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Aruwa CE, Sabiu S. Interplay of poultry-microbiome interactions - influencing factors and microbes in poultry infections and metabolic disorders. Br Poult Sci 2024:1-15. [PMID: 38920059 DOI: 10.1080/00071668.2024.2356666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/06/2024] [Indexed: 06/27/2024]
Abstract
1. The poultry microbiome and its stability at every point in time, either free range or reared under different farming systems, is affected by several environmental and innate factors. The interaction of the poultry birds with their microbiome, as well as several inherent and extraneous factors contribute to the microbiome dynamics. A poor understanding of this could worsen poultry heath and result in disease/metabolic disorders.2. Many diseased states associated with poultry have been linked to dysbiosis state, where the microbiome experiences some perturbation. Dysbiosis itself is too often downplayed; however, it is considered a disease which could lead to more serious conditions in poultry. The management of interconnected factors by conventional and emerging technologies (sequencing, nanotechnology, robotics, 3D mini-guts) could prove to be indispensable in ensuring poultry health and welfare.3. Findings showed that high-throughput technological advancements enhanced scientific insights into emerging trends surrounding the poultry gut microbiome and ecosystem, the dysbiotic condition, and the dynamic roles of intrinsic and exogenous factors in determining poultry health. Yet, a combination of conventional, -omics based and other techniques further enhance characterisation of key poultry microbiome actors, their mechanisms of action, and roles in maintaining gut homoeostasis and health, in a bid to avert metabolic disorders and infections.4. In conclusion, there is an important interplay of innate, environmental, abiotic and biotic factors impacting on poultry gut microbiome homoeostasis, dysbiosis, and overall health. Associated infections and metabolic disorders can result from the interconnected nature of these factors. Emerging concepts (interkingdom or network signalling and neurotransmitter), and future technologies (mini-gut models, cobots) need to include these interactions to ensure accurate control and outcomes.
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Affiliation(s)
- C E Aruwa
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - S Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
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2
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Botta C, Buzzanca D, Chiarini E, Chiesa F, Rubiola S, Ferrocino I, Fontanella E, Rantsiou K, Houf K, Alessandria V. Microbial contamination pathways in a poultry abattoir provided clues on the distribution and persistence of Arcobacter spp. Appl Environ Microbiol 2024; 90:e0029624. [PMID: 38647295 PMCID: PMC11107157 DOI: 10.1128/aem.00296-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/29/2024] [Indexed: 04/25/2024] Open
Abstract
The consumption of contaminated poultry meat is a significant threat for public health, as it implicates in foodborne pathogen infections, such as those caused by Arcobacter. The mitigation of clinical cases requires the understanding of contamination pathways in each food process and the characterization of resident microbiota in the productive environments, so that targeted sanitizing procedures can be effectively implemented. Nowadays these investigations can benefit from the complementary and thoughtful use of culture- and omics-based analyses, although their application in situ is still limited. Therefore, the 16S-rRNA gene-based sequencing of total DNA and the targeted isolation of Arcobacter spp. through enrichment were performed to reconstruct the environmental contamination pathways within a poultry abattoir, as well as the dynamics and distribution of this emerging pathogen. To that scope, broiler's neck skin and caeca have been sampled during processing, while environmental swabs were collected from surfaces after cleaning and sanitizing. Metataxonomic survey highlighted a negligible impact of fecal contamination and a major role of broiler's skin in determining the composition of the resident abattoir microbiota. The introduction of Arcobacter spp. in the environment was mainly conveyed by this source rather than the intestinal content. Arcobacter butzleri represented one of the most abundant species and was extensively detected in the abattoir by both metataxonomic and enrichment methods, showing higher prevalence than other more thermophilic Campylobacterota. In particular, Arcobacter spp. was recovered viable in the plucking sector with high frequency, despite the adequacy of the sanitizing procedure.IMPORTANCEOur findings have emphasized the persistence of Arcobacter spp. in a modern poultry abattoir and its establishment as part of the resident microbiota in specific environmental niches. Although the responses provided here are not conclusive for the identification of the primary source of contamination, this biogeographic assessment underscores the importance of monitoring Arcobacter spp. from the early stages of the production chain with the integrative support of metataxonomic analysis. Through such combined detection approaches, the presence of this pathogen could be soon regarded as hallmark indicator of food safety and quality in poultry slaughtering.
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Affiliation(s)
- Cristian Botta
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Davide Buzzanca
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Elisabetta Chiarini
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Francesco Chiesa
- Department of Veterinary Sciences, University of Torino, Torino, Italy
| | - Selene Rubiola
- Department of Veterinary Sciences, University of Torino, Torino, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | | | - Kalliopi Rantsiou
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Kurt Houf
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Valentina Alessandria
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
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3
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Rios-Galicia B, Sáenz JS, Yergaliyev T, Roth C, Camarinha-Silva A, Seifert J. Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken. Int J Syst Evol Microbiol 2024; 74. [PMID: 38231200 DOI: 10.1099/ijsem.0.006210] [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] [Indexed: 01/18/2024] Open
Abstract
Eight anaerobic strains obtained from crop, jejunum and ileum of chicken were isolated, characterized and genome analysed to observe their metabolic profiles, adaptive strategies and to serve as novel future references. The novel species Ligilactobacillus hohenheimensis sp. nov. (DSM 113870T=LMG 32876T), Limosilactobacillus galli sp. nov. (DSM 113833T=LMG 32623T), Limosilactobacillus avium sp. nov. (DSM 113849T=LMG 32671T), Limosilactobacillus pulli sp. nov. (DSM 115077T=LMG 32877T), Limosilactobacillus viscerum sp. nov. (DSM 113835T=LMG 32625T), Limosilactobacillus difficilis sp. nov. (DSM 114195T=LMG 32875T) and Clostridium butanoliproducens (DSM 115076T=LMG 32878T) are found in the upper gastrointestinal tract and present consistent adaptations that enable us to predict their ecological role. Molecular characterization using 16S rRNA gene analysis and long-read whole genome sequencing, confirmed the description of the novel genus Faecalispora gen. nov. with Faecalispora anaeroviscerum gen. nov. sp. nov. (DSM 113860T=LMG 32675T) as genus type species. After phylogenetic and taxonomic analysis, we recommend the reclassification of the species
Clostridium jeddahense
and
Clostridium sporosphaeroides
to the genus Faecalispora. Exploration of the microbiome from crop and small intestine of chicken expands our knowledge on the taxonomic diversity and adaptive functions of the inhabiting bacteria. The novel species identified in this project are part of a wider cultivation effort that represents the first repository of bacteria obtained from the crop and small intestine of chicken using culturomics, improving the potential handling of chicken microorganisms with biotechnological applications.
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Affiliation(s)
- Bibiana Rios-Galicia
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Johan S Sáenz
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Timur Yergaliyev
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Christoph Roth
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Amélia Camarinha-Silva
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
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4
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Trudeau MP, Mosher W, Tran H, de Rodas B, Karnezos TP, Urriola PE, Gomez A, Saqui-Salces M, Chen C, Shurson GC. Growth Performance, Metabolomics, and Microbiome Responses of Weaned Pigs Fed Diets Containing Growth-Promoting Antibiotics and Various Feed Additives. Animals (Basel) 2023; 14:60. [PMID: 38200791 PMCID: PMC10778031 DOI: 10.3390/ani14010060] [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: 10/26/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
The objective of this study was to determine the potential biological mechanisms of improved growth performance associated with potential changes in the metabolic profiles and intestinal microbiome composition of weaned pigs fed various feed additives. Three separate 42 day experiments were conducted to evaluate the following dietary treatments: chlortetracycline and sulfamethazine (PC), herbal blends, turmeric, garlic, bitter orange extract, sweet orange extract, volatile and semi-volatile milk-derived substances, yeast nucleotide, and cell wall products, compared with feeding a non-supplemented diet (NC). In all three experiments, only pigs fed PC had improved (p < 0.05) ADG and ADFI compared with pigs fed NC. No differences in metabolome and microbiome responses were observed between feed additive treatments and NC. None of the feed additives affected alpha or beta microbiome diversity in the ileum and cecum, but the abundance of specific bacterial taxa was affected by some dietary treatments. Except for feeding antibiotics, none of the other feed additives were effective in improving growth performance or significantly altering the metabolomic profiles, but some additives (e.g., herbal blends and garlic) increased (p < 0.05) the relative abundance of potentially protective bacterial genera that may be beneficial during disease challenge in weaned pigs.
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Affiliation(s)
- Michaela P. Trudeau
- Department of Animal Science, University of Minnesota, St. Paul, MN 55108, USA; (M.P.T.); (P.E.U.); (A.G.); (M.S.-S.)
| | - Wes Mosher
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108, USA; (W.M.); (C.C.)
| | - Huyen Tran
- Purina Animal Nutrition, Gray Summit, MO 63039, USA; (H.T.); (B.d.R.); (T.P.K.)
| | - Brenda de Rodas
- Purina Animal Nutrition, Gray Summit, MO 63039, USA; (H.T.); (B.d.R.); (T.P.K.)
| | | | - Pedro E. Urriola
- Department of Animal Science, University of Minnesota, St. Paul, MN 55108, USA; (M.P.T.); (P.E.U.); (A.G.); (M.S.-S.)
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, St. Paul, MN 55108, USA; (M.P.T.); (P.E.U.); (A.G.); (M.S.-S.)
| | - Milena Saqui-Salces
- Department of Animal Science, University of Minnesota, St. Paul, MN 55108, USA; (M.P.T.); (P.E.U.); (A.G.); (M.S.-S.)
| | - Chi Chen
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108, USA; (W.M.); (C.C.)
| | - Gerald C. Shurson
- Department of Animal Science, University of Minnesota, St. Paul, MN 55108, USA; (M.P.T.); (P.E.U.); (A.G.); (M.S.-S.)
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Yu H, Wang Y, Zhang J, Wang X, Wang R, Bao J, Zhang R. Effects of dustbathing environment on gut microbiota and expression of intestinal barrier and immune-related genes of adult laying hens housed individually in modified traditional cage. Poult Sci 2023; 102:103097. [PMID: 37769487 PMCID: PMC10542639 DOI: 10.1016/j.psj.2023.103097] [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: 06/12/2023] [Revised: 08/25/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023] Open
Abstract
Litters, the composition of sand and peat rich in microbiota, are essential to trigger the dustbathing behavior of chickens. To investigate the effects of a dustbathing environment (DE) on the intestinal health, gut microbiota, and immune responses of laying hens, a total of 72 healthy Hy-Line Brown laying hens at 69 wk of age (WOA) were housed individually in modified traditional cages and randomly divided into 2 groups: one group had free access to litters (CT), while the other one was restricted from litters (CC). The experiment lasted for 42 d. At the end of the experiment, the intestinal histomorphology and immune status of laying hens were determined, and the 16S rRNA sequencing method was used to assess the composition of the intestinal microbial community of birds. Intestinal histomorphology changed, including villus height and villus-to-crypt ratio significantly increased in the CT group (P < 0.01). DE reshaped the microbial community and increased the microbial richness with the higher indicators of Chao1 and observed species and the comparatively abundant beta diversity (P < 0.05). Ten genera, including Faecalibacterium and Coprococcus, declined in laying hens from the CT group (P < 0.05), while Alistipes increased in CT hens (P < 0.05) compared to those hens from the CC group. The expression levels of intestinal barrier-related genes of claudin-1, claudin-4, occludin, ZO-1, and ZO-2 and immune-related genes of IL-4, IL-6, IL-8, IFN-γ, IgA, TLR-2, and TLR-4 were significantly upregulated in the intestine of laying hens in CT group (P < 0.05). DE also increased the serum levels of IL-4, IL-6, IL-8, IFN-γ, and IgA (P < 0.01). The alteration of the gut microbiota by DE is closely related to host immune responses, including Lactobacillus positively correlated with IL-4 and IgA. Thus, a dustbathing environment can improve the welfare of laying hens by changing the intestinal histomorphology, immune response, and the gut microbial community.
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Affiliation(s)
- Hanlin Yu
- College of Animal Science and Technology, Northeast Agricultural University, 150030 Harbin, China
| | - Ye Wang
- College of Animal Science and Technology, Northeast Agricultural University, 150030 Harbin, China
| | - Jiaqi Zhang
- College of Animal Science and Technology, Northeast Agricultural University, 150030 Harbin, China
| | - Xiaoxu Wang
- College of Animal Science and Technology, Northeast Agricultural University, 150030 Harbin, China
| | - Rui Wang
- College of Animal Science and Technology, Northeast Agricultural University, 150030 Harbin, China
| | - Jun Bao
- College of Animal Science and Technology, Northeast Agricultural University, 150030 Harbin, China; Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, 150030 Harbin, China
| | - Runxiang Zhang
- College of Animal Science and Technology, Northeast Agricultural University, 150030 Harbin, China; Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, 150030 Harbin, China.
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6
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Hodak CR, Bescucci DM, Shamash K, Kelly LC, Montina T, Savage PB, Inglis GD. Antimicrobial Growth Promoters Altered the Function but Not the Structure of Enteric Bacterial Communities in Broiler Chicks ± Microbiota Transplantation. Animals (Basel) 2023; 13:ani13060997. [PMID: 36978538 PMCID: PMC10044420 DOI: 10.3390/ani13060997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Non-antibiotic alternatives to antimicrobial growth promoters (AGPs) are required, and understanding the mode of action of AGPs may facilitate the development of effective alternatives. The temporal impact of the conventional antibiotic AGP, virginiamycin, and an AGP alternative, ceragenin (CSA-44), on the structure and function of the broiler chicken cecal microbiota was determined using next-generation sequencing and 1H-nuclear magnetic resonance spectroscopy (NMR)-based metabolomics. To elucidate the impact of enteric bacterial diversity, oral transplantation (±) of cecal digesta into 1-day-old chicks was conducted. Microbiota transplantation resulted in the establishment of a highly diverse cecal microbiota in recipient chicks that did not change between day 10 and day 15 post-hatch. Neither virginiamycin nor CSA-44 influenced feed consumption, weight gain, or feed conversion ratio, and did not affect the structure of the cecal microbiota in chicks possessing a low or high diversity enteric microbiota. However, metabolomic analysis of the cecal contents showed that the metabolome of cecal digesta was affected in birds administered virginiamycin and CSA-44 as a function of bacterial community diversity. As revealed by metabolomics, glycolysis-related metabolites and amino acid synthesis pathways were impacted by virginiamycin and CSA-44. Thus, the administration of AGPs did not influence bacterial community structure but did alter the function of enteric bacterial communities. Hence, alterations to the functioning of the enteric microbiota in chickens may be the mechanism by which AGPs impart beneficial health benefits, and this possibility should be examined in future research.
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Affiliation(s)
- Colten R. Hodak
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Danisa M. Bescucci
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Karen Shamash
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Laisa C. Kelly
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Tony Montina
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Paul B. Savage
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - G. Douglas Inglis
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
- Correspondence:
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7
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Zwirzitz B, Oladeinde A, Johnson J, Zock G, Milfort MC, Fuller AL, Ghareeb AFA, Foutz JC, Teran JA, Woyda R, Abdo Z, Looft T, Lawrence JP, Cudnik D, Aggrey SE. Temporal dynamics of the cecal and litter microbiome of chickens raised in two separate broiler houses. Front Physiol 2023; 14:1083192. [PMID: 36935743 PMCID: PMC10018173 DOI: 10.3389/fphys.2023.1083192] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
In this study, we investigated the dynamics of the ceca and litter microbiome of chickens from post-hatch through pre-harvest. To achieve this, six hundred one-day old Cobb 500 broiler chicks were raised on floor pens for 49 days in two separate houses. We performed short-read and full-length sequencing of the bacterial 16S rRNA gene present in the meconium and in cecal and litter samples collected over the duration of the study. In addition, we determined the antimicrobial resistance (AMR) phenotype of Escherichia coli and Enterococcus spp. isolated from the meconium and the ceca of 49-day old chickens. We monitored the relative humidity, temperature, and ammonia in each house daily and the pH and moisture of litter samples weekly. The overall microbial community structure of the ceca and litter consistently changed throughout the course of the grow-out and correlated with some of the environmental parameters measured (p < 0.05). We found that the ceca and litter microbiome were similar in the two houses at the beginning of the experiment, but over time, the microbial community separated and differed between the houses. When we compared the environmental parameters in the two houses, we found no significant differences in the first half of the growth cycle (day 0-21), but morning temperature, morning humidity, and ammonia significantly differed (p < 0.05) between the two houses from day 22-49. Lastly, the prevalence of AMR in cecal E. coli isolates differed from meconium isolates (p < 0.001), while the AMR phenotype of cecal Enterococcus isolates differed between houses (p < 0.05).
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Affiliation(s)
- Benjamin Zwirzitz
- Department of Food Science and Technology, Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | | | - Jasmine Johnson
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Gregory Zock
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Marie C. Milfort
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | | | - Ahmed F. A. Ghareeb
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - James C. Foutz
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Jose Alexis Teran
- College of Engineering, University of Georgia, Athens, GA, United States
| | - Reed Woyda
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Torey Looft
- USDA-ARS, National Animal Disease Center, Ames, IA, United States
| | | | - Denice Cudnik
- USDA-ARS, U.S. National Poultry Research Center, Athens, GA, United States
| | - Samuel E. Aggrey
- Department of Poultry Science, University of Georgia, Athens, GA, United States
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8
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de Jong IC, Schokker D, Gunnink H, van Wijhe M, Rebel JMJ. Early life environment affects behavior, welfare, gut microbiome composition, and diversity in broiler chickens. Front Vet Sci 2022; 9:977359. [PMID: 36213407 PMCID: PMC9534479 DOI: 10.3389/fvets.2022.977359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/16/2022] [Indexed: 12/11/2022] Open
Abstract
This study aimed to identify whether early-life conditions in broiler chickens could affect their behavior and welfare, and whether or not this was associated with an altered gut microbiome composition or diversity. Broilers were tested in a 2 x 2 factorial design with hatching conditions [home pen (OH) or at the hatchery (HH)] and enrichment (dark brooder (EE) or no brooder (NE) until 14 days of age) as factors (N = 6 per treatment combination). Microbiota composition was measured in the jejunum on days (d) 7, 14, and 35 and in pooled fecal samples on day 14. A novel environment test (NET) was performed on days 1 and 11, and the behavior was observed on days 6, 13, and 33. On day 35, composite asymmetry was determined and footpad dermatitis and hock burn were scored. In their home pen, HH showed more locomotion than OH (P = 0.05), and NE were sitting more and showed more comfort behavior than EE at all ages (P <0.001 and P = 0.001, respectively). On days 6 and 13 NE showed more eating and litter pecking while sitting, but on day 33 the opposite was found (age*enrichment: P = 0.05 and P <0.01, respectively). On days 1 and 11, HH showed more social reinstatement in the NET than OH, and EE showed more social reinstatement than NE (P <0.05). Composite asymmetry scores were lower for EE than NE (P <0.05). EE also had less footpad dermatitis and hock burn than NE (P <0.001). Within OH, NE had a more diverse fecal and jejunal microbiome compared to EE on day 14 (feces: observed richness: P = 0.052; jejunum: observed richness and Shannon: P <0.05); the principal component analysis (PCA) showed differences between NE and EE within both HH and OH in fecal samples on day 14, as well as significant differences in bacterial genera such as Lactobacillus and Lachnospiraceae (P <0.05). On day 35, PCA in jejunal samples only showed a trend (P = 0.068) for differences between NE vs. EE within the OH. In conclusion, these results suggest that especially the dark brooder affected the behavior and had a positive effect on welfare as well as affected the composition and diversity of the microbiome. Whether or not the behavior was modulated by the microbiome or vice versa remains to be investigated.
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Affiliation(s)
- Ingrid C. de Jong
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
- *Correspondence: Ingrid C. de Jong
| | - Dirkjan Schokker
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Henk Gunnink
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Maudia van Wijhe
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Johanna M. J. Rebel
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
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9
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Kers JG, Velkers FC, Fischer EAJ, Stegeman JA, Smidt H, Hermes GDA. Conserved developmental trajectories of the cecal microbiota of broiler chickens in a field study. FEMS Microbiol Ecol 2022; 98:6649812. [PMID: 35878411 PMCID: PMC9423033 DOI: 10.1093/femsec/fiac090] [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: 02/09/2022] [Revised: 06/01/2022] [Accepted: 07/21/2022] [Indexed: 11/15/2022] Open
Abstract
There is great interest in identifying gut microbiota development patterns and underlying assembly rules that can inform strategies to improve broiler health and performance. Microbiota stratification using community types helps to simplify complex and dynamic ecosystem principles of the intestinal microbiota. This study aimed to identify community types to increase insight in intestinal microbiota variation between broilers and to identify factors that explain this variation. A total of 10 well-performing poultry flocks on four farms were followed. From each flock, the cecal content of nine broilers was collected at 7, 14, and 35 days posthatch. A total of two robust community types were observed using different clustering methods, one of which was dominated by 7-day-old broilers, and one by 35-day-old broilers. Broilers, 14-day-old, were divided across both community types. This is the first study that showed conserved cecal microbiota development trajectories in commercial broiler flocks. In addition to the temporal development with age, the cecal microbiota variation between broilers was explained by the flock, body weight, and the different feed components. Our data support a conserved development of cecal microbiota, despite strong influence of environmental factors. Further investigation of mechanisms underlying microbiota development and function is required to facilitate intestinal health promoting management, diagnostics, and nutritional interventions.
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Affiliation(s)
- Jannigje G Kers
- Corresponding author: Department Population Health Sciences, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands. E-mail:
| | - Francisca C Velkers
- Department Population Health Sciences, Faculty of Veterinary Medicine, Division Farm Animal Health, Utrecht University, Yalelaan 7, 3584 CL Utrecht, The Netherlands
| | - Egil A J Fischer
- Department Population Health Sciences, Faculty of Veterinary Medicine, Division Farm Animal Health, Utrecht University, Yalelaan 7, 3584 CL Utrecht, The Netherlands
| | - J Arjan Stegeman
- Department Population Health Sciences, Faculty of Veterinary Medicine, Division Farm Animal Health, Utrecht University, Yalelaan 7, 3584 CL Utrecht, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Gerben D A Hermes
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
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10
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Sztandarski P, Marchewka J, Konieczka P, Zdanowska-Sąsiadek Ż, Damaziak K, Riber AB, Gunnarsson S, Horbańczuk JO. Gut microbiota activity in chickens from two genetic lines and with outdoor-preferring, moderate-preferring, and indoor-preferring ranging profiles. Poult Sci 2022; 101:102039. [PMID: 35952604 PMCID: PMC9385685 DOI: 10.1016/j.psj.2022.102039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/20/2022] [Accepted: 06/25/2022] [Indexed: 11/28/2022] Open
Abstract
Despite the existing research into the gut microbiome of meat chickens, the associations between gut microbiome composition, its activity and chicken outdoor ranging frequency remain unexplored. The aim of this study was to determine the gut microbiota composition, activity and metabolic products in chickens of 2 different lines and 3 ranging profiles. Sixty non-beak trimmed birds, either Sasso or Green-legged Partridge were housed with access to outdoor ranges from wk. 5 to 10 of age. Outdoor ranges were video recorded to obtain frequencies of the birds’ range use. The information about relative abundance of selected bacterial groups in the ceca including Lactobacillus spp., E. coli, Bifidobacterium spp., and Clostridium spp. was obtained with the PCR method. Gut microbiota activity was assessed based on the glycolytic activity of bacterial enzymes including, α-glucosidase, β-glucosidase, α-galactosidase, β-galactosidase, and β-glucuronidase as well as based on the concentration of short-chain fatty acids (SCFA) in the caecal digesta. Statistical analysis was conducted by generalized linear mixed models, applying the breed and ranging profile as fixed effects and pen as a random factor. The lowest relative abundance of Bifidobacterium spp. was found in the cecal content of indoor-preferring Sasso birds (0.01 ± 0.001), as compared to all other birds in the experiment (ranging from 0.03 ± 0.01 to 0.11 ± 0.07; P = 0.0002). The lowest relative abundance of E. coli was identified for all outdoor-preferring birds and indoor- preferring Sasso birds (0.01 ± 0.001; P = 0.0087). Cecal activity of: α-glucosidase, β-glucuronidase and β-galactosidase was higher in Green-legged Partridges, as compared to Sasso (P = 0.013; P = 0.008; P = 0.004). Valeric acid concentrations were higher in moderate Green-legged Partridges than in Sasso of the same ranging profile (2.03 ± 0.16 vs. 1.5 ± 0.17; 0.016). The majority of the current results confirmed an effect of genotype and ranging profile on the various analyzed parameters. In outdoor-preferring birds, the consumption of pasture originating feed sources as a supplement to the indoor accessible cereal-based diet likely caused the positive effects on the birds’ microbial profile.
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Affiliation(s)
- Patryk Sztandarski
- Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzębiec, 05-552 Magdalenka, Poland.
| | - Joanna Marchewka
- Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzębiec, 05-552 Magdalenka, Poland
| | - Paweł Konieczka
- Department of Poultry Science and Apiculture, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, Oczapowskiego 5, 10-719, Olsztyn, Poland
| | - Żaneta Zdanowska-Sąsiadek
- Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzębiec, 05-552 Magdalenka, Poland
| | - Krzysztof Damaziak
- Department of Animal Breeding, Faculty of Animal Breeding, Bioengineering and Conservation, Institute of Animal Science, Warsaw University of Life Sciences, 02-786 Warsaw, Poland
| | - Anja B Riber
- Department of Animal Science, Aarhus University, Aarhus DK-8830, Tjele, Denmark
| | - Stefan Gunnarsson
- Department of Animal Environment and Health, Swedish University of Agricultural Sciences (SLU), S-532 23 Skara, Sweden
| | - Jarosław Olav Horbańczuk
- Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzębiec, 05-552 Magdalenka, Poland
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11
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Goossens E, Dehau T, Ducatelle R, Van Immerseel F. Omics technologies in poultry health and productivity - part 2: future applications in the poultry industry. Avian Pathol 2022; 51:418-423. [PMID: 35675218 DOI: 10.1080/03079457.2022.2085545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The increasing global demand for poultry products, together with the growing consumer concerns related to bird health and welfare, pose a significant challenge to the poultry industry. Therefore, the poultry industry is increasingly implementing novel technologies to optimize and enhance bird welfare and productivity. This second part of a bipartite review on omics technologies in poultry health and productivity highlights the implementation of specific diagnostic biomarkers based on omics-research in the poultry industry, as well as the potential integration of multi-omics in future poultry production. A general discussion of the use of multiple omics technologies in poultry research is provided in part 1. To date, approaches focusing on one or more omics type are widely used in poultry research, but the implementation of these omics techniques in poultry production is not expected in the near future. However, great potential lays in the development of diagnostic tests based on disease- or gut health-specific biomarkers, which are identified through omics research. As the cost of omics technologies is rapidly decreasing, implementation of multi-omics measurements in routine poultry monitoring systems might be feasible in the more distant future. Therefore, the opportunities, challenges and requirements to enable the integration of multi-omics-based monitoring of bird health and productivity in future poultry production are discussed.
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Affiliation(s)
- Evy Goossens
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Tessa Dehau
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Richard Ducatelle
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Filip Van Immerseel
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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12
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Research Progress of the Gut Microbiome in Hybrid Fish. Microorganisms 2022; 10:microorganisms10050891. [PMID: 35630336 PMCID: PMC9146865 DOI: 10.3390/microorganisms10050891] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 02/07/2023] Open
Abstract
Fish, including hybrid species, are essential components of aquaculture, and the gut microbiome plays a vital role in fish growth, behavior, digestion, and immune health. The gut microbiome can be affected by various internal and/or external factors, such as host development, diet, and environment. We reviewed the effects of diet and dietary supplements on intestinal microorganisms in hybrid fish and the difference in the gut microbiome between the hybrid and their hybrids that originate. Then, we summarized the role of the gut microbiome in the speciation and ecological invasion of hybrid fish. Finally, we discussed possible future studies on the gut microbiome in hybrid fish, including the potential interaction with environmental microbiomes, the effects of the gut microbiome on population expansion, and fish conservation and management.
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13
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Kers JG, Saccenti E. The Power of Microbiome Studies: Some Considerations on Which Alpha and Beta Metrics to Use and How to Report Results. Front Microbiol 2022; 12:796025. [PMID: 35310396 PMCID: PMC8928147 DOI: 10.3389/fmicb.2021.796025] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/28/2021] [Indexed: 01/04/2023] Open
Abstract
Background Since sequencing techniques have become less expensive, larger sample sizes are applicable for microbiota studies. The aim of this study is to show how, and to what extent, different diversity metrics and different compositions of the microbiota influence the needed sample size to observe dissimilar groups. Empirical 16S rRNA amplicon sequence data obtained from animal experiments, observational human data, and simulated data were used to perform retrospective power calculations. A wide variation of alpha diversity and beta diversity metrics were used to compare the different microbiota datasets and the effect on the sample size. Results Our data showed that beta diversity metrics are the most sensitive to observe differences as compared with alpha diversity metrics. The structure of the data influenced which alpha metrics are the most sensitive. Regarding beta diversity, the Bray–Curtis metric is in general the most sensitive to observe differences between groups, resulting in lower sample size and potential publication bias. Conclusion We recommend performing power calculations and to use multiple diversity metrics as an outcome measure. To improve microbiota studies, awareness needs to be raised on the sensitivity and bias for microbiota research outcomes created by the used metrics rather than biological differences. We have seen that different alpha and beta diversity metrics lead to different study power: because of this, one could be naturally tempted to try all possible metrics until one or more are found that give a statistically significant test result, i.e., p-value < α. This way of proceeding is one of the many forms of the so-called p-value hacking. To this end, in our opinion, the only way to protect ourselves from (the temptation of) p-hacking would be to publish a statistical plan before experiments are initiated, describing the outcomes of interest and the corresponding statistical analyses to be performed.
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Affiliation(s)
- Jannigje Gerdien Kers
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
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14
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Bindari YR, Gerber PF. Centennial Review: Factors affecting the chicken gastrointestinal microbial composition and their association with gut health and productive performance. Poult Sci 2021; 101:101612. [PMID: 34872745 PMCID: PMC8713025 DOI: 10.1016/j.psj.2021.101612] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 02/08/2023] Open
Abstract
Maintenance of "gut health" is considered a priority in commercial chicken farms, although a precise definition of what constitutes gut health and how to evaluate it is still lacking. In research settings, monitoring of gut microbiota has gained great attention as shifts in microbial community composition have been associated with gut health and productive performance. However, microbial signatures associated with productivity remain elusive because of the high variability of the microbiota of individual birds resulting in multiple and sometimes contradictory profiles associated with poor or high performance. The high costs associated with the testing and the need for the terminal sampling of a large number of birds for the collection of gut contents also make this tool of limited use in commercial settings. This review highlights the existing literature on the chicken digestive system and associated microbiota; factors affecting the gut microbiota and emergence of the major chicken enteric diseases coccidiosis and necrotic enteritis; methods to evaluate gut health and their association with performance; main issues in investigating chicken microbial populations; and the relationship of microbial profiles and production outcomes. Emphasis is given to emerging noninvasive and easy-to-collect sampling methods that could be used to monitor gut health and microbiological changes in commercial flocks.
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Affiliation(s)
- Yugal Raj Bindari
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Priscilla F Gerber
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
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15
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Aruwa CE, Pillay C, Nyaga MM, Sabiu S. Poultry gut health - microbiome functions, environmental impacts, microbiome engineering and advancements in characterization technologies. J Anim Sci Biotechnol 2021; 12:119. [PMID: 34857055 PMCID: PMC8638651 DOI: 10.1186/s40104-021-00640-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/01/2021] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal tract (GIT) health impacts animal productivity. The poultry microbiome has functions which range from protection against pathogens and nutrients production, to host immune system maturation. Fluctuations in the microbiome have also been linked to prevailing environmental conditions. Healthy poultry birds possess a natural resistance to infection. However, the exploration of environmental impacts and other relevant factors on poultry growth and health have been underplayed. Since good performance and growth rate are central to animal production, the host-microbiome relationship remains integral. Prior to the emergence of metagenomic techniques, conventional methods for poultry microbiome studies were used and were low-throughput and associated with insufficient genomic data and high cost of sequencing. Fortunately, the advent of high-throughput sequencing platforms have circumvented some of these shortfalls and paved the way for increased studies on the poultry gut microbiome diversity and functions. Here, we give an up-to-date review on the impact of varied environments on microbiome profile, as well as microbiome engineering and microbiome technology advancements. It is hoped that this paper will provide invaluable information that could guide and inspire further studies on the lingering pertinent questions about the poultry microbiome.
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Affiliation(s)
- Christiana Eleojo Aruwa
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Charlene Pillay
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Martin M Nyaga
- Next Generation Sequencing Unit, Division of Virology, Faculty of Heath Sciences, University of the Free State, Bloemfontein, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa.
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16
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Elling-Staats M, Gilbert M, Smidt H, Kwakkel R. Caecal protein fermentation in broilers: a review. WORLD POULTRY SCI J 2021. [DOI: 10.1080/00439339.2022.2003170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- M.L. Elling-Staats
- Animal Nutrition Group, Wageningen University & Research, Wageningen, The Netherlands
| | - M.S. Gilbert
- Animal Nutrition Group, Wageningen University & Research, Wageningen, The Netherlands
| | - H. Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - R.P. Kwakkel
- Animal Nutrition Group, Wageningen University & Research, Wageningen, The Netherlands
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17
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Abdelli N, Francisco Pérez J, Vilarrasa E, Melo-Duran D, Cabeza Luna I, Karimirad R, Solà-Oriol D. Microencapsulation Improved Fumaric Acid and Thymol Effects on Broiler Chickens Challenged With a Short-Term Fasting Period. Front Vet Sci 2021; 8:686143. [PMID: 34722691 PMCID: PMC8554117 DOI: 10.3389/fvets.2021.686143] [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: 03/26/2021] [Accepted: 09/08/2021] [Indexed: 11/13/2022] Open
Abstract
The first objective of this study was to demonstrate the usefulness of the microencapsulation technique to protect fumaric acid and thymol, avoiding their early absorption and ensuring their slow release throughout the gastrointestinal tract (GIT). For this purpose, the release of a lipid matrix microencapsulated brilliant blue (BB) was assessed in vitro, using a simulated broiler intestinal fluid, and in vivo. In vitro results showed that more than 60% of BB color reached the lower intestine, including 26.6 and 29.7% in the jejunum and ileum, respectively. The second objective was to determine the effects of microencapsulated fumaric acid, thymol, and their mixture on the performance and gut health of broilers challenged with a short-term fasting period (FP). One-day-old male ROSS 308 chickens (n = 280) were randomly distributed into seven treatments, with 10 replicates of four birds each. Dietary treatments consisted of a basal diet as negative control (NC), which was then supplemented by either non-microencapsulated fumaric acid (0.9 g/kg), thymol (0.6 g/kg), or a mixture of them. The same additive doses were also administered in a microencapsulated form (1.5 and 3 g/kg for the fumaric acid and thymol, respectively). At day 21, chickens were subjected to a 16.5-h short-term FP to induce an increase in intestinal permeability. Growth performance was assessed weekly. At day 35, ileal tissue and cecal content were collected from one bird per replicate to analyze intestinal histomorphology and microbiota, respectively. No treatment effect was observed on growth performance from day 1 to 21 (p > 0.05). Microencapsulated fumaric acid, thymol, or their mixture improved the overall FCR (feed conversion ratio) and increased ileal villi height-to-crypt depth ratio (VH:CD) (p < 0.001) on day 35 of the experiment. The microencapsulated mixture of fumaric acid and thymol increased cecal abundance of Bacteroidetes, Bacillaceae, and Rikenellaceae, while decreasing that of Pseudomonadaceae. These results indicate that the microencapsulation technique used in the current study can be useful to protect fumaric acid and thymol, avoiding early absorption, ensure their slow release throughout the GIT, and improve their effects on fasted broiler chickens.
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Affiliation(s)
- Nedra Abdelli
- Animal Nutrition and Welfare Service (SNIBA), Department of Animal and Science, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - José Francisco Pérez
- Animal Nutrition and Welfare Service (SNIBA), Department of Animal and Science, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Diego Melo-Duran
- Animal Nutrition and Welfare Service (SNIBA), Department of Animal and Science, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Razzagh Karimirad
- Department of Animal Science, Lorestan University, Khorramabad, Iran
| | - David Solà-Oriol
- Animal Nutrition and Welfare Service (SNIBA), Department of Animal and Science, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain
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18
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Oost MJ, Velkers FC, Kraneveld AD, Venema K. Development of the in vitro Cecal Chicken ALIMEntary tRact mOdel-2 to Study Microbiota Composition and Function. Front Microbiol 2021; 12:726447. [PMID: 34707583 PMCID: PMC8542841 DOI: 10.3389/fmicb.2021.726447] [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: 06/17/2021] [Accepted: 09/16/2021] [Indexed: 01/04/2023] Open
Abstract
The digestive system of the chicken plays an important role in metabolism, immunity, and chicken health and production performance. The chicken ceca harbor a diverse microbial community and play a crucial role in the microbial fermentation and production of energy-rich short-chain fatty acids (SCFA). For humans, dogs, and piglets in vitro digestive system models have been developed and are used to study the microbiota composition and metabolism after intervention studies. For chickens, most research on the cecal microbiota has been performed in in vivo experiments or in static in vitro models that may not accurately resemble the in vivo situations. This paper introduces an optimized digestive system model that simulates the conditions in the ceca of the chicken, i.e., the Chicken ALIMEntary tRact mOdel-2 (CALIMERO-2). The system is based on the well-validated TNO in vitro model of the colon-2 (TIM-2) and is the first dynamic in vitro digestion model for chickens species. To validate this model, the pH, temperature, and different types of microbial feeding were compared and analyzed, to best mimic the conditions in the chicken ceca. The bacterial composition, as well as the metabolite production at 72 h, showed no significant difference between the different microbial feedings. Moreover, we compared the CALIMERO-2 digestive samples to the original inoculum and found some significant shifts in bacterial composition after the fermentation started. Over time the bacterial diversity increased and became more similar to the original inoculum. We can conclude that CALIMERO-2 is reproducible and can be used as a digestive system model for the chicken ceca, in which the microbial composition and activity can be maintained and shows similar results to the in vivo cecum. CALIMERO-2 can be used to study effects on composition and activity of the chicken cecum microbiota in response to in-feed interventions.
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Affiliation(s)
- Miriam J Oost
- Centre for Healthy Eating and Food Innovation, Faculty of Science and Engineering, Maastricht University-Campus Venlo, Venlo, Netherlands.,Division Farm Animal Health, Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Francisca C Velkers
- Division Farm Animal Health, Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Koen Venema
- Centre for Healthy Eating and Food Innovation, Department of Human Biology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Venlo, Netherlands
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19
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Lundberg R, Scharch C, Sandvang D. The link between broiler flock heterogeneity and cecal microbiome composition. Anim Microbiome 2021; 3:54. [PMID: 34332648 PMCID: PMC8325257 DOI: 10.1186/s42523-021-00110-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 07/06/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Despite low genetic variation of broilers and deployment of considerate management practices, there still exists considerable body weight (BW) heterogeneity within broiler flocks which adversely affects the commercial value. The purpose of this study was to investigate the role of the cecal microbiome in weight differences between animals. Understanding how the gut microbiome may contribute to flock heterogeneity helps to pave the road for identifying methods to improve flock uniformity and performance. RESULTS Two hundred eighteen male broiler chicks were housed in the same pen, reared for 37 days, and at study end the 25 birds with highest BW (Big) and the 25 birds with lowest BW (Small) were selected for microbiome analysis. Cecal contents were analyzed by a hybrid metagenomic sequencing approach combining long and short read sequencing. We found that Big birds displayed higher microbial alpha diversity, higher microbiome uniformity (i.e. lower beta diversity within the group of Big birds), higher levels of SCFA-producing and health-associated bacterial taxa such as Lachnospiraceae, Faecalibacterium, Butyricicoccus and Christensenellales, and lower levels of Akkermansia muciniphila and Escherichia coli as compared to Small birds. CONCLUSION Cecal microbiome characteristics could be linked to the size of broiler chickens. Differences in alpha diversity, beta diversity and taxa abundances all seem to be directly associated with growth differences observed in an otherwise similar broiler flock.
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Affiliation(s)
- Randi Lundberg
- Chr. Hansen A/S, Boege Allé 10-12, 2970, Hoersholm, Denmark.
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20
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Wen C, van Dixhoorn I, Schokker D, Woelders H, Stockhofe-Zurwieden N, Rebel JMJ, Smidt H. Environmentally enriched housing conditions affect pig welfare, immune system and gut microbiota in early life. Anim Microbiome 2021; 3:52. [PMID: 34321110 PMCID: PMC8320228 DOI: 10.1186/s42523-021-00115-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/16/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Conventional pig housing and management conditions are associated with gastrointestinal pathophysiology and disease susceptibility in early life. Developing new strategies to reduce both therapeutic and prophylactic antibiotic use is urgent for the sustainable swine production globally. To this end, housing methodology providing effective environmental enrichment could be a promising alternative approach to reduce antibiotic usage, as it has been proven to positively influence pig welfare and immune status and reduce susceptibility to infections. It is, however, poorly understood how this enriched housing affects systemic and local pulmonary immune status and gut microbiota colonization during early life. In the present study, we compared the effects of two housing conditions, i.e., conventional housing: (CH) versus enriched housing (EH), on immune status and gut microbiota from birth until 61 days of age. RESULTS The expected benefits of enrichment on pig welfare were confirmed as EH pigs showed more positive behaviour, less aggression behaviour during the weaning transition and better human animal relation during the post weaning phase. Regarding the pigs' immune status, EH pigs had higher values of haemoglobin and mean corpuscular volume in haematological profiles and higher percentages of T cells and cytotoxic T cells in peripheral blood. Furthermore, EH pigs showed higher ex vivo secretion of IL1ß and TNF-α after lipopolysaccharide stimulation of whole blood than CH pigs. The structure of the developing faecal microbiota of CH and EH pigs significantly differed as early as day 12 with an increase in the relative abundance of several bacterial groups known to be involved in the production of short chain fatty acids, such as Prevotella_2, Christensenellaceae_R_7_group and Ruminococcus gauvreauii group. Furthermore, the main difference between both housing conditions post weaning was that on day 61, CH pigs had significantly larger inter-individual variation of ileal and colonic microbiota than EH pigs. In addition to housing, other intrinsic factors (e.g., sex) were associated with gut microbiota development and immune competence. CONCLUSIONS In addition to the known welfare benefits for pigs, environmentally enriched housing also positively drives important aspects of the development of the immune system and the establishment of gut microbiota in early life. Consequently, EH may contribute to increasing productivity of pigs and reducing antibiotic use.
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Affiliation(s)
- Caifang Wen
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ingrid van Dixhoorn
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Dirkjan Schokker
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Henri Woelders
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Johanna M. J. Rebel
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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21
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Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria. mSystems 2021; 6:6/3/e01300-20. [PMID: 34006629 PMCID: PMC8269260 DOI: 10.1128/msystems.01300-20] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The gut microbiome is crucial for both maturation of the immune system and colonization resistance against enteric pathogens. Although chicken are important domesticated animals, the impact of their gut microbiome on the immune system is understudied. Therefore, we investigated the effect of microbiome-based interventions on host mucosal immune responses. Increased levels of IgA and IgY were observed in chickens exposed to maternal feces after hatching compared with strict hygienic conditions. This was accompanied by increased gut bacterial diversity as assessed by 16S rRNA gene amplicon sequencing. Cultivation work allowed the establishment of a collection of 43 bacterial species spanning 4 phyla and 19 families, including the first cultured members of 3 novel genera and 4 novel species that were taxonomically described. This resource is available at www.dsmz.de/chibac. A synthetic community consisting of nine phylogenetically diverse and dominant species from this collection was designed and found to be moderately efficient in boosting immunoglobulin levels when provided to chickens early in life. IMPORTANCE The immune system plays a crucial role in sustaining animal health. Its development is markedly influenced by early microbial colonization of the gastrointestinal tract. As chicken are fully dependent on environmental microbes after hatching, extensive hygienic measures in production facilities are detrimental to the microbiota, resulting in low colonization resistance against pathogens. To combat enteric infections, antibiotics are frequently used, which aggravates the issue by altering gut microbiota colonization. Intervention strategies based on cultured gut bacteria are proposed to influence immune responses in chicken.
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Schreuder J, Velkers FC, Bossers A, Bouwstra RJ, de Boer WF, van Hooft P, Stegeman JA, Jurburg SD. Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range. Front Microbiol 2021; 11:626713. [PMID: 33584593 PMCID: PMC7876281 DOI: 10.3389/fmicb.2020.626713] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/24/2020] [Indexed: 01/04/2023] Open
Abstract
Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 and 4.4% of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition.
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Affiliation(s)
- Janneke Schreuder
- Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Francisca C Velkers
- Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Alex Bossers
- Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | | | - Willem F de Boer
- Wildlife Ecology and Conservation Group, Wageningen University and Research, Wageningen, Netherlands
| | - Pim van Hooft
- Wildlife Ecology and Conservation Group, Wageningen University and Research, Wageningen, Netherlands
| | - J Arjan Stegeman
- Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Stephanie D Jurburg
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
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23
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Banaszak M, Biesek J, Bogucka J, Dankowiakowska A, Olszewski D, Bigorowski B, Grabowicz M, Adamski M. Impact of aluminosilicates on productivity, carcass traits, meat quality, and jejunum morphology of broiler chickens. Poult Sci 2020; 99:7169-7177. [PMID: 33248634 PMCID: PMC7704995 DOI: 10.1016/j.psj.2020.08.073] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/15/2020] [Accepted: 08/27/2020] [Indexed: 11/29/2022] Open
Abstract
The aim of the study was to compare production results and quality of meat, as well as histological features of the jejunum in broiler chickens administered feed with 1% addition of zeolite or halloysite, with the addition of aluminosilicates to litter (4.50 kg/m2) throughout the rearing. In the experiment, 300 male broilers were used for 6 wk. They were divided into 3 groups, each of 10 repetitions (10 birds each). Group 1 was a control, halloysite was added to feed and litter in group 2, while zeolite was applied instead of halloysite in group 3. After rearing, 10 selected birds from each group were slaughtered. Selected production properties and degree of footpad dermatitis were examined, and histomorphometric examination of the jejunum was performed. The lowest yield and the highest proportion of neck with skin in the carcass were demonstrated in group 2 (P < 0.05). The lowest percentage of skin with subcutaneous fat was found in group 3 (P < 0.05). A decrease in lightness (L∗) and yellowness (b∗) was demonstrated in group 2, while redness (a∗) was the lowest in group 3 (P < 0.05). Group 2 was characterized by the lowest water-holding capacity in breast muscles, and in group 3, in leg muscles (P < 0.05). In group 3, the highest fat content and the lowest water content in the breast muscles (P < 0.05) were found. The leg muscles in groups 2 and 3 were characterized by the highest a∗, and in group 2, by b∗. The control group had the lowest protein and the highest fat content in leg muscles. In the intestine from group 2, a higher height (P < 0.05) and surface area (P < 0.01) of intestinal villi were found, in comparison to group 3. The width of intestinal villi was higher in groups 2 and 1 than in group 3 (P < 0.05), similarly the depth of intestinal crypts. The addition of zeolite could be proposed because of the obtained production results, while the halloysite had a positive effect on the histomorphometric features of the jejunum.
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Affiliation(s)
- Mirosław Banaszak
- Department of Animal Breeding, Faculty of Animal Breeding and Biology, UTP - University of Science and Technology in Bydgoszcz, 85-084 Bydgoszcz, Poland
| | - Jakub Biesek
- Department of Animal Breeding, Faculty of Animal Breeding and Biology, UTP - University of Science and Technology in Bydgoszcz, 85-084 Bydgoszcz, Poland.
| | - Joanna Bogucka
- Department of Animal Physiology, Physiotherapy and Nutrition, Faculty of Animal Breeding and Biology, UTP - University of Science and Technology in Bydgoszcz, 85-084 Bydgoszcz, Poland
| | - Agata Dankowiakowska
- Department of Animal Physiology, Physiotherapy and Nutrition, Faculty of Animal Breeding and Biology, UTP - University of Science and Technology in Bydgoszcz, 85-084 Bydgoszcz, Poland
| | | | - Bartosz Bigorowski
- Department of Animal Breeding, Faculty of Animal Breeding and Biology, UTP - University of Science and Technology in Bydgoszcz, 85-084 Bydgoszcz, Poland
| | - Małgorzata Grabowicz
- Department of Animal Physiology, Physiotherapy and Nutrition, Faculty of Animal Breeding and Biology, UTP - University of Science and Technology in Bydgoszcz, 85-084 Bydgoszcz, Poland
| | - Marek Adamski
- Department of Animal Breeding, Faculty of Animal Breeding and Biology, UTP - University of Science and Technology in Bydgoszcz, 85-084 Bydgoszcz, Poland
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24
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Meijerink N, Kers JG, Velkers FC, van Haarlem DA, Lamot DM, de Oliveira JE, Smidt H, Stegeman JA, Rutten VPMG, Jansen CA. Early Life Inoculation With Adult-Derived Microbiota Accelerates Maturation of Intestinal Microbiota and Enhances NK Cell Activation in Broiler Chickens. Front Vet Sci 2020; 7:584561. [PMID: 33330708 PMCID: PMC7710667 DOI: 10.3389/fvets.2020.584561] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/26/2020] [Indexed: 01/06/2023] Open
Abstract
Studies in mammals, including chickens, have shown that the development of the immune system is affected by interactions with intestinal microbiota. Early life microbial colonization may affect the development of innate and adaptive immunity and may contribute to lasting effects on health and resilience of broiler chickens. We inoculated broiler chickens with adult-derived-microbiota (AM) to investigate their effects on intestinal microbiota composition and natural killer (NK) cells, amongst other immune cells. We hypothesized that AM inoculation directly upon hatch (day 0) would induce an alteration in microbiota composition shortly after hatch, and subsequently affect (subsets of) intestinal NK cells and their activation. Microbiota composition of caecal and ileal content of chickens of 1, 3, 7, 14, 21, and 35 days of age was assessed by sequencing of 16S ribosomal RNA gene amplicons. In parallel, subsets and activation of intestinal NK cells were analyzed by flow cytometry. In caecal content of 1- and 3-day-old AM chickens, a higher alpha-diversity (Faith's phylogenetic diversity) was observed compared to control chickens, whereas ileal microbiota were unaffected. Regarding beta-diversity, caecal microbiota profiles could be clustered into three distinct community types. Cluster A represented caecal microbiota of 1-day-old AM chickens and 1- and 3-day-old control chickens. Cluster B included microbiota of seven of eight 3- and 7-day-old AM and 7-day-old control chickens, and cluster C comprised microbiota of all chickens of 14-days and older, independent of inoculation. In 3-day-old AM chickens an increase in the percentages of intestinal IL-2Rα+NK cells and activated NK cells was observed compared to control chickens of the same age. In addition, an increase in relative numbers of intestinal cytotoxic CD8αα+T cells was observed in 14- and 21-day-old AM chickens. Taken together, these results indicate that early exposure to AM shapes and accelerates the maturation of caecal microbiota, which is paralleled by an increase in IL-2Rα+NK cells and enhanced NK cell activation. The observed association between early life development of intestinal microbiota and immune system indicates possibilities to apply microbiota-targeted strategies that can accelerate maturation of intestinal microbiota and strengthen the immune system, thereby improving the health and resilience of broiler chickens.
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Affiliation(s)
- Nathalie Meijerink
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Jannigje G. Kers
- Division Farm Animal Health, Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Francisca C. Velkers
- Division Farm Animal Health, Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Daphne A. van Haarlem
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - David M. Lamot
- Cargill Animal Nutrition and Health Innovation Center, Velddriel, Netherlands
| | | | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - J. Arjan Stegeman
- Division Farm Animal Health, Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Victor P. M. G. Rutten
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Christine A. Jansen
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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Dame-Korevaar A, Kers JG, van der Goot J, Velkers FC, Ceccarelli D, Mevius DJ, Stegeman A, Fischer EAJ. Competitive Exclusion Prevents Colonization and Compartmentalization Reduces Transmission of ESBL-Producing Escherichia coli in Broilers. Front Microbiol 2020; 11:566619. [PMID: 33304325 PMCID: PMC7693455 DOI: 10.3389/fmicb.2020.566619] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/21/2020] [Indexed: 11/13/2022] Open
Abstract
Extended spectrum beta-lactamase (ESBL)-producing bacteria are resistant to extended-spectrum cephalosporins and are common in broilers. Interventions are needed to reduce the prevalence of ESBL-producing bacteria in the broiler production pyramid. This study investigated two different interventions. The effect of a prolonged supply of competitive exclusion (CE) product and compartmentalization on colonization and transmission, after challenge with a low dose of ESBL-producing Escherichia coli, in broilers kept under semi-field conditions, were examined. One-day-old broilers (Ross 308) (n = 400) were housed in four experimental rooms, subdivided in one seeder (S/C1)-pen and eight contact (C2)-pens. In two rooms, CE product was supplied from day 0 to 7. At day 5, seeder-broilers were inoculated with E. coli strain carrying bla CTX-M- 1 on plasmid IncI1 (CTX-M-1-E. coli). Presence of CTX-M-1-E. coli was determined using cloacal swabs (day 5-21 daily) and cecal samples (day 21). Time until colonization and cecal excretion (log10 CFU/g) were analyzed using survival analysis and linear regression. Transmission coefficients within and between pens were estimated using maximum likelihood. The microbiota composition was assessed by 16S ribosomal RNA gene amplicon sequencing in cecal content of broilers on days 5 and 21. None of the CE broilers was CTX-M-1-E. coli positive. In contrast, in the untreated rooms 187/200 of the broilers were CTX-M-1-E. coli positive at day 21. Broilers in C2-pens were colonized later than seeder-broilers (Time to event Ratio 3.53, 95% CI 3.14 to 3.93). The transmission coefficient between pens was lower than within pens (3.28 × 10-4 day-2, 95% CI 2.41 × 10-4 to 4.32 × 10-4 vs. 6.12 × 10-2 day-2, 95% CI 4.78 × 10-2 to 7.64 × 10-2). The alpha diversity of the cecal microbiota content was higher in CE broilers than in control broilers at days 5 and 21. The supply of a CE product from day 0 to 7 prevented colonization of CTX-M-1-E. coli after challenge at day 5, likely as a result of CE induced effects on the microbiota composition. Furthermore, compartmentalization reduced transmission rate between broilers. Therefore, a combination of compartmentalization and supply of a CE product may be a useful intervention to reduce transmission and prevent colonization of ESBL/pAmpC-producing bacteria in the broiler production pyramid.
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Affiliation(s)
- Anita Dame-Korevaar
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Jannigje G. Kers
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Jeanet van der Goot
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Francisca C. Velkers
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Dik J. Mevius
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Arjan Stegeman
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Egil A. J. Fischer
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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26
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Kers JG, de Oliveira JE, Fischer EAJ, Tersteeg‐Zijderveld MHG, Konstanti P, Stegeman JA(A, Smidt H, Velkers FC. Associations between phenotypic characteristics and clinical parameters of broilers and intestinal microbial development throughout a production cycle: A field study. Microbiologyopen 2020; 9:e1114. [PMID: 33068065 PMCID: PMC7658455 DOI: 10.1002/mbo3.1114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/09/2020] [Accepted: 08/18/2020] [Indexed: 01/09/2023] Open
Abstract
Disturbances in intestinal health are a common problem affecting commercial broiler chickens worldwide. Several studies have revealed associations between health, production performance, and intestinal microbiota. This study aimed to describe the development of the intestinal microbiota of broilers within a production cycle to evaluate to what extent clinical parameters and phenotypic characteristics can explain the intestinal microbiota variation. Of four well-performing flocks within two farms, the cecal content was collected of nine broilers at 0, 2, 4, or 5, 7, 11, or 12, 14, 21, 28, 35, and 40 days of the production cycle. In total, 342 samples were analyzed using 16S ribosomal RNA gene amplicon sequencing. Variables as macroscopic gut abnormalities, gut lesions, age, individual body weight, sex, footpad integrity, the color of ceca, and foam in cecal content were determined. Ileum tissue was collected for histological quantification of villus length and crypt depth. Flock infection levels of the intestinal disease coccidiosis were measured in pooled feces from the poultry house. Increases in phylogenetic diversity were observed from hatch until day 21 of age. Constrained multivariate analysis indicated that age, farm, body weight, ileum crypt depth, cecal color, and the coccidiosis lesion score were important variables to describe the variation in cecal microbiota. These results contribute to determining relevant variables in flocks that may be indicative of the intestinal microbiota composition. Moreover, this knowledge increases the awareness of interactions between the intestinal microbiota and broiler health as well as their relative importance.
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Affiliation(s)
- Jannigje G. Kers
- Department of Population Health SciencesDivision of Farm Animal HealthFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Jean E. de Oliveira
- Cargill Animal Nutrition and HealthInnovation Center VelddrielVelddrielThe Netherlands
| | - Egil A. J. Fischer
- Department of Population Health SciencesDivision of Farm Animal HealthFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Monique H. G. Tersteeg‐Zijderveld
- Department of Population Health SciencesInstitute for Risk Assessment SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Prokopis Konstanti
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Jan Arend (Arjan) Stegeman
- Department of Population Health SciencesDivision of Farm Animal HealthFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Hauke Smidt
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Francisca C. Velkers
- Department of Population Health SciencesDivision of Farm Animal HealthFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
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27
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Schreuder J, Velkers FC, Bouwstra RJ, Beerens N, Stegeman JA, de Boer WF, van Hooft P, Elbers ARW, Bossers A, Jurburg SD. An observational field study of the cloacal microbiota in adult laying hens with and without access to an outdoor range. Anim Microbiome 2020; 2:28. [PMID: 33499947 PMCID: PMC7807755 DOI: 10.1186/s42523-020-00044-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Laying hens with access to outdoor ranges are exposed to additional environmental factors and microorganisms, including potential pathogens. Differences in composition of the cloacal microbial community between indoor- and outdoor-housed layers may serve as an indicator for exposure to the outdoor environment, including its pathogens, and may yield insights into factors affecting the chickens' microbiota community dynamics. However, little is known about the influence of outdoor housing on microbiota community composition in commercial layer flocks. We performed a cross-sectional field study to evaluate differences in the cloacal microbiota of indoor- vs outdoor-layers across farms. Eight layer flocks (four indoor, four outdoor) from five commercial poultry farms were sampled. Indoor and outdoor flocks with the same rearing flock of origin, age, and breed were selected. In each flock, cloacal swabs were taken from ten layers, and microbiota were analysed with 16S rRNA gene amplicon sequencing. RESULTS Housing type (indoor vs outdoor), rearing farm, farm and poultry house within the farm all significantly contributed to bacterial community composition. Poultry house explained most of the variation (20.9%), while housing type only explained 0.2% of the variation in community composition. Bacterial diversity was higher in indoor-layers than in outdoor-layers, and indoor-layers also had more variation in their bacterial community composition. No phyla or genera were found to be differentially abundant between indoor and outdoor poultry houses. One amplicon sequence variant was exclusively present in outdoor-layers across all outdoor poultry houses, and was identified as Dietzia maris. CONCLUSIONS This study shows that exposure to an outdoor environment is responsible for a relatively small proportion of the community variation in the microbiota of layers. The poultry house, farm, and rearing flock play a much greater role in determining the cloacal microbiota composition of adult laying hens. Overall, measuring differences in cloacal microbiota of layers as an indicator for the level of exposure to potential pathogens and biosecurity seems of limited practical use. To gain more insight into environmental drivers of the gut microbiota, future research should aim at investigating community composition of commercial layer flocks over time.
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Affiliation(s)
- Janneke Schreuder
- Faculty of Veterinary Medicine, Department Population Health Sciences, Utrecht University, Yalelaan 7, 3584 CL Utrecht, The Netherlands
| | - Francisca C. Velkers
- Faculty of Veterinary Medicine, Department Population Health Sciences, Utrecht University, Yalelaan 7, 3584 CL Utrecht, The Netherlands
| | | | - Nancy Beerens
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - J. Arjan Stegeman
- Faculty of Veterinary Medicine, Department Population Health Sciences, Utrecht University, Yalelaan 7, 3584 CL Utrecht, The Netherlands
| | - Willem F. de Boer
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, the Netherlands
| | - P. van Hooft
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Armin R. W. Elbers
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Alex Bossers
- Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Stephanie D. Jurburg
- Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, the Netherlands
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
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28
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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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