breast Cancer in Korean Women. J Microbiol Biotechnol 2021; 31:1643-1655. [PMID: 34584037 PMCID: PMC9705848 DOI: 10.4014/jmb.2106.06039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/31/2021] [Accepted: 09/23/2021] [Indexed: 12/15/2022]
Abstract
Recent studies have reported dysbiosis of the microbiome in breast tissue collected from patients with breast cancer and the association between the microbiota and disease progression. However, the role of the microbiota in breast tissue remains unclear, possibly due to the complexity of breast cancer and various factors, including racial and geographical differences, influencing microbiota in breast tissue. Here, to determine the potential role of microbiota in breast tumor tissue, we analyzed 141 tissue samples based on three different tissue types (tumor, adjacent normal, and lymph node tissues) from the same patients with breast cancer in Korea. The microbiota was not simply distinguishable based on tissue types. However, the microbiota could be divided into two cluster types, even within the same tissue type, and the clinicopathologic factors were differently correlated in the two cluster types. Risk of regional recurrence was also significantly different between the microbiota cluster types (p = 0.014). In predicted function analysis, the pentose and glucuronate interconversions were significantly different between the cluster types (q < 0.001), and Enterococcus was the main genus contributing to these differences (q < 0.01). Results showed that the microbiota of breast tissue could interact with the host and influence the risk of regional recurrence. Although further studies would be recommended to validate our results, this study could expand our understanding on the breast tissue microbiota, and the results might be applied to develop novel prediction methods and treatments for patients with breast cancer.
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Affiliation(s)
- Hyo-Eun Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do 24252, Republic of Korea
| | - Jongjin Kim
- Department of Surgery, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul 07061, Republic of Korea
| | - Sejung Maeng
- Department of Surgery, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul 07061, Republic of Korea
| | - Bumjo Oh
- Department of Family Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul 07061, Republic of Korea
| | - Ki-Tae Hwang
- Department of Surgery, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul 07061, Republic of Korea,Corresponding authors K.T. Hwang Phone: +82-2-870-2275 Fax: +82-2-831-2826 E-mail:
| | - Bong-Soo Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do 24252, Republic of Korea,The Korean Institute of Nutrition, Hallym University, Chuncheon, Gangwon-do 24252, Republic of Korea,
B.S. Kim Phone: +82-33-248-2093 Fax: +82-33-256-3420 E-mail:
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12
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Gichure JN, Kamau Njage PM, Wambui JM, Dykes GA, Buys EM, Coorey R. Systematic-review and meta-analysis on effect of decontamination interventions on prevalence and concentration of Campylobacter spp. during primary processing of broiler chickens. Food Microbiol 2021; 102:103923. [PMID: 34809949 DOI: 10.1016/j.fm.2021.103923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022]
Abstract
Scientific advances in pathogen decontamination offer great potential to reduce Campylobacter spp. during primary processing. The aim of this study was to collate data from eligible studies using systematic review, meta-analysis followed by meta-regression. Random effect meta-analysis revealed heterogenous (τ2 = 0.6, I2 = 98 %) pooled reduction in Campylobacter concentration of 0.6 log10 CFU/carcass and a decrease in relative risk of Campylobacter spp. prevalence in broiler carcasses by 57.2 %. Decontamination interventions during Inside-Outside-Carcass-Wash were most effective on concentration (0.8 log10 CFU/carcass) while those during evisceration were most effective on prevalence (78.0 % decrease in relative risk). Physical decontamination was more effective on Campylobacter prevalence (68.7 % decrease in relative risk) compared chemical treatment (30.3 %). Application through immersion was superior on Campylobacter concentration (0.9 log10 CFU/carcass odds reduction) to spraying (0.5 log10 CFU/carcass odds reduction). Publication bias and small study effect were observed in trials on Campylobacter prevalence but not for concentration. The meta-regression revealed four and seven potential modifier variables for concentration and prevalence respectively. This meta-analysis provides an overview of the expected magnitude in Campylobacter spp. concentration and prevalence with application of decontamination interventions on broiler carcasses along the slaughter process and forms a basis of quantitative microbial risk assessment and derivation of intervention measures. Even though modest microbial concentration reduction is reported there was a large decrease in contamination prevalence during processing interventions.
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Affiliation(s)
- Josphat N Gichure
- Department of Food Science, Nutrition and Technology, South Eastern Kenya University, P.O. Box 170-90200, Kitui, Kenya.
| | - Patrick Murigu Kamau Njage
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, Denmark
| | - Joseph M Wambui
- Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, 8057, Zurich, Switzerland
| | - Gary A Dykes
- School of Molecular and Life Sciences, Faculty of Science and Engineering, Curtin University, GPO Box U1987, Perth, Western Australia, 6845, Australia
| | - Elna M Buys
- Department of Consumer and Food Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Ranil Coorey
- School of Molecular and Life Sciences, Faculty of Science and Engineering, Curtin University, GPO Box U1987, Perth, Western Australia, 6845, Australia
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13
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Song L, Wu X, Xie J, Zhang H, Yang H, Zeng Q, Yang X, Xie W. Kaempferia galanga Linn. Extract – A potential antibacterial agent for preservation of poultry products. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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The changing microbiome of poultry meat; from farm to fridge. Food Microbiol 2021; 99:103823. [PMID: 34119108 DOI: 10.1016/j.fm.2021.103823] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 11/20/2022]
Abstract
Chickens play host to a diverse community of microorganisms which constitute the microflora of the live bird. Factors such as diet, genetics and immune system activity affect this complex population within the bird, while external influences including weather and exposure to other animals alter the development of the microbiome. Bacteria from these settings including Campylobacter and Salmonella play an important role in the quality and safety of end-products from these birds. Further steps, including washing and chilling, within the production cycle aim to control the proliferation of these microbes as well as those which cause product spoilage. These steps impose specific selective pressures upon the microflora of the meat product. Within the next decade, it is forecast that poultry meat, particularly chicken will become the most consumed meat globally. However, as poultry meat is a frequently cited reservoir of zoonotic disease, understanding the development of its microflora is key to controlling the proliferation of important spoilage and pathogenic bacterial groups present on the bird. Whilst several excellent reviews exist detailing the microbiome of poultry during primary production, others focus on fate of important poultry pathogens such as Campylobacter and Salmonella spp. At farm and retail level, and yet others describe the evolution of spoilage microbes during spoilage. This review seeks to provide the poultry industry and research scientists unfamiliar with food technology process with a holistic overview of the key changes to the microflora of broiler chickens at each stage of the production and retail cycle.
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Microbiota of Chicken Breast and Thigh Fillets Stored under Different Refrigeration Temperatures Assessed by Next-Generation Sequencing. Foods 2021; 10:foods10040765. [PMID: 33916748 PMCID: PMC8066510 DOI: 10.3390/foods10040765] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/17/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022] Open
Abstract
Chicken is one of the most widely consumed meats worldwide. The exploration of the bacterial diversity of chicken meat may provide new insights into the chicken-associated microbiome that will lead to moderation of food spoilage or safety. This study was undertaken to explore the bacterial communities of chicken breast and thigh fillets stored at refrigeration (0 °C and 5 °C) and slightly abuse (10 °C) temperatures for 5 days through conventional cultural methods along with next-generation sequencing (NGS) analysis. Total viable counts (TVC), Brochothrix thermosphacta, Pseudomonas spp., and lactic acid bacteria (LAB) were enumerated, while the bacterial communities were mapped through 16S rRNA gene amplicon sequencing. Chicken breast and thigh fillets possessed a complex bacterial structure that incorporated a total of >200 Operational Taxonomic Units (OTUs) at the genus level. The core microbiota of fresh samples consisted of Acinetobacter, Brochothrix, Flavobacterium, Pseudomonas, Psychrobacter, and Vibrionaceae (family). These genera persisted until the end of storage in >80% of samples, except Psychrobacter and Flavobacterium, while Photobacterium was also identified. Hierarchical clustering showed a distinction of samples based on storage time and chicken part. Conventional plate counting with growth media commonly used in spoilage studies did not always correspond to the microbial community profiles derived from NGS analysis, especially in Pseudomonas, Acinetobacter, Photobacterium, and Vibrionaceae. Results of the present study highlight Photobacterium and Vibrionaceae, in general, as potent chicken meat spoilers and suggest the necessity to combine classical microbiological methods along with NGS technologies to characterize chicken meat spoilage microbiota.
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Lee JJ, Yong D, Suk KT, Kim DJ, Woo HJ, Lee SS, Kim BS. Alteration of Gut Microbiota in Carbapenem-Resistant Enterobacteriaceae Carriers during Fecal Microbiota Transplantation According to Decolonization Periods. Microorganisms 2021; 9:microorganisms9020352. [PMID: 33578974 PMCID: PMC7916679 DOI: 10.3390/microorganisms9020352] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
Fecal microbiota transplantation (FMT) has been suggested as an alternative therapeutic option to decolonize carbapenem-resistant Enterobacteriaceae (CRE). However, the analysis of gut microbiota alteration in CRE carriers during FMT is still limited. Here, gut microbiota changes in CRE carriers were evaluated during FMT according to decolonization periods. The decolonization of 10 CRE carriers was evaluated after FMT, using serial consecutive rectal swab cultures. Alterations of gut microbiota before and after FMT (56 serial samples) were analyzed using high-throughput sequencing. The decolonization rates of CRE carriers were 40%, 50%, and 90% within 1, 3 and 5 months after initial FMT, respectively. Gut microbiota significantly changed after FMT (p = 0.003). Microbiota alteration was different between the early decolonization carriers (EDC) and late decolonization carriers (LDC). Microbiota convergence in carriers to donors was detected in EDC within 4 weeks, and keystone genera within the Bacteroidetes were found in the gut microbiota of EDC before FMT. The relative abundance of Klebsiella was lower in EDC than in LDC, before and after FMT. Our results indicate that FMT is a potential option for CRE decolonization. The gut microbiota of CRE carriers could be used to predict decolonization timing after FMT, and determine repeated FMT necessity.
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Affiliation(s)
- Jin-Jae Lee
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Korea;
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea; (K.T.S.); (D.J.K.)
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Ki Tae Suk
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea; (K.T.S.); (D.J.K.)
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Hallym University, Chuncheon Sacred Heart Hospital, Chuncheon 24253, Korea
| | - Dong Joon Kim
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea; (K.T.S.); (D.J.K.)
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Hallym University, Chuncheon Sacred Heart Hospital, Chuncheon 24253, Korea
| | - Heung-Jeong Woo
- Department of Internal Medicine, Division of Infectious Diseases, Hallym University Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong 18450, Korea;
| | - Seung Soon Lee
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea; (K.T.S.); (D.J.K.)
- Department of Internal Medicine, Division of Infectious Diseases, Hallym University Chuncheon Sacred Heart Hospital, Hallym University College of Medicine, Chuncheon 24252, Korea
- Correspondence: (S.S.L.); (B.-S.K.)
| | - Bong-Soo Kim
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Korea;
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea; (K.T.S.); (D.J.K.)
- Correspondence: (S.S.L.); (B.-S.K.)
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Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes. mSystems 2020; 5:5/5/e00589-20. [PMID: 32900871 PMCID: PMC7483511 DOI: 10.1128/msystems.00589-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Chicken has recently overtaken beef as the most-consumed meat in the United States. The growing popularity of chicken is accompanied by frequent occurrences of foodborne pathogens and increasing concerns over antibiotic usage. Our study represents a proof-of-concept investigation into the possibility and practicality of leveraging microbiome-informed food safety and quality. Through a longitudinal and cross-sectional survey, we established the chicken microbiome as a robust and multifaceted food microbiology attribute that could provide a variety of safety and quality information and retain systematic signals characteristic of overall processing environments. Microorganisms and their communities on foods are important determinants and indicators of food safety and quality. Despite growing interests in studying food and food-related microbiomes, how effective and practical it is to glean various food safety and quality information from food commodity microbiomes remains underinvestigated. Microbiomes of retail chicken breast from 4 processing establishments in 3 major U.S. broiler production states displayed longitudinal consistency over 7 months and cross-sectional distinctiveness associated with individual processing environments. Packaging type and processing environment but not antibiotic usage and seasonality affected composition and diversity of the microbiomes. Low abundances of antimicrobial resistance genes were found on chicken breasts, and no significant resistome difference was observed between antibiotic-free and conventional products. Benchmarked by culture enrichment, shotgun metagenomics sequencing delivered sensitive and specific detection of Salmonella enterica from chicken breasts. IMPORTANCE Chicken has recently overtaken beef as the most-consumed meat in the United States. The growing popularity of chicken is accompanied by frequent occurrences of foodborne pathogens and increasing concerns over antibiotic usage. Our study represents a proof-of-concept investigation into the possibility and practicality of leveraging microbiome-informed food safety and quality. Through a longitudinal and cross-sectional survey, we established the chicken microbiome as a robust and multifaceted food microbiology attribute that could provide a variety of safety and quality information and retain systematic signals characteristic of overall processing environments.
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Hwang BK, Choi H, Choi SH, Kim BS. Analysis of Microbiota Structure and Potential Functions Influencing Spoilage of Fresh Beef Meat. Front Microbiol 2020; 11:1657. [PMID: 32793151 PMCID: PMC7387507 DOI: 10.3389/fmicb.2020.01657] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/25/2020] [Indexed: 11/13/2022] Open
Abstract
Beef is one of the most consumed food worldwide, and it is prone to spoilage by bacteria. This risk could be caused by resident microbiota and their alterations in fresh beef meat during processing. However, scarce information is available regarding potential spoilage factors due to resident microbiota in fresh beef meat. In this study, we analyzed the microbiota composition and their predicted functions on fresh beef meat. A total of 120 beef meat samples (60 fresh ground and 60 non-ground beef samples) were collected from three different sites in South Korea on different months, and the microbiota were analyzed by the MiSeq system. Our results showed that although the microbiota in beef meat were varied among sampling site and months, the dominant phyla were the same with shared core bacteria. Notably, psychrotrophic genera, related to spoilage, were detected in all samples, and their prevalence increased significantly in July. These genera could inhibit the growth of other microbes with using glucose by fermentation. The results of this study extend our understanding of initial microbiota in fresh beef meat and potential functions influencing spoilage and can be useful to develop the preventive measures to reduce the spoilage of beef meat products.
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Affiliation(s)
- Bo Kyoung Hwang
- Department of Agricultural Biotechnology, Center of Food Safety and Toxicology, Seoul National University, Seoul, South Korea
| | - HyeLim Choi
- Department of Agricultural Biotechnology, Center of Food Safety and Toxicology, Seoul National University, Seoul, South Korea
| | - Sang Ho Choi
- Department of Agricultural Biotechnology, Center of Food Safety and Toxicology, Seoul National University, Seoul, South Korea
| | - Bong-Soo Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, South Korea
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Vásquez-Ampuero JM, Tasayco-Alcántara WR. Presencia de patógenos en carne cruda de pollo en centros de expendio, Huánuco-Perú. JOURNAL OF THE SELVA ANDINA RESEARCH SOCIETY 2020. [DOI: 10.36610/j.jsars.2020.110200130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Vásquez-Ampuero JM, Tasayco-Alcántara WR. Presence of pathogens in raw chicken meat in retail centers, Huánuco-Peru. JOURNAL OF THE SELVA ANDINA RESEARCH SOCIETY 2020. [DOI: 10.36610/j.jsars.2020.110200130x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Hosnedlova B, Vernerova K, Kizek R, Bozzi R, Kadlec J, Curn V, Kouba F, Fernandez C, Machander V, Horna H. Associations between IGF1, IGFBP2 and TGFß3 Genes Polymorphisms and Growth Performance of Broiler Chicken Lines. Animals (Basel) 2020; 10:E800. [PMID: 32380764 PMCID: PMC7277336 DOI: 10.3390/ani10050800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 01/18/2023] Open
Abstract
Marker-assisted selection based on fast and accurate molecular analysis of individual genes is considered an acceptable tool in the speed-up of the genetic improvement of production performance in chickens. The objective of this study was to detect the single nucleotide polymorphisms (SNPs) in the IGF1, IGFBP2 and TGFß3 genes, and to investigate their associations with growth performance (body weight (BW) and average daily gain (ADG) at 14, 21, 28, 35 and 42 days of age) and carcass traits in broilers. Performance (carcass) data (weight before slaughter; weights of the trunk, giblets, abdominal fat, breast muscle and thigh muscle; slaughter value and slaughter percentage), as well as blood samples for DNA extraction and SNP analysis, were obtained from 97 chickens belonging to two different lines (Hubbard F15 and Cobb E) equally divided between the two sexes. The genotypes were detected using polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) methods with specific primers and restrictase for each gene. The statistical analysis discovered significant associations (p < 0.05) between the TGFβ3 SNP and the following parameters: BW at 21, 28 and 35 days, trunk weight and slaughter value. Association analysis of BWs (at 21, 28 and 35 days) and SNPs was always significant for codominant, dominant and overdominant genetic models, showing a possible path for genomic selection in these chicken lines. Slaughter value was significant for codominant, recessive and overdominant patterns, whereas other carcass traits were not influenced by SNPs. Based on the results of this study, we suggested that the TGFβ3 gene could be used as a candidate gene marker for chicken growth traits in the Hubbard F15 and Cobb E population selection programs, whereas for carcass traits further investigation is needed.
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Affiliation(s)
- Bozena Hosnedlova
- Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic;
| | - Katerina Vernerova
- Biotechnological Centre, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (K.V.); (V.C.)
| | - Rene Kizek
- Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic;
- Department of Human Pharmacology and Toxicology, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackého 1946/1, 612 42 Brno, Czech Republic
- Department of Biomedical and Environmental Analyses, Faculty of Pharmacy with Division of Laboratory Medicine, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland
| | - Riccardo Bozzi
- Food, Environment and Forestry, Animal Science Section, Department of Agriculture, University of Florence, Via delle Cascine, 5, 50144 Firenze, Italy;
| | - Jaromir Kadlec
- Department of Agricultural Products’ Quality, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic;
| | - Vladislav Curn
- Biotechnological Centre, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (K.V.); (V.C.)
| | - Frantisek Kouba
- State Veterinary Administration, Regional Veterinary Administration of the South Bohemian Region, Severní 9, 370 10 České Budějovice, Czech Republic;
| | - Carlos Fernandez
- School of Pharmacy and Life Sciences, Robert Gordon University, Garthdee Road, Aberdeen AB10 7QB, UK;
| | - Vlastislav Machander
- International Testing of Poultry, Ústrašice 63, 390 02 Tábor, Czech Republic; (V.M.); (H.H.)
| | - Hana Horna
- International Testing of Poultry, Ústrašice 63, 390 02 Tábor, Czech Republic; (V.M.); (H.H.)
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