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Bonilla-Espadas M, Zafrilla B, Lifante-Martínez I, Camacho M, Orgilés-Calpena E, Arán-Aís F, Bertazzo M, Bonete MJ. Selective Isolation and Identification of Microorganisms with Dual Capabilities: Leather Biodegradation and Heavy Metal Resistance for Industrial Applications. Microorganisms 2024; 12:1029. [PMID: 38792858 PMCID: PMC11124520 DOI: 10.3390/microorganisms12051029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Tanning, crucial for leather production, relies heavily on chromium yet poses risks due to chromium's oxidative conversion, leading to significant wastewater and solid waste generation. Physico-chemical methods are typically used for heavy metal removal, but they have drawbacks, prompting interest in eco-friendly biological remediation techniques like biosorption, bioaccumulation, and biotransformation. The EU Directive (2018/850) mandates alternatives to landfilling or incineration for industrial textile waste management, highlighting the importance of environmentally conscious practices for leather products' end-of-life management, with composting being the most researched and viable option. This study aimed to isolate microorganisms from tannery wastewater and identify those responsible for different types of tanned leather biodegradation. Bacterial shifts during leather biodegradation were observed using a leather biodegradation assay (ISO 20136) with tannery and municipal wastewater as the inoculum. Over 10,000 bacterial species were identified in all analysed samples, with 7 bacterial strains isolated from tannery wastewaters. Identification of bacterial genera like Acinetobacter, Brevundimonas, and Mycolicibacterium provides insights into potential microbial candidates for enhancing leather biodegradability, wastewater treatment, and heavy metal bioremediation in industrial applications.
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Affiliation(s)
- Manuela Bonilla-Espadas
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Basilio Zafrilla
- Grupo Biotecnología de Extremófilos, Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Universidad de Alicante, 03690 Alicante, Spain; (B.Z.); (M.C.)
| | - Irene Lifante-Martínez
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Mónica Camacho
- Grupo Biotecnología de Extremófilos, Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Universidad de Alicante, 03690 Alicante, Spain; (B.Z.); (M.C.)
| | - Elena Orgilés-Calpena
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Francisca Arán-Aís
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Marcelo Bertazzo
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - María-José Bonete
- Grupo Biotecnología de Extremófilos, Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Universidad de Alicante, 03690 Alicante, Spain; (B.Z.); (M.C.)
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Fonseca A, Kenney S, Van Syoc E, Bierly S, Dini-Andreote F, Silverman J, Boney J, Ganda E. Investigating antibiotic free feed additives for growth promotion in poultry: effects on performance and microbiota. Poult Sci 2024; 103:103604. [PMID: 38484563 PMCID: PMC10951610 DOI: 10.1016/j.psj.2024.103604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/24/2024] Open
Abstract
The poultry industry is evolving towards antibiotic-free production to meet market demands and decelerate the increasing spread of the antimicrobial resistance. The growing need for antibiotic free products has challenged producers to decrease or completely stop using antimicrobials as feed supplements in broiler diet to improve feed efficiency, growth rate, and intestinal health. Natural feed additives (e.g., probiotics and phytobiotics) are promising alternatives to substitute antimicrobial growth promoters. The goal of our study was to characterize the effects of a Probiotic and an Essential Oils blend on broilers' performance and perform a time-series analysis to describe their excreta microbiome. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 d in 32 randomly allocated cages. Treatments consisted of 4 experimental diets: a basal diet, and a basal diet mixed with an Antibiotic (bacitracin methylene disalicylate), an essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Body weight (on 1, 10, and 21d), and feed intake (10d and 21d) were recorded and feed conversion ratio was calculated. Droppings were collected daily (1-21d) to characterize broilers' excreta microbiota by targeted sequencing of the bacterial 16S rRNA gene. The Probiotic significantly improved feed conversion ratio for starter phase 1 to 10d (P = 0.03), grower phase 10 to 21d (P = 0.05), and total period 1 to 21d (P = 0.01) compared to the Antibiotic. Feed supplements did not affect alpha diversity but did impact microbial beta diversity (P < 0.01). Age also impacted microbiome turnover as differences in alpha and beta diversity were detected. Furthermore, when compared to the basal diet, the probiotic and antibiotic significantly impacted relative abundance of Bifidobacterium (log2 fold change -1.44, P = 0.03), Intestinimonas (log2 fold change 0.560, P < 0.01) and Ligilactobacillus (log2 fold change -1.600, P < 0.01). Overall, Probiotic supplementation but not essential oils supplementation positively impacted broilers' growth performance by directly causing directional shifts in broilers' excreta microbiota structure.
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Affiliation(s)
- Ana Fonseca
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA
| | - Sophia Kenney
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA
| | - Emily Van Syoc
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA; Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Stephanie Bierly
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA
| | - Francisco Dini-Andreote
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA; Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Justin Silverman
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA; College of Information Sciences and Technology, The Pennsylvania State University, University Park, PA, USA; Department of Statistics, The Pennsylvania State University, University Park, PA, USA; Department of Medicine, The Pennsylvania State University, University Park, PA, USA; Institute for Computational and Data Science, The Pennsylvania State University, University Park, PA, USA
| | - John Boney
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA
| | - Erika Ganda
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA.
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3
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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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Craven H, Erlandsson H, McGuinness D, McGuinness D, Mafra D, Ijaz U, Bergman P, Shiels P, Stenvinkel P. A normative microbiome is not restored following kidney transplantation. Clin Sci (Lond) 2023; 137:1563-1575. [PMID: 37756543 PMCID: PMC10582644 DOI: 10.1042/cs20230779] [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: 07/18/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 09/29/2023]
Abstract
Dialysis and kidney transplantation (Ktx) mitigate some of the physiological deficits in chronic kidney disease (CKD), but it remains to be determined if these mitigate microbial dysbiosis and the production of inflammatory microbial metabolites, which contribute significantly to the uraemic phenotype. We have investigated bacterial DNA signatures present in the circulation of CKD patients and those receiving a KTx. Our data are consistent with increasing dysbiosis as CKD progresses, with an accompanying increase in trimethylamine (TMA) producing pathobionts Pseudomonas and Bacillus. Notably, KTx patients displayed a significantly different microbiota compared with CKD5 patients, which surprisingly included further increase in TMA producing Bacillus and loss of salutogenic Lactobacilli. Only two genera (Viellonella and Saccharimonidales) showed significant differences in abundance following KTx that may reflect a reciprocal relationship between TMA producers and utilisers, which supersedes restoration of a normative microbiome. Our metadata analysis confirmed that TMA N-oxide (TMAO) along with one carbon metabolism had significant impact upon both inflammatory burden and the composition of the microbiome. This indicates that these metabolites are key to shaping the uraemic microbiome and might be exploited in the development of dietary intervention strategies to both mitigate the physiological deficits in CKD and enable the restoration of a more salutogenic microbiome.
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Affiliation(s)
- Hannah Craven
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Molecular Biosciences, Davidson Bld, Glasgow, U.K
| | - Helen Erlandsson
- Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Dagmara McGuinness
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Molecular Biosciences, Davidson Bld, Glasgow, U.K
| | | | - Denise Mafra
- Fluminense Federal University (UFF), Niterói, RJ, Brazil
| | | | - Peter Bergman
- Department of Laboratory Medicine, Division of Clinical Immunology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Paul G. Shiels
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Molecular Biosciences, Davidson Bld, Glasgow, U.K
| | - Peter Stenvinkel
- Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Karolinska Institutet, Stockholm, Sweden
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Lorenzo-Rebenaque L, Casto-Rebollo C, Diretto G, Frusciante S, Rodríguez JC, Ventero MP, Molina-Pardines C, Vega S, Marin C, Marco-Jiménez F. Modulation of Caecal Microbiota and Metabolome Profile in Salmonella-Infected Broilers by Phage Therapy. Int J Mol Sci 2023; 24:15201. [PMID: 37894882 PMCID: PMC10607084 DOI: 10.3390/ijms242015201] [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: 09/20/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Bacteriophage therapy is considered one of the most promising tools to control zoonotic bacteria, such as Salmonella, in broiler production. Phages exhibit high specificity for their targeted bacterial hosts, causing minimal disruption to the niche microbiota. However, data on the gut environment's response to phage therapy in poultry are limited. This study investigated the influence of Salmonella phage on host physiology through caecal microbiota and metabolome modulation using high-throughput 16S rRNA gene sequencing and an untargeted metabolomics approach. We employed 24 caecum content samples and 24 blood serum samples from 4-, 5- and 6-week-old broilers from a previous study where Salmonella phages were administered via feed in Salmonella-infected broilers, which were individually weighed weekly. Phage therapy did not affect the alpha or beta diversity of the microbiota. Specifically, we observed changes in the relative abundance of 14 out of the 110 genera using the PLS-DA and Bayes approaches. On the other hand, we noted changes in the caecal metabolites (63 up-accumulated and 37 down-accumulated out of the 1113 caecal metabolites). Nevertheless, the minimal changes in blood serum suggest a non-significant physiological response. The application of Salmonella phages under production conditions modulates the caecal microbiome and metabolome profiles in broilers without impacting the host physiology in terms of growth performance.
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Affiliation(s)
- Laura Lorenzo-Rebenaque
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Cristina Casto-Rebollo
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain;
| | - Gianfranco Diretto
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Via Anguillarese, 301, Santa Maria di Galeria, 00123 Rome, Italy; (G.D.); (S.F.)
| | - Sarah Frusciante
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Via Anguillarese, 301, Santa Maria di Galeria, 00123 Rome, Italy; (G.D.); (S.F.)
| | - Juan Carlos Rodríguez
- Microbiology Department, Dr. Balmis University General Hospital, Microbiology Division, Miguel Hernández University, ISABIAL, 03010 Alicante, Spain;
| | - María-Paz Ventero
- Microbiology Department, Dr. Balmis University General Hospital, ISABIAL, 03010 Alicante, Spain; (M.-P.V.); (C.M.-P.)
| | - Carmen Molina-Pardines
- Microbiology Department, Dr. Balmis University General Hospital, ISABIAL, 03010 Alicante, Spain; (M.-P.V.); (C.M.-P.)
| | - Santiago Vega
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Clara Marin
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Francisco Marco-Jiménez
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain;
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Gunther NW, Nunez A, Bagi L, Abdul-Wakeel A, Ream A, Liu Y, Uhlich G. Butyrate decreases Campylobacter jejuni motility and biofilm partially through influence on LysR expression. Food Microbiol 2023; 115:104310. [PMID: 37567643 DOI: 10.1016/j.fm.2023.104310] [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: 02/17/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 08/13/2023]
Abstract
The food pathogen Campylobacter jejuni both colonizes the lower intestines of poultry and infects the lower intestines of humans. The lower intestines of both poultry and humans are also home to a wide range of commensal organisms which compete with an organism like C. jejuni for space and resources. The commensal organisms are believed to protect humans against infection by pathogens of the digestive tract like C. jejuni. The short chain fatty acid (SCFA) butyrate is a metabolite commonly produced by commensal organisms within both the poultry and human digestive tract. We investigated the effect that physiologically relevant concentrations of butyrate have on C. jejuni under in vitro conditions. Butyrate at concentrations of 5 and 20 mM negatively impacted C. jejuni motility and biofilm formation. These two traits are believed important for C. jejuni's ability to infect the lower intestines of humans. Additionally, 20 mM butyrate concentrations were observed to influence the expression of a range of different Campylobacter proteins. Constitutive expression of one of these proteins, LysR, within a C. jejuni strain partially lessened the negative influence butyrate had on the bacteria's motility.
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Affiliation(s)
- Nereus W Gunther
- Molecular Characterization of Foodborne Pathogens Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, USA.
| | - Alberto Nunez
- Emeritis, U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, USA
| | - Lori Bagi
- Molecular Characterization of Foodborne Pathogens Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, USA
| | - Aisha Abdul-Wakeel
- Molecular Characterization of Foodborne Pathogens Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, USA
| | - Amy Ream
- Molecular Characterization of Foodborne Pathogens Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, USA
| | - Yanhong Liu
- Molecular Characterization of Foodborne Pathogens Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, USA
| | - Gaylen Uhlich
- Molecular Characterization of Foodborne Pathogens Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, USA
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Ameer A, Cheng Y, Saleem F, Uzma, McKenna A, Richmond A, Gundogdu O, Sloan WT, Javed S, Ijaz UZ. Temporal stability and community assembly mechanisms in healthy broiler cecum. Front Microbiol 2023; 14:1197838. [PMID: 37779716 PMCID: PMC10534011 DOI: 10.3389/fmicb.2023.1197838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
In recent years, there has been an unprecedented advancement in in situ analytical approaches that contribute to the mechanistic understanding of microbial communities by explicitly incorporating ecology and studying their assembly. In this study, we have analyzed the temporal profiles of the healthy broiler cecal microbiome from day 3 to day 35 to recover the stable and varying components of microbial communities. During this period, the broilers were fed three different diets chronologically, and therefore, we have recovered signature microbial species that dominate during each dietary regime. Since broilers were raised in multiple pens, we have also parameterized these as an environmental condition to explore microbial niches and their overlap. All of these analyses were performed in view of different parameters such as body weight (BW-mean), feed intake (FI), feed conversion ratio (FCR), and age (days) to link them to a subset of microbes that these parameters have a bearing upon. We found that gut microbial communities exhibited strong and statistically significant specificity for several environmental variables. Through regression models, genera that positively/negatively correlate with the bird's age were identified. Some short-chain fatty acids (SCFAs)-producing bacteria, including Izemoplasmatales, Gastranaerophilales, and Roseburia, have a positive correlation with age. Certain pathogens, such as Escherichia-Shigella, Sporomusa, Campylobacter, and Enterococcus, negatively correlated with the bird's age, which indicated a high disease risk in the initial days. Moreover, the majority of pathways involved in amino acid biosynthesis were also positively correlated with the bird's age. Some probiotic genera associated with improved performance included Oscillospirales; UCG-010, Shuttleworthia, Bifidobacterium, and Butyricicoccaceae; UCG-009. In general, predicted antimicrobial resistance genes (piARGs) contributed at a stable level, but there was a slight increase in abundance when the diet was changed. To the best of the authors' knowledge, this is one of the first studies looking at the stability, complexity, and ecology of natural broiler microbiota development in a temporal setting.
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Affiliation(s)
- Aqsa Ameer
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Youqi Cheng
- Water and Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Farrukh Saleem
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Uzma
- Water and Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Ozan Gundogdu
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - William T. Sloan
- Water and Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Sundus Javed
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Umer Zeeshan Ijaz
- Water and Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, United Kingdom
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
- College of Science and Engineering, University of Galway, Galway, Ireland
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El-Saadony MT, Saad AM, Yang T, Salem HM, Korma SA, Ahmed AE, Mosa WFA, Abd El-Mageed TA, Selim S, Al Jaouni SK, Zaghloul RA, Abd El-Hack ME, El-Tarabily KA, Ibrahim SA. Avian campylobacteriosis, prevalence, sources, hazards, antibiotic resistance, poultry meat contamination, and control measures: a comprehensive review. Poult Sci 2023; 102:102786. [PMID: 37454641 PMCID: PMC10371856 DOI: 10.1016/j.psj.2023.102786] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/05/2023] [Accepted: 05/13/2023] [Indexed: 07/18/2023] Open
Abstract
Avian campylobacteriosis is a vandal infection that poses human health hazards. Campylobacter is usually colonized in the avian gut revealing mild signs in the infected birds, but retail chicken carcasses have high contamination levels of Campylobacter spp. Consequently, the contaminated avian products constitute the main source of human infection with campylobacteriosis and result in severe clinical symptoms such as diarrhea, abdominal pain, spasm, and deaths in sensitive cases. Thus, the current review aims to shed light on the prevalence of Campylobacter in broiler chickens, Campylobacter colonization, bird immunity against Campylobacter, sources of poultry infection, antibiotic resistance, poultry meat contamination, human health hazard, and the use of standard antimicrobial technology during the chicken processing of possible control strategies to overcome such problems.
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Affiliation(s)
- Mohamed T El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Ahmed M Saad
- Department of Biochemistry, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Tao Yang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, 571199, China
| | - Heba M Salem
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Sameh A Korma
- Department of Food Science, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Ahmed Ezzat Ahmed
- Biology Department, College of Science, King Khalid University, Abha, 61413, Saudi Arabia; Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, 61413, Saudi Arabia
| | - Walid F A Mosa
- Plant Production Department (Horticulture-Pomology), Faculty of Agriculture, Saba Basha, Alexandria University, Alexandria, 21531, Egypt
| | - Taia A Abd El-Mageed
- Department of Soils and Water, Faculty of Agriculture, Fayoum University, Fayoum, 63514, Egypt
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, 72388, Saudi Arabia
| | - Soad K Al Jaouni
- Department of Hematology/Oncology, Yousef Abdulatif Jameel Scientific Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Rashed A Zaghloul
- Department Agricultural Microbiology, Faculty of Agriculture, Benha University, Moshtohor, Qaluybia, 13736, Egypt
| | - Mohamed E Abd El-Hack
- Poultry Department, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates.
| | - Salam A Ibrahim
- Food Microbiology and Biotechnology Laboratory, Carver Hall, College of Agriculture and Environmental Sciences, North Carolina A & T State University, Greensboro, NC, 27411-1064
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Aziz I, Noreen Z, Ijaz UZ, Gundogdu O, Hamid MH, Muhammad N, Khan A, Bokhari H. A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome. Sci Rep 2023; 13:6802. [PMID: 37185286 PMCID: PMC10133260 DOI: 10.1038/s41598-023-32491-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/28/2023] [Indexed: 05/17/2023] Open
Abstract
Stunted growth is an emerging global challenge affecting children under the age of 5 years in low- and middle-income countries. Despite such a high global prevalence of stunting, the mechanism of pathogenesis and the role of associated gut microbiota is poorly understood. The present study was designed to investigate the association of pathogenic strains of E. coli with the residential gut microbiota of stunted growth children. A total of 64 stool sample were collected from children aged ≤ 5 years, and were processed for isolation and molecular characterization of diarrheagenic E. coli. Selected stool samples (n = 39 including three normal controls) were then analysed for microbial community profiling using 16S ribosomal RNA (rRNA) gene sequencing. Furthermore, associations between changes in the microbiota in the presence of different E. coli strains was explored. Pathotyping of the isolated E. coli (n = 64) has shown that 39.68% belonged to one of the five pathotypes of E. coli whilst the remaining ones were non-typeable. Amongst the different pathotypes, EPEC was found to be the most prevalent (52%; n = 13), followed by EAEC (20%; n = 5), EIEC (12%; n = 3), EHEC (8%; n = 2) and ETEC 2 (8%; n = 2). Phylogrouping analysis has shown that majority of the strains belonged to B2 (28.12%). Microbial diversity is shown to be significant and varied when the samples are organized under the recovered phylogroups. Moreover, based on predictive metabolism, the colonization of these strains were found to be significantly associated with energy utilization pathways such as Denovoprine-2 and glyoxylate-by. Differential analysis has shown that Escherichia-Shigella and Enterococcus were altered for the children with stunted growth.
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Affiliation(s)
- Israr Aziz
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Zobia Noreen
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | | | - Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Muhammad Haroon Hamid
- Department of Pediatrics/Department of Preventive Pediatrics, Mayo Hospital, King Edward Medical University, Lahore, Pakistan
| | - Nazir Muhammad
- Department of Pediatrics/Department of Preventive Pediatrics, Mayo Hospital, King Edward Medical University, Lahore, Pakistan
| | - Abdullah Khan
- Paediatric Unit, Saidu Teaching Hospitals, Swat, Saidu Sharif, Pakistan
| | - Habib Bokhari
- Department of Biosciences, COMSATS University, Islamabad, Pakistan.
- Department of Biosciences, Kohsar University, Murree, Pakistan.
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10
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Doster E, Pinnell LJ, Noyes NR, Parker JK, Anderson CA, Booker CW, Hannon SJ, McAllister TA, Gow SP, Belk KE, Morley PS. Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle. Front Microbiol 2022; 13:970358. [PMID: 36583056 PMCID: PMC9792868 DOI: 10.3389/fmicb.2022.970358] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/10/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction Use of antimicrobial drugs (AMDs) in food producing animals has received increasing scrutiny because of concerns about antimicrobial resistance (AMR) that might affect consumers. Previously, investigations regarding AMR have focused largely on phenotypes of selected pathogens and indicator bacteria, such as Salmonella enterica or Escherichia coli. However, genes conferring AMR are known to be distributed and shared throughout microbial communities. The objectives of this study were to employ target-enriched metagenomic sequencing and 16S rRNA gene amplicon sequencing to investigate the effects of AMD use, in the context of other management and environmental factors, on the resistome and microbiome in beef feedlot cattle. Methods This study leveraged samples collected during a previous longitudinal study of cattle at beef feedlots in Canada. This included fecal samples collected from randomly selected individual cattle, as well as composite-fecal samples from randomly selected pens of cattle. All AMD use was recorded and characterized across different drug classes using animal defined daily dose (ADD) metrics. Results Overall, fecal resistome composition was dominated by genes conferring resistance to tetracycline and macrolide-lincosamide-streptogramin (MLS) drug classes. The diversity of bacterial phyla was greater early in the feeding period and decreased over time in the feedlot. This decrease in diversity occurred concurrently as the microbiome represented in different individuals and different pens shifted toward a similar composition dominated by Proteobacteria and Firmicutes. Some antimicrobial drug exposures in individuals and groups were associated with explaining a statistically significant proportion of the variance in the resistome, but the amount of variance explained by these important factors was very small (<0.6% variance each), and smaller than associations with other factors measured in this study such as time and feedlot ID. Time in the feedlot was associated with greater changes in the resistome for both individual animals and composite pen-floor samples, although the proportion of the variance associated with this factor was small (2.4% and 1.2%, respectively). Discussion Results of this study are consistent with other investigations showing that, compared to other factors, AMD exposures did not have strong effects on antimicrobial resistance or the fecal microbial ecology of beef cattle.
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Affiliation(s)
- Enrique Doster
- Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, CO, United States,Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, United States
| | - Lee J. Pinnell
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, United States
| | - Noelle R. Noyes
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Jennifer K. Parker
- Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, CO, United States
| | - Cameron A. Anderson
- Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, CO, United States
| | | | | | | | - Sheryl P. Gow
- Public Health Agency of Canada, Saskatoon, SK, Canada
| | - Keith E. Belk
- Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, CO, United States
| | - Paul S. Morley
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, United States,*Correspondence: Paul S. Morley,
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11
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Moran ET, Bedford MR. Large intestinal dynamics differ between fowl and swine: Anatomical modifications, microbial collaboration, and digestive advantages from fibrolytic enzymes. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 11:160-170. [PMID: 36254218 PMCID: PMC9550523 DOI: 10.1016/j.aninu.2022.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/21/2022] [Accepted: 07/14/2022] [Indexed: 06/16/2023]
Abstract
The large intestinal systems of fowl and swine recover nutrients from ileal indigesta by a strategically different manner. Indigesta with fowl enter a short colon where retro-peristalsis using urine from the urodeum carries small particulates and solutes into both ceca while coarse materials collect in the cloaca. Fowl repetitively add fine and soluble materials into both ceca to continue fermentation until complexity of the remainder exceeds microbial action, then contents apart from faeces are entirely evacuated. Indigesta with swine initially enter a short cecum followed by a lengthy progression through to the rectal ampulla. Wall out-pocketings of circular muscle or haustrae occur throughout the length of the pig's cecum and helicoidal colon. Each pocket carries contents acquired earlier in the cecum. Motility collects fines and solutes into haustrae during their progression through the colon whereas coarse particulates assemble in the core. Haustrae contents continually ferment during movement to the distal colon with resulting volatile fatty acids (VFA) and electrolytes being absorbed. Mucin loosely covers the lumen surface in caeca as well as helicoidal colon that may capture microbes from active intestinal contents as well as release others to sustain fermentation. The microbial community continually modifies to accommodate fibre complexity as encountered. Resistant starches (RS) and simple oligosaccharides rapidly ferment to yield VFA while encouraging butyric acid in the cecum and anterior colon, whereas non-starch polysaccharides (NSP) complexity requires extended durations through the remaining colon that enhance acetic acid. Residual fibre eventually results in undue complexity for fermentation and consolidates at termination of the colon. These compact pellets are placed on core contents to form faeces having a nodular surface. Acetic, propionic, and butyric acids represent the bulk of VFA and are derived from non-digestible carbohydrates. Fibrolytic enzymes, when supplemented to feed, may increase the proportion of oligosaccharides and simpler NSP to further the rate as well as extent of fermentation. Active absorption of VFA by mucosal enterocytes employs its ionized form together with Na+, whereas direct membrane passage occurs when non-dissociated. Most absorbed VFA favour use by the host with a portion of butyric acid together with by-products from protein digestion being retained to reform mucin and sustain mucosal integrity.
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Affiliation(s)
- Edwin T. Moran
- Poultry Science Department, Auburn University, AL 36830-5416, USA
| | - Michael R. Bedford
- AB Vista, Woodstock Court, Blenheim Road, Marlborough, Wiltshire SN8 4AN, UK
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12
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Interactions of Microbiota and Mucosal Immunity in the Ceca of Broiler Chickens Infected with Eimeria tenella. Vaccines (Basel) 2022; 10:vaccines10111941. [PMID: 36423036 PMCID: PMC9693493 DOI: 10.3390/vaccines10111941] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
The purpose of the study was to investigate the effects of Eimeria tenella infection on the cecal microbiome, the protein concentration of cecal content, cecal mucosal immunity, and serum endotoxin levels in broilers. Three hundred sixty 14-day-old broilers were allocated to five infection doses with six replicates. The five infection doses were: ID0: 0, ID1: 6250, ID2: 12,500, ID3: 25,000, and ID4: 50,000 Eimeria tenella oocysts. Eimeria tenella infection significantly increased the relative abundance of the phylum Proteobacteria, which includes diverse pathogenic bacteria, and significantly decreased the relative abundance of the phylum Firmicutes. Protein concentration of the cecal content was linearly increased (p < 0.05), and the concentration of secretory immunoglobulin A (sIgA) in the cecal content was linearly decreased by Eimeria tenella infection (p < 0.05). Goblet cell density was linearly reduced in the ceca by Eimeria tenella infection (p < 0.05). Eimeria tenella infection tended to linearly decrease the relative mRNA expression of antimicrobial peptide genes such as avian beta-defensin 9 (AvBD9; p = 0.10) and liver-expressed antimicrobial peptide 2 (LEAP2; p = 0.08) in the cecal tissue. Therefore, Eimeria tenella infection negatively modulated cecal microbiota via impairing cecal mucosal immunity and increasing protein concentration in the cecal content in broilers.
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13
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Proszkowiec-Weglarz M, Miska KB, Ellestad LE, Schreier LL, Kahl S, Darwish N, Campos P, Shao J. Delayed access to feed early post-hatch affects the development and maturation of gastrointestinal tract microbiota in broiler chickens. BMC Microbiol 2022; 22:206. [PMID: 36002800 PMCID: PMC9404604 DOI: 10.1186/s12866-022-02619-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 08/17/2022] [Indexed: 11/24/2022] Open
Abstract
Background The first two weeks of post-hatch (PH) growth in broilers (meat-type birds) are critical for gut development and microbiota colonization. In the current broiler production system, chicks may not receive feed and water for 24 to 72 h due to variations in hatching time and hatchery management. Post-hatch feed delay affects body weight, feed efficiency, mortality, and gut development. The goal of this study was to investigate changes in the microbiome in broiler chickens early PH and the effect of delayed access to feed on the microbiota. Results Chicks either received feed and water immediately after hatch or access to feed was delayed for 48 h to mimic commercial hatchery settings (treatment, TRT). Both groups were sampled (n = 6) at -48, 0, 4 h, and 1 (24 h), 2 (48 h), 3 (72 h), 4 (96 h), 6 (144 h), 8 (192 h), 10 (240 h), 12 (288 h) and 14 (336 h) days PH. Ileal (IL) and cecal (CE) epithelial scrapings (mucosal bacteria, M) and digesta (luminal bacteria, L) were collected for microbiota analysis. Microbiota was determined by sequencing the V3-V4 region of bacterial 16S rRNA and analyzed using QIIME2. The microbiota of early ileal and cecal samples were characterized by high abundance of unclassified bacteria. Among four bacterial populations (IL-L, IL-M, CE-L, CE-M), IL-M was the least affected by delayed access to feed early PH. Both alpha and beta diversities were affected by delayed access to feed PH in IL-L, CE-M and CE-L. However, the development effect was more pronounced. In all four bacterial populations, significant changes due to developmental effect (time relative to hatch) was observed in taxonomic composition, with transient changes of bacterial taxa during the first two weeks PH. Delayed access to feed has limited influence on bacterial composition with only a few genera and species affected in all four bacterial populations. Predicted function based on 16S rRNA was also affected by delayed access to feed PH with most changes in metabolic pathway richness observed in IL-L, CE-L and CE-M. Conclusions These results show transient changes in chicken microbiota biodiversity during the first two weeks PH and indicate that delayed access to feed affects microbiota development. Proper microbiota development could be an important factor in disease prevention and antibiotic use in broiler chickens. Moreover, significant differences in response to delayed access to feed PH between luminal and mucosal bacterial populations strongly suggests the need for separate analysis of these two populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02619-6.
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Affiliation(s)
- Monika Proszkowiec-Weglarz
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Northeast Area (NEA), Animal Biosciences and Biotechnology Laboratory (ABBL), Beltsville, 10300 Baltimore Avenue, B-200, Rm. 100B, BARC-East, Beltsville, MD, 20705, USA.
| | - Katarzyna B Miska
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Northeast Area (NEA), Animal Biosciences and Biotechnology Laboratory (ABBL), Beltsville, 10300 Baltimore Avenue, B-200, Rm. 100B, BARC-East, Beltsville, MD, 20705, USA
| | - Laura E Ellestad
- Department of Poultry Science, University of Georgia, Athens, GA, 30602, USA
| | - Lori L Schreier
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Northeast Area (NEA), Animal Biosciences and Biotechnology Laboratory (ABBL), Beltsville, 10300 Baltimore Avenue, B-200, Rm. 100B, BARC-East, Beltsville, MD, 20705, USA
| | - Stanislaw Kahl
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Northeast Area (NEA), Animal Biosciences and Biotechnology Laboratory (ABBL), Beltsville, 10300 Baltimore Avenue, B-200, Rm. 100B, BARC-East, Beltsville, MD, 20705, USA
| | - Nadia Darwish
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Northeast Area (NEA), Animal Biosciences and Biotechnology Laboratory (ABBL), Beltsville, 10300 Baltimore Avenue, B-200, Rm. 100B, BARC-East, Beltsville, MD, 20705, USA.,United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Northeast Area (NEA), Statistic Group, Beltsville, MD, 20705, USA
| | - Philip Campos
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Northeast Area (NEA), Animal Biosciences and Biotechnology Laboratory (ABBL), Beltsville, 10300 Baltimore Avenue, B-200, Rm. 100B, BARC-East, Beltsville, MD, 20705, USA.,United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Northeast Area (NEA), Statistic Group, Beltsville, MD, 20705, USA
| | - Jonathan Shao
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Northeast Area (NEA), Statistic Group, Beltsville, MD, 20705, USA
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14
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Gradisteanu Pircalabioru G, Liaw J, Gundogdu O, Corcionivoschi N, Ilie I, Oprea L, Musat M, Chifiriuc MC. Effects of the Lipid Profile, Type 2 Diabetes and Medication on the Metabolic Syndrome—Associated Gut Microbiome. Int J Mol Sci 2022; 23:ijms23147509. [PMID: 35886861 PMCID: PMC9318871 DOI: 10.3390/ijms23147509] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 02/08/2023] Open
Abstract
Metabolic syndrome (MetSyn) is a major health problem affecting approximately 25% of the worldwide population. Since the gut microbiota is highly connected to the host metabolism, several recent studies have emerged to characterize the role of the microbiome in MetSyn development and progression. To this end, our study aimed to identify the microbiome patterns which distinguish MetSyn from type 2 diabetes mellitus (T2DM). We performed 16S rRNA amplicon sequencing on a cohort of 70 individuals among which 40 were MetSyn patients. The microbiome of MetSyn patients was characterised by reduced diversity, loss of butyrate producers (Subdoligranulum, Butyricicoccus, Faecalibacterium prausnitzii) and enrichment in the relative abundance of fungal populations. We also show a link between the gut microbiome and lipid metabolism in MetSyn. Specifically, low-density lipoproteins (LDL) and high-density lipoproteins (HDL) display a positive effect on gut microbial diversity. When interrogating the signature of gut microbiota in a subgroup of patients harbouring both MetSyn and T2DM conditions, we observed a significant increase in taxa such as Bacteroides, Clostridiales, and Erysipelotrichaceae. This preliminary study shows for the first time that T2DM brings unique signatures of gut microbiota in MetSyn patients. We also highlight the impact of metformin treatment on the gut microbiota. Metformin administration was linked to changes in Prevotellaceae, Rickenellaceae, and Clostridiales. Further research focusing on the microbiome-metabolome patterns is needed to clarify the exact association of various gut microbial communities with the progression of T2DM and the occurrence of various complications in MetSyn patients.
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Affiliation(s)
| | - Janie Liaw
- Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK;
| | - Ozan Gundogdu
- Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK;
- Correspondence: (G.G.P.); (O.G.)
| | - Nicolae Corcionivoschi
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast BT9 5PX, UK;
- Faculty of Bioengineering of Animal Resources, Banat University of Agricultural Sciences and Veterinary Medicine—King Michael I of Romania, 300645 Timisoara, Romania
| | | | - Luciana Oprea
- National Institute of Endocrinology C.I. Parhon, 011863 Bucharest, Romania; (L.O.); (M.M.)
| | - Madalina Musat
- National Institute of Endocrinology C.I. Parhon, 011863 Bucharest, Romania; (L.O.); (M.M.)
- Department of Endocrinology, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Mariana-Carmen Chifiriuc
- Research Institute of University of Bucharest (ICUB), 300645 Bucharest, Romania;
- Romanian Academy, 010071 Bucharest, Romania
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15
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Colles FM, Karasova D, Crhanova M, Preston SG, Smith AL, Dawkins MS, Rychlik I, Gebhardt-Henrich SG. High resolution parallel sequencing reveals multi-strain Campylobacter in broiler chicken flocks testing ‘negative’ by conventional culture methods: implications for control of Campylobacter infection. Poult Sci 2022; 101:102048. [PMID: 35952602 PMCID: PMC9372630 DOI: 10.1016/j.psj.2022.102048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022] Open
Abstract
Contaminated chicken meat is a major source of human Campylobacteriosis and rates of infection remain high, despite efforts to limit the colonisation of broiler (meat) chicken flocks on farms. Using conventional testing methods of culture or qPCR, Campylobacter is typically detected amongst broiler flocks from 3 wk of age, leading to the assumption that infection is introduced horizontally into chicken rearing houses at this time. In this study, we use parallel sequencing of a fragment of the Campylobacter outer membrane protein, encoded by the porA gene, to test for presence of Campylobacter DNA amongst fresh fecal samples collected from broiler flocks aged 23 to 28 d. Campylobacter DNA was detected in all of the 290 samples tested using the porA target, and in 48% of samples using 16S bacterial profiling, irrespective of whether or not Campylobacter could be detected using conventional qPCR thresholds. A single porAf2 variant was predominant among flocks that would be determined to be Campylobacter ‘positive’ by conventional means, but a diverse pattern was seen among flocks that were Campylobacter ‘negative’. The ability to routinely detect low levels of Campylobacter amongst broiler flocks at a much earlier age than would conventionally be identified requires a re-examination of how and when biosecurity measures are best applied for live birds. In addition, it may be useful to investigate why single Campylobacter variants proliferate in some broiler flocks and not others.
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16
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Mota-Gutierrez J, Lis L, Lasagabaster A, Nafarrate I, Ferrocino I, Cocolin L, Rantsiou K. Campylobacter spp. prevalence and mitigation strategies in the broiler production chain. Food Microbiol 2022; 104:103998. [DOI: 10.1016/j.fm.2022.103998] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/13/2022] [Accepted: 01/28/2022] [Indexed: 12/15/2022]
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17
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Clavere-Graciette AG, McWhirt ME, Hoopes LA, Bassos-Hull K, Wilkinson KA, Stewart FJ, Pratte ZA. Microbiome differences between wild and aquarium whitespotted eagle rays (Aetobatus narinari). Anim Microbiome 2022; 4:34. [PMID: 35606841 PMCID: PMC9128078 DOI: 10.1186/s42523-022-00187-8] [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] [Received: 08/24/2021] [Accepted: 05/09/2022] [Indexed: 11/15/2022] Open
Abstract
Background Animal-associated microbiomes can be influenced by both host and environmental factors. Comparing wild animals to those in zoos or aquariums can help disentangle the effects of host versus environmental factors, while also testing whether managed conditions foster a ‘natural’ host microbiome. Focusing on an endangered elasmobranch species—the whitespotted eagle ray Aetobatus narinari—we compared the skin, gill, and cloaca microbiomes of wild individuals to those at Georgia Aquarium. Whitespotted eagle ray microbiomes from Georgia Aquarium were also compared to those of cownose rays (Rhinoptera bonasus) in the same exhibit, allowing us to explore the effect of host identity on the ray microbiome.
Results Long-term veterinary monitoring indicated that the rays in managed care did not have a history of disease and maintained health parameters consistent with those of wild individuals, with one exception. Aquarium whitespotted eagle rays were regularly treated to control parasite loads, but the effects on animal health were subclinical. Microbiome α- and β-diversity differed between wild versus aquarium whitespotted eagle rays at all body sites, with α-diversity significantly higher in wild individuals. β-diversity differences in wild versus aquarium whitespotted eagle rays were greater for skin and gill microbiomes compared to those of the cloaca. At each body site, we also detected microbial taxa shared between wild and aquarium eagle rays. Additionally, the cloaca, skin, and gill microbiomes of aquarium eagle rays differed from those of cownose rays in the same exhibit. Potentially pathogenic bacteria were at low abundance in all wild and aquarium rays.
Conclusion For whitespotted eagle rays, managed care was associated with a microbiome differing significantly from that of wild individuals. These differences were not absolute, as the microbiome of aquarium rays shared members with that of wild counterparts and was distinct from that of a cohabitating ray species. Eagle rays under managed care appear healthy, suggesting that their microbiomes are not associated with compromised host health. However, the ray microbiome is dynamic, differing with both environmental factors and host identity. Monitoring of aquarium ray microbiomes over time may identify taxonomic patterns that co-vary with host health. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00187-8.
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Affiliation(s)
| | - Mary E McWhirt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Lisa A Hoopes
- Department of Research and Conservation, Georgia Aquarium, Atlanta, GA, USA
| | - Kim Bassos-Hull
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,Chicago Zoological Society's Sarasota Dolphin Research Program, c/o Mote Marine Laboratory, Sarasota, FL, USA
| | - Krystan A Wilkinson
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,Chicago Zoological Society's Sarasota Dolphin Research Program, c/o Mote Marine Laboratory, Sarasota, FL, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, USA
| | - Zoe A Pratte
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, USA.
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18
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Bedford MR, Apajalahti JH. The role of feed enzymes in maintaining poultry intestinal health. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:1759-1770. [PMID: 34802157 PMCID: PMC9300167 DOI: 10.1002/jsfa.11670] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/21/2021] [Accepted: 11/20/2021] [Indexed: 06/13/2023]
Abstract
Gut health or intestinal health is frequently discussed without any clear definition as to its meaning. It is suggested that this should be defined as intestinal integrity and functionality as both are a pre-requisite for the health of the intestine itself and the host. The health of the intestine is dependent upon a successful evolution of the absorptive capacity of the intestine, which in turn is influenced by the co-evolution of the intestinal immune systems and the microbiota. Nutrient supply plays a significant role in this process and from the perspective of the microbiota this changes with age as the intestines and upper gastrointestinal tract (GIT) microbiota become more effective in nutrient removal. Feed enzymes play a significant role in this process. Phytases can improve digestion of minerals, amino acids and energy and as a result reduce the availability of nutrients in the lower intestines for the microbiota. Protease can have a similar effect with amino acid supply. Non-starch polysaccharidases (NSPases) have a unique role in that they not only improve diet digestibility from the hosts perspective, thus limiting nutrient supply to the microbiota, but they also release soluble fragments of fibre from the insoluble matrix and/or depolymerize high molecular weight viscous fibre fractions in to smaller, more fermentable carbohydrate fractions. This results in a more favourable balance between fermentable carbohydrate to protein supply, a ratio which is deemed critical to maintaining good intestinal health. The dynamic nature of this complex evolution needs greater consideration if antibiotic free production is to succeed. © 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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19
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Clavijo V, Morales T, Vives-Flores MJ, Reyes Muñoz A. The gut microbiota of chickens in a commercial farm treated with a Salmonella phage cocktail. Sci Rep 2022; 12:991. [PMID: 35046416 PMCID: PMC8770602 DOI: 10.1038/s41598-021-04679-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/29/2021] [Indexed: 12/25/2022] Open
Abstract
The microbiota in broiler chicken intestines affects the animals' health, metabolism, and immunity both positively and negatively. Accordingly, it has a significant impact on animal productivity. Phages, host-specific parasites of bacterial cells, are a promising antimicrobial alternative that selectively target pathogens without disturbing the microbiota. The purpose of this study is to further characterize the commensal microbial community at production scale in broiler chickens treated with a Salmonella phage treatment. We evaluated the cecal microbiota of broilers reared in a commercial farming system where a phage cocktail against Salmonella, SalmoFree was supplied to animals. To do so, two field trials were conducted, incorporating three doses of phages in the broilers' drinking water. Our results showed that the core microbiome (taxa that were present in more than 50% of samples) contained species that are key to microbiota adaptation in the last stage of the production cycle. Among these, there are some important degraders of complex polysaccharides and producers of short chain fatty acids (SCFA) such as Eisenbergiella and Lachnoclostridium. The phage cocktail did not affect the normal development of the microbiota's structure. The addition of the phage cocktail resulted in a significant reduction in Campylobacter and an increase in Butyricimonas, Helicobacter and Rikenellaceae, which are common inhabitants in chicken gut with known negative and positive effects on their health and metabolism. Altogether, we consider that these results contribute valuable information to the implementation of large-scale phage therapy technologies.
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Affiliation(s)
- Viviana Clavijo
- Grupo de Investigación en Biología Computacional y Ecología Microbiana, Universidad de los Andes, Cra 1 #18A-12, Bogotá, Colombia
- Centro de Investigaciones Microbiológicas, Universidad de los Andes, Carrera 1 Este #19A-40, Bogotá, Colombia
| | - Tatiana Morales
- Centro de Investigaciones Microbiológicas, Universidad de los Andes, Carrera 1 Este #19A-40, Bogotá, Colombia
| | | | - Alejandro Reyes Muñoz
- Grupo de Investigación en Biología Computacional y Ecología Microbiana, Universidad de los Andes, Cra 1 #18A-12, Bogotá, Colombia.
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Carrera 1 Este #19A-40, Bogotá, Colombia.
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, 63108, USA.
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20
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Frau A, Ijaz UZ, Slater R, Jonkers D, Penders J, Campbell BJ, Kenny JG, Hall N, Lenzi L, Burkitt MD, Pierik M, Darby AC, Probert CSJ. Inter-kingdom relationships in Crohn's disease explored using a multi-omics approach. Gut Microbes 2022; 13:1930871. [PMID: 34241567 PMCID: PMC8274447 DOI: 10.1080/19490976.2021.1930871] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The etiology of Crohn's disease (CD) is multifactorial. Bacterial and fungal microbiota are involved in the onset and/or progression of the disease. A bacterial dysbiosis in CD patients is accepted; however, less is known about the mycobiome and the relationships between the two communities. We investigated the interkingdom relationships, their metabolic consequences, and the changes in the fungal community during relapse and remission in CD.Two cohorts were evaluated: a British cohort (n = 63) comprising CD and ulcerative colitis patients, and controls. The fungal and bacterial communities of biopsy and fecal samples were analyzed, with the fecal volatiles; datasets were also integrated; and a Dutch cohort (n = 41) comprising CD patients and healthy controls was analyzed for stability of the gut mycobiome.A dysbiosis of the bacterial community was observed in biopsies and stool. Results suggest Bacteroides is likely key in CD and may modulate Candida colonization. A dysbiosis of the fungal community was observed only in the Dutch cohort; Malassezia and Candida were increased in patients taking immunosuppressants. Longitudinal analysis showed an increase in Cyberlindnera in relapse. Saccharomyces was dominant in all fecal samples, but not in biopsies, some of which did not yield fungal reads; amino acid degradation was the main metabolic change associated with CD and both bacteria and fungi might be implicated.We have shown that Bacteroides and yeasts may play a role in CD; understanding their role and relationship in the disease would shed new light on the development and treatment of CD.
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Affiliation(s)
- Alessandra Frau
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK,CONTACT Alessandra Frau Department of Molecular and Clinical Cancer Medicine, Nuffield Building, Ashton Street, LiverpoolL69 3GE, UK
| | - Umer Z. Ijaz
- School of Engineering, University of Glasgow, Glasgow, UK,Umer Z. Ijaz School of Engineering, University of Glasgow, Glasgow, UK
| | - Rachael Slater
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daisy Jonkers
- School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - John Penders
- School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Barry J. Campbell
- Department of Infection & Microbiomes, University of Liverpool, Liverpool, UK
| | | | - Neil Hall
- Earlham Institute, Norwich, UK,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | - Luca Lenzi
- Centre for Genomic Research, University of Liverpool, Liverpool, UK
| | - Michael D. Burkitt
- Division of Diabetes, Endocrinology and Gastroenterology, University of Manchester, Manchester, UK
| | - Marieke Pierik
- School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Alistair C. Darby
- Department of Infection & Microbiomes, University of Liverpool, Liverpool, UK
| | - Christopher S. J. Probert
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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21
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Asare PT, Greppi A, Pennacchia A, Brenig K, Geirnaert A, Schwab C, Stephan R, Lacroix C. In vitro Modeling of Chicken Cecal Microbiota Ecology and Metabolism Using the PolyFermS Platform. Front Microbiol 2022; 12:780092. [PMID: 34987487 PMCID: PMC8721126 DOI: 10.3389/fmicb.2021.780092] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/15/2021] [Indexed: 12/30/2022] Open
Abstract
Continuous in vitro fermentation models provide a useful tool for a fast, reproducible, and direct assessment of treatment-related changes in microbiota metabolism and composition independent of the host. In this study, we used the PolyFermS model to mimic the conditions of the chicken cecum and evaluated three nutritive media for in vitro modeling of the chicken cecal microbiota ecology and metabolism. We observed that our model inoculated with immobilized cecal microbiota and fed with a modified Viande Levure medium (mVL-3) reached a high bacterial cell density of up to approximately 10.5 log cells per mL and stable microbiota composition, akin to the host, during 82 days of continuous operation. Relevant bacterial functional groups containing primary fibrolytic (Bacteroides, Bifidobacteriaceae, Ruminococcaceae), glycolytic (Enterococcus), mucolytic (Bacteroides), proteolytic (Bacteroides), and secondary acetate-utilizing butyrate-producing and propionate-producing (Lachnospiraceae) taxa were preserved in vitro. Besides, conserved metabolic and functional Kyoto Encyclopedia of Genes and Genomes pathways were observed between in vitro microbiota and cecal inoculum microbiota as predicted by functional metagenomics analysis. Furthermore, we demonstrated that the continuous inoculation provided by the inoculum reactor generated reproducible metabolic profiles in second-stage reactors comparable to the chicken cecum, allowing for the simultaneous investigation and direct comparison of different treatments with a control. In conclusion, we showed that PolyFermS is a suitable model for mimicking chicken cecal microbiota fermentation allowing ethical and ex vivo screening of environmental factors, such as dietary additives, on chicken cecal fermentation. We report here for the first time a fermentation medium (mVL-3) that closely mimics the substrate conditions in the chicken cecum and supports the growth and metabolic activity of the cecal bacterial akin to the host. Our PolyFermS chicken cecum model is a useful tool to study microbiota functionality and structure ex vivo.
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Affiliation(s)
- Paul Tetteh Asare
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Anna Greppi
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Alessia Pennacchia
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Katharina Brenig
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Hygiene and Safety, University of Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
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22
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Souza MN, Wolf JM, Zanetti NS, Fonseca ASK, Ikuta N, Lunge VR. Direct Detection and Quantification of Bacterial Pathogens from Broiler Cecal Samples in the Slaughter Line by Real-Time PCR. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2022. [DOI: 10.1590/1806-9061-2021-1505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- MN Souza
- Universidade Luterana do Brasil, Brazil
| | - JM Wolf
- Universidade Luterana do Brasil, Brazil
| | | | | | - N Ikuta
- Simbios Biotecnologia, Brazil
| | - VR Lunge
- Universidade Luterana do Brasil, Brazil; Simbios Biotecnologia, Brazil
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23
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Nothaft H, Perez-Muñoz ME, Yang T, Murugan AVM, Miller M, Kolarich D, Plastow GS, Walter J, Szymanski CM. Improving Chicken Responses to Glycoconjugate Vaccination Against Campylobacter jejuni. Front Microbiol 2021; 12:734526. [PMID: 34867850 PMCID: PMC8637857 DOI: 10.3389/fmicb.2021.734526] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/04/2021] [Indexed: 01/03/2023] Open
Abstract
Campylobacter jejuni is a common cause of diarrheal disease worldwide. Human infection typically occurs through the ingestion of contaminated poultry products. We previously demonstrated that an attenuated Escherichia coli live vaccine strain expressing the C. jejuni N-glycan on its surface reduced the Campylobacter load in more than 50% of vaccinated leghorn and broiler birds to undetectable levels (responder birds), whereas the remainder of the animals was still colonized (non-responders). To understand the underlying mechanism, we conducted three vaccination and challenge studies using 135 broiler birds and found a similar responder/non-responder effect. Subsequent genome-wide association studies (GWAS), analyses of bird sex and levels of vaccine-induced IgY responses did not correlate with the responder versus non-responder phenotype. In contrast, antibodies isolated from responder birds displayed a higher Campylobacter-opsonophagocytic activity when compared to antisera from non-responder birds. No differences in the N-glycome of the sera could be detected, although minor changes in IgY glycosylation warrant further investigation. As reported before, the composition of the microbiota, particularly levels of OTU classified as Clostridium spp., Ruminococcaceae and Lachnospiraceae are associated with the response. Transplantation of the cecal microbiota of responder birds into new birds in combination with vaccination resulted in further increases in vaccine-induced antigen-specific IgY responses when compared to birds that did not receive microbiota transplants. Our work suggests that the IgY effector function and microbiota contribute to the efficacy of the E. coli live vaccine, information that could form the basis for the development of improved vaccines targeted at the elimination of C. jejuni from poultry.
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Affiliation(s)
- Harald Nothaft
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Maria Elisa Perez-Muñoz
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Tianfu Yang
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Abarna V M Murugan
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, QLD, Australia
| | | | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, QLD, Australia.,ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, Southport, QLD, Australia
| | - Graham S Plastow
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Livestock Gentec, Edmonton, AB, Canada
| | - Jens Walter
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Christine M Szymanski
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada.,Department of Microbiology and Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
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24
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Hansen ZA, Cha W, Nohomovich B, Newton DW, Lephart P, Salimnia H, Khalife W, Shade A, Rudrik JT, Manning SD. Comparing gut resistome composition among patients with acute Campylobacter infections and healthy family members. Sci Rep 2021; 11:22368. [PMID: 34785751 PMCID: PMC8595376 DOI: 10.1038/s41598-021-01927-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/02/2021] [Indexed: 12/04/2022] Open
Abstract
Campylobacter commonly causes foodborne infections and antibiotic resistance is an imminent concern. It is not clear, however, if the human gut 'resistome' is affected by Campylobacter during infection. Application of shotgun metagenomics on stools from 26 cases with Campylobacter infections and 44 healthy family members (controls) identified 406 unique antibiotic resistance genes (ARGs) representing 153 genes/operons, 40 mechanisms, and 18 classes. Cases had greater ARG richness (p < 0.0001) and Shannon diversity (p < 0.0001) than controls with distinct compositions (p = 0.000999; PERMANOVA). Cases were defined by multidrug resistance genes and were dominated by Proteobacteria (40.8%), specifically those representing Escherichia (20.9%). Tetracycline resistance genes were most abundant in controls, which were dominated by Bacteroidetes (45.3%) and Firmicutes (44.4%). Hierarchical clustering of cases identified three clusters with distinct resistomes. Case clusters 1 and 3 differed from controls containing more urban and hospitalized patients. Relative to family members of the same household, ARG composition among matched cases was mostly distinct, though some familial controls had similar profiles that could be explained by a shorter time since exposure to the case. Together, these data indicate that Campylobacter infection is associated with an altered resistome composition and increased ARG diversity, raising concerns about the role of infection in the spread of resistance determinants.
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Affiliation(s)
- Zoe A Hansen
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Wonhee Cha
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Brian Nohomovich
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Paul Lephart
- University of Michigan, Ann Arbor, MI, 48109, USA
| | | | | | - Ashley Shade
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA
| | - James T Rudrik
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, 48913, USA
| | - Shannon D Manning
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA.
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25
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Yan W, Zhou Q, Yuan Z, Fu L, Wen C, Yang N, Sun C. Impact of the gut microecology on Campylobacter presence revealed by comparisons of the gut microbiota from chickens raised on litter or in individual cages. BMC Microbiol 2021; 21:290. [PMID: 34686130 PMCID: PMC8532315 DOI: 10.1186/s12866-021-02353-5] [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] [Received: 07/17/2021] [Accepted: 10/11/2021] [Indexed: 11/10/2022] Open
Abstract
Background Poultry is the major reservoir of Campylobacter that contributes to human campylobacteriosis and threatens food safety. Litter contact has been linked to Campylobacter colonization, but the gut microecological impact underlying this link remains not fully clear. Here, we sought to investigate the impact of the gut microecology on the presence of Campylobacter by examining the microbiota in the duodenum, jejunum, ileum, ceca, and feces from chickens raised on commercial litter and in individual cages at 0–57 days of age. Results Through litter contact, the presence of Campylobacter was found to benefit from microecological competition among Lactobacillus, Helicobacter, and genera that are halotolerant and aerobic or facultatively anaerobic in the upper intestine, such as Corynebacterium and Brachybacterium. The presence was also promoted by the increased abundance in obligate anaerobic fermentation microbes, especially members of the orders Clostridiales and Bacteroidales. The longitudinal analysis supported the vertical or pseudo-vertical transmission but suggested that colonization might occur immensely at 7–28 days of age. We observed a host genetic effect on the gut microecology, which might lead to increased heterogeneity of the microecological impact on Campylobacter colonization. Conclusions The findings advance the understanding of the gut microecological impact on Campylobacter presence in the chicken gut under conditions of litter contact and suggest that manipulations of the gut microecology, as well as the microbes identified in the Campylobacter association networks, might be important for the development of intervention strategies. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02353-5.
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Affiliation(s)
- Wei Yan
- Poultry Science Laboratory, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.,National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Qianqian Zhou
- Poultry Science Laboratory, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.,National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Zhongyang Yuan
- Poultry Science Laboratory, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.,National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Liang Fu
- Poultry Science Laboratory, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.,National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Chaoliang Wen
- Poultry Science Laboratory, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.,National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Ning Yang
- Poultry Science Laboratory, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.,National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Congjiao Sun
- Poultry Science Laboratory, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. .,National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China.
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26
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Wyszyńska AK, Godlewska R. Lactic Acid Bacteria - A Promising Tool for Controlling Chicken Campylobacter Infection. Front Microbiol 2021; 12:703441. [PMID: 34650524 PMCID: PMC8506037 DOI: 10.3389/fmicb.2021.703441] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/23/2021] [Indexed: 11/19/2022] Open
Abstract
Since 2005, campylobacteriosis has been the most common zoonotic disease in Europe. The main reservoir of pathogenic Campylobacter strains is broilers, which makes raw and undercooked poultry meat two major sources of disease. Infection in chicken flocks is most often asymptomatic, despite a high level of colonization reaching 106-109cfu/g in animal ceca. It is widely believed that controlling the level of colonization of the birds' digestive tract by pathogenic strains is a good way to increase food safety. Many treatments have been proposed to combat or at least reduce the level of colonization in animals reservoirs: probiotics, bacteriophages, vaccines, and anti-Campylobacter bacteriocins. This review focuses on the effects of Campylobacter infection on the chicken microbiome and colonization control strategies using probiotics (mostly lactic acid bacteria, LAB), which are live microorganisms included in the diet of animals as feed additives or supplements. Probiotics are not only an alternative to antibiotics, which were used for years as animal growth promoters, but they also constitute an effective protective barrier against excessive colonization of the digestive system by pathogenic bacteria, including Campylobacter. Moreover, one of the many beneficial functions of probiotics is the ability to manipulate the host's microbiota. Recently, there have also been some promising attempts to use lactic acid bacteria as a delivery system of oral vaccine against Campylobacter. Recombinant LAB strains induce primarily a mucosal immune response against foreign antigens, accompanied by at most a low-level immune response against carrier strains. Since the main barrier against the invasion of pathogens in the gastrointestinal tract is the intestinal mucosal membrane, the development of effective oral vaccines to protect animals against enteric infection is very reasonable.
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27
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Robinson L, Liaw J, Omole Z, Xia D, van Vliet AHM, Corcionivoschi N, Hachani A, Gundogdu O. Bioinformatic Analysis of the Campylobacter jejuni Type VI Secretion System and Effector Prediction. Front Microbiol 2021; 12:694824. [PMID: 34276628 PMCID: PMC8285248 DOI: 10.3389/fmicb.2021.694824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/07/2021] [Indexed: 12/30/2022] Open
Abstract
The Type VI Secretion System (T6SS) has important roles relating to bacterial antagonism, subversion of host cells, and niche colonisation. Campylobacter jejuni is one of the leading bacterial causes of human gastroenteritis worldwide and is a commensal coloniser of birds. Although recently discovered, the T6SS biological functions and identities of its effectors are still poorly defined in C. jejuni. Here, we perform a comprehensive bioinformatic analysis of the C. jejuni T6SS by investigating the prevalence and genetic architecture of the T6SS in 513 publicly available genomes using C. jejuni 488 strain as reference. A unique and conserved T6SS cluster associated with the Campylobacter jejuni Integrated Element 3 (CJIE3) was identified in the genomes of 117 strains. Analyses of the T6SS-positive 488 strain against the T6SS-negative C. jejuni RM1221 strain and the T6SS-positive plasmid pCJDM202 carried by C. jejuni WP2-202 strain defined the “T6SS-containing CJIE3” as a pathogenicity island, thus renamed as Campylobacter jejuni Pathogenicity Island-1 (CJPI-1). Analysis of CJPI-1 revealed two canonical VgrG homologues, CJ488_0978 and CJ488_0998, harbouring distinct C-termini in a genetically variable region downstream of the T6SS operon. CJPI-1 was also found to carry a putative DinJ-YafQ Type II toxin-antitoxin (TA) module, conserved across pCJDM202 and the genomic island CJIE3, as well as several open reading frames functionally predicted to encode for nucleases, lipases, and peptidoglycan hydrolases. This comprehensive in silico study provides a framework for experimental characterisation of T6SS-related effectors and TA modules in C. jejuni.
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Affiliation(s)
- Luca Robinson
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Janie Liaw
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Zahra Omole
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Dong Xia
- Comparative Biomedical Sciences, Royal Veterinary College, London, United Kingdom
| | - Arnoud H M van Vliet
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Nicolae Corcionivoschi
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Bioengineering of Animal Science Resources, Banat University of Agricultural Sciences and Veterinary Medicine - King Michael the I of Romania, Timisoara, Romania
| | - Abderrahman Hachani
- The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
| | - Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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28
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Craven H, McGuinness D, Buchanan S, Galbraith N, McGuinness DH, Jones B, Combet E, Mafra D, Bergman P, Ellaway A, Stenvinkel P, Ijaz UZ, Shiels PG. Socioeconomic position links circulatory microbiota differences with biological age. Sci Rep 2021; 11:12629. [PMID: 34135381 PMCID: PMC8209159 DOI: 10.1038/s41598-021-92042-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/20/2021] [Indexed: 12/23/2022] Open
Abstract
Imbalanced nutrition is associated with accelerated ageing, possibly mediated by microbiota. An analysis of the circulatory microbiota obtained from the leukocytes of participants in the MRC Twenty-07 general population cohort was performed. We now report that in this cohort, the most biologically aged exhibit a significantly higher abundance of circulatory pathogenic bacteria, including Neisseria, Rothia and Porphyromonas, while those less biologically aged possess more circulatory salutogenic (defined as being supportive of human health and wellbeing) bacteria, including Lactobacillus, Lachnospiraceae UCG-004 and Kocuria. The presence of these salutogenic bactreria is consistent with a capacity to metabolise and produce Nrf2 agonists. We also demonstrate that associated one carbon metabolism, notably betaine levels, did not vary with chronological age, but displayed a difference with socioeconomic position (SEP). Those at lower SEP possessed significantly lower betaine levels indicative of a poorer diet and poorer health span and consistent with reduced global DNA methylation levels in this group. Our data suggest a clear route to improving age related health and resilience based on dietary modulation of the microbiota.
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Affiliation(s)
- Hannah Craven
- Wolfson Wohl Translational Research Centre, Institute of Cancer Sciences, MVLS, Garscube Estate, University of Glasgow, Switchback Road, Glasgow, G61 1QH, UK
| | - Dagmara McGuinness
- Wolfson Wohl Translational Research Centre, Institute of Cancer Sciences, MVLS, Garscube Estate, University of Glasgow, Switchback Road, Glasgow, G61 1QH, UK
| | - Sarah Buchanan
- Wolfson Wohl Translational Research Centre, Institute of Cancer Sciences, MVLS, Garscube Estate, University of Glasgow, Switchback Road, Glasgow, G61 1QH, UK
| | | | | | - Brian Jones
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Emilie Combet
- School of Medicine, University of Glasgow, Glasgow, UK
| | - Denise Mafra
- Fluminense Federal University (UFF), Niterói, RJ, Brazil
| | - Peter Bergman
- Division of Renal Medicine M99, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Anne Ellaway
- Institute of Health and Wellbeing, MVLS, University of Glasgow, Glasgow, UK
| | - Peter Stenvinkel
- Division of Renal Medicine M99, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Umer Z Ijaz
- School of Engineering, University of Glasgow, Glasgow, UK.
| | - Paul G Shiels
- Wolfson Wohl Translational Research Centre, Institute of Cancer Sciences, MVLS, Garscube Estate, University of Glasgow, Switchback Road, Glasgow, G61 1QH, UK.
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29
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Foodborne Pathogen Campylobacter. Microorganisms 2021; 9:microorganisms9061241. [PMID: 34200984 PMCID: PMC8227710 DOI: 10.3390/microorganisms9061241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 05/27/2021] [Accepted: 06/03/2021] [Indexed: 12/24/2022] Open
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30
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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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Slater R, Frau A, Hodgkinson J, Archer D, Probert C. A Comparison of the Colonic Microbiome and Volatile Organic Compound Metabolome of Anoplocephala perfoliata Infected and Non-Infected Horses: A Pilot Study. Animals (Basel) 2021; 11:ani11030755. [PMID: 33803473 PMCID: PMC7999024 DOI: 10.3390/ani11030755] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/25/2021] [Accepted: 03/05/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary In horses, tapeworm infection is associated with specific forms of colic (abdominal pain) that can be life-threatening without surgical treatment. There is growing evidence that intestinal parasites interact with the gut bacteria, and the consequences of these interactions may influence the ability of the host to resist infection and parasite-associated disease. We aimed to compare the intestinal bacteria and the gases produced by metabolic processes in the gut between horses that had varying levels of tapeworms and those with no tapeworm present. Overall, the diversity of gut bacteria was similar in horses with and without tapeworms. There were some decreases in beneficial bacteria in horses with tapeworms, indicating a possible negative consequence of infection. Intestinal gases correlated with some bacteria indicating their functionality and use as potential markers of active bacteria. Our study validates further research investigating tapeworm and gut bacteria interactions in the horse. Abstract Anoplocephala perfoliata is a common equine tapeworm associated with an increased risk of colic (abdominal pain) in horses. Identification of parasite and intestinal microbiota interactions have consequences for understanding the mechanisms behind parasite-associated colic and potential new methods for parasite control. A. perfoliata was diagnosed by counting of worms in the caecum post-mortem. Bacterial DNA was extracted from colonic contents and sequenced targeting of the 16S rRNA gene (V4 region). The volatile organic compound (VOC) metabolome of colonic contents was characterised using gas chromatography mass spectrometry. Bacterial diversity (alpha and beta) was similar between tapeworm infected and non-infected controls. Some compositional differences were apparent with down-regulation of operational taxonomic units (OTUs) belonging to the symbiotic families of Ruminococcaceae and Lachnospiraceae in the tapeworm-infected group. Overall tapeworm burden accounted for 7–8% of variation in the VOC profile (permutational multivariate analysis of variance). Integration of bacterial OTUs and VOCs demonstrated moderate to strong correlations indicating the potential of VOCs as markers for bacterial OTUs in equine colonic contents. This study has shown potential differences in the intestinal microbiome and metabolome of A. perfoliata infected and non-infected horses. This pilot study did not control for extrinsic factors including diet, disease history and stage of infection.
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Affiliation(s)
- Rachael Slater
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 3GE, UK; (A.F.); (C.P.)
- Correspondence:
| | - Alessandra Frau
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 3GE, UK; (A.F.); (C.P.)
| | - Jane Hodgkinson
- Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Leahurst Campus, Chester High Road, Wirral CH64 7TE, UK; (J.H.); (D.A.)
| | - Debra Archer
- Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Leahurst Campus, Chester High Road, Wirral CH64 7TE, UK; (J.H.); (D.A.)
| | - Chris Probert
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 3GE, UK; (A.F.); (C.P.)
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Elmi A, Nasher F, Dorrell N, Wren B, Gundogdu O. Revisiting Campylobacter jejuni Virulence and Fitness Factors: Role in Sensing, Adapting, and Competing. Front Cell Infect Microbiol 2021; 10:607704. [PMID: 33614526 PMCID: PMC7887314 DOI: 10.3389/fcimb.2020.607704] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/11/2020] [Indexed: 12/18/2022] Open
Abstract
Campylobacter jejuni is the leading cause of bacterial foodborne gastroenteritis world wide and represents a major public health concern. Over the past two decades, significant progress in functional genomics, proteomics, enzymatic-based virulence profiling (EBVP), and the cellular biology of C. jejuni have improved our basic understanding of this important pathogen. We review key advances in our understanding of the multitude of emerging virulence factors that influence the outcome of C. jejuni–mediated infections. We highlight, the spatial and temporal dynamics of factors that promote C. jejuni to sense, adapt and survive in multiple hosts. Finally, we propose cohesive research directions to obtain a comprehensive understanding of C. jejuni virulence mechanisms.
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Affiliation(s)
- Abdi Elmi
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Fauzy Nasher
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Nick Dorrell
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Brendan Wren
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Hakeem MJ, Lu X. Survival and Control of Campylobacter in Poultry Production Environment. Front Cell Infect Microbiol 2021; 10:615049. [PMID: 33585282 PMCID: PMC7879573 DOI: 10.3389/fcimb.2020.615049] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022] Open
Abstract
Campylobacter species are Gram-negative, motile, and non-spore-forming bacteria with a unique helical shape that changes to filamentous or coccoid as an adaptive response to environmental stresses. The relatively small genome (1.6 Mbp) of Campylobacter with unique cellular and molecular physiology is only understood to a limited extent. The overall strict requirement of this fastidious microorganism to be either isolated or cultivated in the laboratory settings make itself to appear as a weak survivor and/or an easy target to be inactivated in the surrounding environment of poultry farms, such as soil, water source, dust, surfaces and air. The survival of this obligate microaerobic bacterium from poultry farms to slaughterhouses and the final poultry products indicates that Campylobacter has several adaptive responses and/or environmental niches throughout the poultry production chain. Many of these adaptive responses remain puzzles. No single control method is yet known to fully address Campylobacter contamination in the poultry industry and new intervention strategies are required. The aim of this review article is to discuss the transmission, survival, and adaptation of Campylobacter species in the poultry production environments. Some approved and novel control methods against Campylobacter species throughout the poultry production chain will also be discussed.
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Affiliation(s)
- Mohammed J Hakeem
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada.,Department of Food Science and Human Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Xiaonan Lu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada.,Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Ste Anne de Bellevue, QC, Canada
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34
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Corcionivoschi N, Thompson SA, Gundogdu O. Editorial: Developments in Campylobacter, Helicobacter & Related Organisms Research - CHRO 2019. Front Microbiol 2021; 11:622582. [PMID: 33488566 PMCID: PMC7820174 DOI: 10.3389/fmicb.2020.622582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/14/2020] [Indexed: 11/24/2022] Open
Affiliation(s)
- Nicolae Corcionivoschi
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute (AFBI), Belfast, United Kingdom
| | - Stuart A Thompson
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Ozan Gundogdu
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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35
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Takeshita N, Watanabe T, Ishida-Kuroki K, Sekizaki T. Transition of microbiota in chicken cecal droppings from commercial broiler farms. BMC Vet Res 2021; 17:10. [PMID: 33407476 PMCID: PMC7789685 DOI: 10.1186/s12917-020-02688-7] [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: 02/27/2020] [Accepted: 11/23/2020] [Indexed: 11/11/2022] Open
Abstract
Background Chickens are major sources of human nutrition worldwide, but the chicken intestinal microbiota can be a source of bacterial infection. The microbiota has potential to regulate the colonization of pathogens by competitive exclusion, production of antimicrobial compounds, and stimulation of the mucosal immune system. But information on the microbiota in commercial broiler chickens is limited because of the difficulty of conducting studies at commercial farms. To obtain fundamental information that can be used to control pathogens in chickens, we determined the 6-week dynamics of microbiota in chicken cecal droppings from commercial broiler farms. Results Cecal droppings from four chickens were collected once a week from 1 to 6 weeks of age at three commercial broiler farms. A total of 168 samples were collected from 7 flocks and subjected to 16S rRNA amplicon sequencing. Despite the farms have distinctly different climate conditions, the microbiota in the same growth stages were similar among farms. Moreover, as the chickens grew and the feed types were switched, the richness and diversity of the microbiota gradually increased and convergence of the composition of the microbiota was apparent. Notably, minor bacterial taxa (i.e. OTUs with relative abundance < 0.05%) within the microbiota were changed by the chicken age, switching of feed types, and presence of Campylobacter. In particular, the effects of switching of feed types on the microbiota were larger than the effects of age and Campylobacter. Conclusions Irrespective of the locations of the farms, the microbiota of chicken cecum, especially minor bacteria, was successively changed more affected by feed types than by ages. Switching of feed types inducing the alteration of the microbiota may be associated with the colonization of pathogens in the chicken gut. These results will also help with extrapolation of studies in experimental animals to those in the commercial farms. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-020-02688-7.
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Affiliation(s)
- Nachiko Takeshita
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takayasu Watanabe
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.,Present Address: Department of Chemistry, Nihon University School of Dentistry, Kanda-Surugadai 1-8-13, Chiyoda-ku, Tokyo, 101-8310, Japan
| | - Kasumi Ishida-Kuroki
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tsutomu Sekizaki
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
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Broom LJ. Evidence-based consideration of dietary ‘alternatives’ to anticoccidial drugs to help control poultry coccidial infections. WORLD POULTRY SCI J 2021. [DOI: 10.1080/00439339.2021.1873713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Leon J. Broom
- Gut Health Consultancy, Exeter, UK
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
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37
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Emanowicz M, Meade J, Bolton D, Golden O, Gutierrez M, Byrne W, Egan J, Lynch H, O'Connor L, Coffey A, Lucey B, Whyte P. The impact of key processing stages and flock variables on the prevalence and levels of Campylobacter on broiler carcasses. Food Microbiol 2020; 95:103688. [PMID: 33397618 DOI: 10.1016/j.fm.2020.103688] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/11/2020] [Accepted: 11/14/2020] [Indexed: 01/01/2023]
Abstract
This study examined the impact of key processing stages and flock variables on the prevalence of Campylobacter on broiler carcasses. Overall, the prevalence of Campylobacter was 62% in caeca, and 68%, 65% and 62% in neck skin samples collected after evisceration, final wash and carcass chilling, respectively. Campylobacter were found in 32% of caeca, and 52%, 40% and 32% of neck skin samples collected after evisceration, final wash and carcass chilling, respectively from first thin broiler batches. Final thin broiler batches were more frequently contaminated with prevalences of 83% found in caeca, 80% in neck skin samples collected after evisceration and 83% found in neck skin samples collected after both final wash and carcass chilling stages (p < 0.05). Thinning status had a significant effect on Campylobacter counts with significantly higher counts observed in samples from final thin batches (p < 0.05). Highest Campylobacter concentrations in neck skin samples were observed at the evisceration stage in both first and final thin samples, with counts ranging from 2.0 to 3.8 log10 CFU/g and 2.3 to 4.8 log10 CFU/g in first and final thin batches, respectively. All first thin samples had counts below the European Union (EU) Process Hygiene Criterion threshold level of 3 log10 CFU/g after chilling while 52% of final thin batches had counts above this limit.
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Affiliation(s)
- Malgorzata Emanowicz
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Joseph Meade
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Declan Bolton
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland
| | - Olwen Golden
- National Reference Laboratory Campylobacter, Department of Agriculture, Food and the Marine Laboratories, Backweston Campus, Celbridge, Ireland
| | - Montserrat Gutierrez
- National Reference Laboratory Campylobacter, Department of Agriculture, Food and the Marine Laboratories, Backweston Campus, Celbridge, Ireland
| | - William Byrne
- National Reference Laboratory Campylobacter, Department of Agriculture, Food and the Marine Laboratories, Backweston Campus, Celbridge, Ireland
| | - John Egan
- National Reference Laboratory Campylobacter, Department of Agriculture, Food and the Marine Laboratories, Backweston Campus, Celbridge, Ireland
| | - Helen Lynch
- National Reference Laboratory Campylobacter, Department of Agriculture, Food and the Marine Laboratories, Backweston Campus, Celbridge, Ireland
| | - Lisa O'Connor
- Food Safety Authority of Ireland, IFSC, Dublin 1, Ireland
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown Campus, Cork, Ireland
| | - Brigid Lucey
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown Campus, Cork, Ireland
| | - Paul Whyte
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
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Rebollada-Merino A, Ugarte-Ruiz M, Hernández M, Miguela-Villoldo P, Abad D, Rodríguez-Lázaro D, de Juan L, Domínguez L, Rodríguez-Bertos A. Reduction of Salmonella Typhimurium Cecal Colonisation and Improvement of Intestinal Health in Broilers Supplemented with Fermented Defatted 'Alperujo', an Olive Oil By-Product. Animals (Basel) 2020; 10:E1931. [PMID: 33096645 PMCID: PMC7589156 DOI: 10.3390/ani10101931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/14/2020] [Accepted: 10/20/2020] [Indexed: 12/29/2022] Open
Abstract
Salmonella spp. contaminates egg and poultry meat leading to foodborne infections in humans. The emergence of antimicrobial-resistant strains has limited the use of antimicrobials. We aimed to determine the effects of the food supplement, fermented defatted 'alperujo' (FDA), a modified olive oil by-product, on Salmonella Typhimurium colonisation in broilers. One hundred and twenty 1-day-old broilers were divided into four experimental groups-two control groups and two treated groups, and challenged with S. Typhimurium at day 7 or 21. On days 7, 14, 21, 28, 35, and 42 of life, duodenum and cecum tissue samples were collected for histopathological and histomorphometric studies. Additionally, cecum content was collected for Salmonella spp. detection by culture and qPCR, and for metagenomic analysis. Our results showed a significant reduction of Salmonella spp. in the cecum of 42-day-old broilers, suggesting that fermented defatted 'alperujo' limits Salmonella Typhimurium colonization in that cecum and may contribute to diminishing the risk of carcass contamination at the time of slaughter. The improvement of the mucosal integrity, observed histologically and morphometrically, may contribute to enhancing intestinal health and to limiting Salmonella spp. colonisation in the host, mitigating production losses. These results could provide evidence that FDA would contribute to prophylactic and therapeutic measures to reduce salmonellosis prevalence in poultry farms.
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Affiliation(s)
- Agustín Rebollada-Merino
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain; (A.R.-M.); (P.M.-V.); (L.d.J.); (L.D.); (A.R.-B.)
- Department of Internal Medicine and Animal Surgery, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain; (A.R.-M.); (P.M.-V.); (L.d.J.); (L.D.); (A.R.-B.)
| | - Marta Hernández
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León, 47071 Valladolid, Spain; (M.H.); (D.A.); (D.R.-L.)
- Área de Microbiología, Departamento de Biotecnología y Ciencia de los Alimentos, Universidad de Burgos, 09001 Burgos, Spain
| | - Pedro Miguela-Villoldo
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain; (A.R.-M.); (P.M.-V.); (L.d.J.); (L.D.); (A.R.-B.)
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - David Abad
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León, 47071 Valladolid, Spain; (M.H.); (D.A.); (D.R.-L.)
| | - David Rodríguez-Lázaro
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León, 47071 Valladolid, Spain; (M.H.); (D.A.); (D.R.-L.)
- Área de Microbiología, Departamento de Biotecnología y Ciencia de los Alimentos, Universidad de Burgos, 09001 Burgos, Spain
| | - Lucía de Juan
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain; (A.R.-M.); (P.M.-V.); (L.d.J.); (L.D.); (A.R.-B.)
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain; (A.R.-M.); (P.M.-V.); (L.d.J.); (L.D.); (A.R.-B.)
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - Antonio Rodríguez-Bertos
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain; (A.R.-M.); (P.M.-V.); (L.d.J.); (L.D.); (A.R.-B.)
- Department of Internal Medicine and Animal Surgery, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
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McKenna A, Ijaz UZ, Kelly C, Linton M, Sloan WT, Green BD, Lavery U, Dorrell N, Wren BW, Richmond A, Corcionivoschi N, Gundogdu O. Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter. MICROBIOME 2020; 8:128. [PMID: 32907634 PMCID: PMC7488076 DOI: 10.1186/s40168-020-00908-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/17/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND The factors affecting host-pathogen ecology in terms of the microbiome remain poorly studied. Chickens are a key source of protein with gut health heavily dependent on the complex microbiome which has key roles in nutrient assimilation and vitamin and amino acid biosynthesis. The chicken gut microbiome may be influenced by extrinsic production system parameters such as Placement Birds/m2 (stocking density), feed type and additives. Such parameters, in addition to on-farm biosecurity may influence performance and also pathogenic bacterial numbers such as Campylobacter. In this study, three different production systems 'Normal' (N), 'Higher Welfare' (HW) and 'Omega-3 Higher Welfare' (O) were investigated in an industrial farm environment at day 7 and day 30 with a range of extrinsic parameters correlating performance with microbial dynamics and Campylobacter presence. RESULTS Our data identified production system N as significantly dissimilar from production systems HW and O when comparing the prevalence of genera. An increase in Placement Birds/m2 density led to a decrease in environmental pressure influencing the microbial community structure. Prevalence of genera, such as Eisenbergiella within HW and O, and likewise Alistipes within N were representative. These genera have roles directly relating to energy metabolism, amino acid, nucleotide and short chain fatty acid (SCFA) utilisation. Thus, an association exists between consistent and differentiating parameters of the production systems that affect feed utilisation, leading to competitive exclusion of genera based on competition for nutrients and other factors. Campylobacter was identified within specific production system and presence was linked with the increased diversity and increased environmental pressure on microbial community structure. Addition of Omega-3 though did alter prevalence of specific genera, in our analysis did not differentiate itself from HW production system. However, Omega-3 was linked with a positive impact on weight gain. CONCLUSIONS Overall, our results show that microbial communities in different industrial production systems are deterministic in elucidating the underlying biological confounders, and these recommendations are transferable to farm practices and diet manipulation leading to improved performance and better intervention strategies against Campylobacter within the food chain. Video Abstract.
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Affiliation(s)
- Aaron McKenna
- Moy Park, 39 Seagoe Industrial Estate, Portadown, Craigavon, Co. Armagh, BT63 5QE, UK
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Biological Sciences Building, Belfast, BT9 5DL, Northern Ireland
| | | | - Carmel Kelly
- Food Microbiology Unit, Agri-Food and Biosciences Institute, Newforge Lane, Belfast, BT9 5PX, UK
| | - Mark Linton
- Food Microbiology Unit, Agri-Food and Biosciences Institute, Newforge Lane, Belfast, BT9 5PX, UK
| | - William T Sloan
- School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
| | - Brian D Green
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Biological Sciences Building, Belfast, BT9 5DL, Northern Ireland
| | - Ursula Lavery
- Moy Park, 39 Seagoe Industrial Estate, Portadown, Craigavon, Co. Armagh, BT63 5QE, UK
| | - Nick Dorrell
- Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Brendan W Wren
- Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Anne Richmond
- Moy Park, 39 Seagoe Industrial Estate, Portadown, Craigavon, Co. Armagh, BT63 5QE, UK
| | - Nicolae Corcionivoschi
- Food Microbiology Unit, Agri-Food and Biosciences Institute, Newforge Lane, Belfast, BT9 5PX, UK.
| | - Ozan Gundogdu
- Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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Duquenoy A, Ania M, Boucher N, Reynier F, Boucinha L, Andreoni C, Thomas V. Caecal microbiota compositions from 7-day-old chicks reared in high-performance and low-performance industrial farms and systematic culturomics to select strains with anti-Campylobacter activity. PLoS One 2020; 15:e0237541. [PMID: 32834007 PMCID: PMC7446796 DOI: 10.1371/journal.pone.0237541] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/28/2020] [Indexed: 12/12/2022] Open
Abstract
There is growing interest in exploring the chickens' intestinal microbiota and understanding its interactions with the host. The objective is to optimize this parameter in order to increase the productivity of farm animals. With the goal to isolate candidate probiotic strains, specific culturomic methods were used in our study to culture commensal bacteria from 7-days old chicks raised in two farms presenting long history of high performance. A total of 347 isolates were cultured, corresponding to at least 64 species. Among the isolates affiliated to the Firmicutes, 26 had less than 97% identity of their partial 16S sequence with that of the closest described species, while one presented less than 93% identity, thus revealing a significant potential for new species in this ecosystem. In parallel, and in order to better understand the differences between the microbiota of high-performing and low-performing animals, caecal contents of animals collected from these two farms and from a third farm with long history of low performance were collected and sequenced. This compositional analysis revealed an enrichment of Faecalibacterium-and Campylobacter-related sequences in lower-performing animals whereas there was a higher abundance of enterobacteria-related sequences in high-performing animals. We then investigated antibiosis activity against C. jejuni ATCC 700819 and C. jejuni field isolate as a first phenotypic trait to select probiotic candidates. Antibiosis was found to be limited to a few strains, including several lactic acid bacteria, a strain of Bacillus horneckiae and a strain of Escherichia coli. The antagonist activity depended on test conditions that mimicked the evolution of the intestinal environment of the chicken during its lifetime, i.e. temperature (37°C or 42°C) and oxygen levels (aerobic or anaerobic conditions). This should be taken into account according to the stage of development of the animal at which administration of the active strain is envisaged.
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Rebollada-Merino A, Ugarte-Ruiz M, Hernández M, Miguela-Villoldo P, Abad D, Cuesta-Álvaro P, Rodríguez-Lázaro D, de Juan L, Domínguez L, Rodríguez-Bertos A. Dietary supplementation with fermented defatted "alperujo" induces modifications of the intestinal mucosa and cecal microbiota of broiler chickens. Poult Sci 2020; 99:5308-5315. [PMID: 33142446 PMCID: PMC7647715 DOI: 10.1016/j.psj.2020.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/06/2020] [Accepted: 07/25/2020] [Indexed: 12/04/2022] Open
Abstract
Nutraceuticals are not only nutritionally beneficial for animals but also their use as feed supplements may reduce environmental contamination. The effect of fermented defatted “alperujo,” an olive oil by-product, supplementation on the intestinal health of broiler chickens was assessed by analyzing the intestinal mucosal morphology of the duodenum and the cecum. The microbiota of the cecum was also characterized by analyzing the V3-V4 region of the 16S rRNA gene on days 7, 14, 21, 28, 35, and 42. Supplemented broilers from 14 to 35 D of age showed an increase in villus height in the duodenum. This increase likely improved digestibility and absorption capacity during growth, leading to the observed increase in BW at day 35 of life. A progressive increase in crypt depth in both the duodenum and the cecum was also observed. This modification likely enhanced epithelial renewal, thus safeguarding the turnover capacity of the intestinal mucosa. Our molecular analysis of cecal microbiota suggests that this dietary supplement may favor the growth of certain bacteria and may control the spread of pathogenic bacteria by means of competitive exclusion.
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Affiliation(s)
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Marta Hernández
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León, 47071 Valladolid, Spain; Área de Microbiología, Departamento de Biotecnología y Ciencia de los Alimentos, Universidad de Burgos, 09001 Burgos, Spain
| | - Pedro Miguela-Villoldo
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain; Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - David Abad
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León, 47071 Valladolid, Spain
| | - Pedro Cuesta-Álvaro
- Computing Services, Research Support, Complutense University of Madrid, 28040 Madrid, Spain
| | - David Rodríguez-Lázaro
- Área de Microbiología, Departamento de Biotecnología y Ciencia de los Alimentos, Universidad de Burgos, 09001 Burgos, Spain
| | - Lucía de Juan
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain; Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain; Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - Antonio Rodríguez-Bertos
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain; Department of Internal Medicine and Animal Surgery, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
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A One Health approach to prevention, treatment, and control of campylobacteriosis. Curr Opin Infect Dis 2020; 32:453-460. [PMID: 31305492 DOI: 10.1097/qco.0000000000000570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW To review recent findings regarding the control and treatment of campylobacteriosis. RECENT FINDINGS The application of improved diagnostics has led to an upward shift in the attributable burden of Campylobacter infections, in both the United States and Europe as well as in resource-poor settings. Increased focus has brought a fundamental feature of campylobacteriosis -- the ability to cause relapsing disease back into focus, and expanding data on antimicrobial resistance has lead from a switch in first-line therapy for severe diarrhea from quinolones to azithromycin in most contexts, even as evidence of expanding macrolide resistance emerges. SUMMARY Campylobacter spp. infection is a common infection worldwide. Antibiotic-resistant Campylobacter spp. has become an emerging threat with the increase in industrial poultry production, as well as the broad use of antibiotics in both animals and humans.
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Effects of Vitamin B2 Supplementation in Broilers Microbiota and Metabolome. Microorganisms 2020; 8:microorganisms8081134. [PMID: 32727134 PMCID: PMC7464963 DOI: 10.3390/microorganisms8081134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/24/2020] [Accepted: 07/24/2020] [Indexed: 01/04/2023] Open
Abstract
The study of the microbiome in broiler chickens holds great promise for the development of strategies for health maintenance and performance improvement. Nutritional strategies aimed at modulating the microbiota-host relationship can improve chickens' immunological status and metabolic fitness. Here, we present the results of a pilot trial aimed at analyzing the effects of a nutritional strategy involving vitamin B2 supplementation on the ileum, caeca and litter microbiota of Ross 308 broilers, as well as on the metabolic profile of the caecal content. Three groups of chickens were administered control diets and diets supplemented with two different dosages of vitamin B2. Ileum, caeca, and litter samples were obtained from subgroups of birds at three time points along the productive cycle. Sequencing of the 16S rRNA V3-V4 region and NMR metabolomics were used to explore microbiota composition and the concentration of metabolites of interest, including short-chain fatty acids. Vitamin B2 supplementation significantly modulated caeca microbiota, with the highest dosage being more effective in increasing the abundance of health-promoting bacterial groups, including Bifidobacterium, resulting in boosted production of butyrate, a well-known health-promoting metabolite, in the caeca environment.
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Maki JJ, Bobeck EA, Sylte MJ, Looft T. Eggshell and environmental bacteria contribute to the intestinal microbiota of growing chickens. J Anim Sci Biotechnol 2020; 11:60. [PMID: 32537141 PMCID: PMC7288515 DOI: 10.1186/s40104-020-00459-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/08/2020] [Indexed: 12/14/2022] Open
Abstract
Background The initial intestinal microbiota acquired from different sources has profound impacts on animal health and productivity. In modern poultry production practices, the source(s) of the establishing microbes and their overall contribution during development of gastrointestinal tract communities are still unclear. Using fertilized eggs from two independent sources, we assessed the impact of eggshell- and environmental-associated microbial communities on the successional processes and bacterial community structure throughout the intestinal tract of chickens for up to 6 weeks post-hatch. Results Culturing and sequencing techniques identified a viable, highly diverse population of anaerobic bacteria on the eggshell. The jejunal, ileal, and cecal microbial communities for the egg-only, environment-only, and conventionally raised birds generally displayed similar successional patterns characterized by increasing community richness and evenness over time, with strains of Enterococcus, Romboutsia, and unclassified Lachnospiraceae abundant for all three input groups in both trials. Bacterial community structures differed significantly based on trial and microbiota input with the exception of the egg-exposed and conventional birds in the jejunum at week 1 and the ileum at week 6. Cecal community structures were different based on trial and microbiota input source, and cecal short-chain fatty acid profiles at week 6 highlighted functional differences as well. Conclusion We identified distinct intestinal microbial communities and differing cecal short-chain fatty acid profiles between birds exposed to the microbiota associated with either the eggshell or environment, and those of conventionally hatched birds. Our data suggest the eggshell plays an appreciable role in the development of the chicken intestinal microbiota, especially in the jejunum and ileum where the community structure of the eggshell-only birds was similar to the structure of conventionally hatched birds. Our data identify a complex interplay between the eggshell and environmental microbiota during establishment and succession within the chicken gut. Further studies should explore the ability of eggshell- and environment-derived microbes to shape the dynamics of succession and how these communities can be targeted through interventions to promote gut health and mitigate food-borne pathogen colonization in poultry.
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Affiliation(s)
- Joel J Maki
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, US Department of Agriculture, 1920 Dayton Ave, Ames, IA 50010 USA.,Interdepartmental Microbiology Graduate Program, Iowa State University
- , Ames, IA 50011 USA.,Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN 37830 USA
| | | | - Matthew J Sylte
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, US Department of Agriculture, 1920 Dayton Ave, Ames, IA 50010 USA
| | - Torey Looft
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, US Department of Agriculture, 1920 Dayton Ave, Ames, IA 50010 USA
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Flaujac Lafontaine GM, Richards PJ, Connerton PL, O’Kane PM, Ghaffar NM, Cummings NJ, Fish NM, Connerton IF. Prebiotic Driven Increases in IL-17A Do Not Prevent Campylobacter jejuni Colonization of Chickens. Front Microbiol 2020; 10:3030. [PMID: 32010094 PMCID: PMC6972505 DOI: 10.3389/fmicb.2019.03030] [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: 09/23/2019] [Accepted: 12/17/2019] [Indexed: 01/13/2023] Open
Abstract
Worldwide Campylobacter jejuni is a leading cause of foodborne disease. Contamination of chicken meat with digesta from C. jejuni-positive birds during slaughter and processing is a key route of transmission to humans through the food chain. Colonization of chickens with C. jejuni elicits host innate immune responses that may be modulated by dietary additives to provide a reduction in the number of campylobacters colonizing the gastrointestinal tract and thereby reduce the likelihood of human exposure to an infectious dose. Here we report the effects of prebiotic galacto-oligosaccharide (GOS) on broiler chickens colonized with C. jejuni when challenged at either an early stage in development at 6 days of age or 20 days old when campylobacters are frequently detected in commercial flocks. GOS-fed birds had increased growth performance, but the levels of C. jejuni colonizing the cecal pouches were unchanged irrespective of the age of challenge. Dietary GOS modulated the immune response to C. jejuni by increasing cytokine IL-17A expression at colonization. Correspondingly, reduced diversity of the cecal microbiota was associated with Campylobacter colonization in GOS-fed birds. In birds challenged at 6 days-old the reduction in microbial diversity was accompanied by an increase in the relative abundance of Escherichia spp. Whilst immuno-modulation of the Th17 pro-inflammatory response did not prevent C. jejuni colonization of the intestinal tract of broiler chickens, the study highlights the potential for combinations of prebiotics, and specific competitors (synbiotics) to engage with the host innate immunity to reduce pathogen burdens.
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Affiliation(s)
- Geraldine M. Flaujac Lafontaine
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Philip J. Richards
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Phillippa L. Connerton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Peter M. O’Kane
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Nacheervan M. Ghaffar
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Nicola J. Cummings
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Neville M. Fish
- Saputo Dairy UK, Dairy Crest Innovation Centre, Harper Adams University, Newport, United Kingdom
| | - Ian F. Connerton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
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Galacto-Oligosaccharides Modulate the Juvenile Gut Microbiome and Innate Immunity To Improve Broiler Chicken Performance. mSystems 2020; 5:5/1/e00827-19. [PMID: 31937680 PMCID: PMC6967391 DOI: 10.1128/msystems.00827-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Improvements in growth performance and health are key goals in broiler chicken production. Inclusion of prebiotic galacto-oligosaccharides (GOS) in broiler feed enhanced the growth rate and feed conversion of chickens relative to those obtained with a calorie-matched control diet. Comparison of the cecal microbiota identified key differences in abundances of Lactobacillus spp. Increased levels of Lactobacillus johnsonii in GOS-fed juvenile birds at the expense of Lactobacillus crispatus were linked to improved performance (growth rate and market weight). Investigation of the innate immune responses highlighted increases of ileal and cecal interleukin-17A (IL-17A) gene expression counterposed to a decrease in IL-10. Quantification of the autochthonous Lactobacillus spp. revealed a correlation between bird performance and L. johnsonii abundance. Shifts in the cecal populations of key Lactobacillus spp. of juvenile birds primed intestinal innate immunity without harmful pathogen challenge.IMPORTANCE Improvements in the growth rate of broiler chickens can be achieved through dietary manipulation of the naturally occurring bacterial populations while mitigating the withdrawal of antibiotic growth promoters. Prebiotic galacto-oligosaccharides (GOS) are manufactured as a by-product of dairy cheese production and can be incorporated into the diets of juvenile chickens to improve their health and performance. This study investigated the key mechanisms behind this progression and pinpointed L. johnsonii as a key species that facilitates the enhancements in growth rate and gut health. The study identified the relationships between the GOS diet, L. johnsonii intestinal populations, and cytokine immune effectors to improve growth.
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Kers JG, Fischer EAJ, Stegeman JA, Smidt H, Velkers FC. Comparison of Different Invasive and Non-Invasive Methods to Characterize Intestinal Microbiota throughout a Production Cycle of Broiler Chickens. Microorganisms 2019; 7:E431. [PMID: 31658673 PMCID: PMC6843853 DOI: 10.3390/microorganisms7100431] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/25/2019] [Accepted: 10/07/2019] [Indexed: 12/21/2022] Open
Abstract
In the short life of broiler chickens, their intestinal microbiota undergoes many changes. To study underlying biological mechanisms and factors that influence the intestinal microbiota development, longitudinal data from flocks and individual birds is needed. However, post-mortem collection of samples hampers longitudinal data collection. In this study, invasively collected cecal and ileal content, cloacal swabs collected from the same bird, and boot sock samples and cecal droppings from the litter of the broilers' poultry house, were collected on days 0, 2, 7, 14 and 35 post-hatch. The different sample types were evaluated on their applicability and reliability to characterize the broiler intestinal microbiota. The microbiota of 247 samples was assessed by 16S ribosomal RNA gene amplicon sequencing. Analyses of α and β measures showed a similar development of microbiota composition of cecal droppings compared to cecal content. Furthermore, the composition of cecal content samples was comparable to that of the boot socks until day 14 post-hatch. This study shows that the value of non-invasive sample types varies at different ages and depends on the goal of the microbiota characterization. Specifically, cecal droppings and boot socks may be useful alternatives for cecal samples to determine intestinal microbiota composition longitudinally.
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Affiliation(s)
- Jannigje G Kers
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, 3584 CL Utrecht, The Netherlands.
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands.
| | - Egil A J Fischer
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, 3584 CL Utrecht, The Netherlands.
| | - J Arjan Stegeman
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, 3584 CL Utrecht, The Netherlands.
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands.
| | - Francisca C Velkers
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, 3584 CL Utrecht, The Netherlands.
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