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Yuan B, Md Ahsanul K, Rong L, Han S, Pan Y, Hou G, Li S. Exploring the relationship between rearing system and carcass traits of Danzhou chicken: a microbial perspective. Poult Sci 2024; 103:104186. [PMID: 39260026 PMCID: PMC11416224 DOI: 10.1016/j.psj.2024.104186] [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: 06/11/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 09/13/2024] Open
Abstract
This study investigated the effects of free-range (FR) and cage-rearing (CR) systems on intestinal health, carcass traits, and microbial diversity in the Danzhou chicken breed. Two groups of 125 hens in each group, aged 42 wk, were reared under FR and CR systems. At 50 wk, 50 hens from each group were randomly selected for carcass analysis and 10 hens for intestinal morphology and microbiota profiling. Results indicated a significant increase in villus height (VH) in the duodenum (P < 0.05), jejunum (P < 0.01), and ileum (P < 0.001) of the CR group. Additionally, the ratio of VH to crypt depth (VR) significantly (P < 0.001) increased in the jejunum, while crypt depth (CD) decreased significantly (P < 0.001) in the same section in the CR group. Carcass traits, including dress weight (DW), eviscerated with giblet weight (EGW), eviscerated weight (EW), and leg muscle weight (LW) significantly improved (P < 0.05) in the CR group. Microbial diversity showed significant β-diversity differences, with Lactobacillus, Enterococcus, and Oxalobacteraceae as dominant biomarkers in the CR group. Conversely, Actinomycetaceae, Erysipelotrichaceae, Coriobacteriaceae, Eubacterium, Actinomyces, Scardovia, and Lachnospiraceae were dominant in the FG group. Correlation analysis showed duodenum Lactobacillus was positively correlated with VH (P < 0.05), EW (P < 0.05), and LW (P < 0.001). Jejunum Lactobacillus was positively correlated considerably with VH (P < 0.01), VR (P < 0.05), DW (P < 0.05), EGW (P < 0.01), and LW (P < 0.001). Ileum Lactobacillus was positively correlated with EGW (P < 0.01), EW (P < 0.05), and LW (P < 0.01). Aeriscardovia in duodenum was positively (P < 0.01) associated with EGW. Enterococcus in the duodenum was positively (P < 0.05) associated with EGW and in Jejunum positively correlated with VH (P < 0.05) and VR (P < 0.01). The study concludes that cage rearing improves intestinal health, carcass traits, and microbial diversity in Danzhou chickens, with Lactobacillus and Enterococcus playing key roles.
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Affiliation(s)
- Bo Yuan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
| | - Kabir Md Ahsanul
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China; Biotechnology Division, Bangladesh Livestock Research Institute, Savar, Dhaka-1341, Bangladesh
| | - Li Rong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
| | - Shaobo Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
| | - Yangming Pan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
| | - Guanyu Hou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
| | - Shijun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China; Key Laboratory of Smart Farming for Agricultural Animals, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei Province 430070, China
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Saint-Martin V, Guillory V, Chollot M, Fleurot I, Kut E, Roesch F, Caballero I, Helloin E, Chambellon E, Ferguson B, Velge P, Kempf F, Trapp S, Guabiraba R. The gut microbiota and its metabolite butyrate shape metabolism and antiviral immunity along the gut-lung axis in the chicken. Commun Biol 2024; 7:1185. [PMID: 39300162 DOI: 10.1038/s42003-024-06815-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 08/30/2024] [Indexed: 09/22/2024] Open
Abstract
The gut microbiota exerts profound influence on poultry immunity and metabolism through mechanisms that yet need to be elucidated. Here we used conventional and germ-free chickens to explore the influence of the gut microbiota on transcriptomic and metabolic signatures along the gut-lung axis in poultry. Our results demonstrated a differential regulation of certain metabolites and genes associated with innate immunity and metabolism in peripheral tissues of germ-free birds. Furthermore, we evidenced the gut microbiota's capacity to regulate mucosal immunity in the chicken lung during avian influenza virus infection. Finally, by fine-analysing the antiviral pathways triggered by the short-chain fatty acid (SCFA) butyrate in chicken respiratory epithelial cells, we found that it regulates interferon-stimulated genes (ISGs), notably OASL, via the transcription factor Sp1. These findings emphasize the pivotal role of the gut microbiota and its metabolites in shaping homeostasis and immunity in poultry, offering crucial insights into the mechanisms governing the communication between the gut and lungs in birds.
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Affiliation(s)
| | | | | | | | - Emmanuel Kut
- INRAE, ISP, Université de Tours, 37380, Nouzilly, France
| | | | | | | | | | - Brian Ferguson
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Philippe Velge
- INRAE, ISP, Université de Tours, 37380, Nouzilly, France
| | - Florent Kempf
- INRAE, ISP, Université de Tours, 37380, Nouzilly, France
| | - Sascha Trapp
- INRAE, ISP, Université de Tours, 37380, Nouzilly, France
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da Silva JMS, Almeida AMDS, Borsanelli AC, de Athayde FRF, Nascente EDP, Batista JMM, Gouveia ABVS, Stringhini JH, Leandro NSM, Café MB. Intestinal Microbiome Profiles in Broiler Chickens Raised with Different Probiotic Strains. Microorganisms 2024; 12:1639. [PMID: 39203481 PMCID: PMC11357238 DOI: 10.3390/microorganisms12081639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 07/22/2024] [Accepted: 08/09/2024] [Indexed: 09/03/2024] Open
Abstract
The composition of the intestinal microbiota can influence the metabolism and overall functioning of avian organisms. Therefore, the objective of this study was to evaluate the effect of three different probiotics and an antibiotic on the microbiomes of 1.400 male Cobb® broiler raised for 42 days. The experiment was conducted with the following treatments: positive control diet (basal diet + antibiotic); negative control diet (basal diet without antibiotic and without probiotic); basal diet + Normal Avian Gut Flora (NAGF); basal diet + multiple colonizing strain probiotics (MCSPs); and basal diet + non-colonizing single strain probiotics (NCSSPs). The antibiotic (enramycin-antibiotic growth promoter) and probiotics were administered orally during all experiment (1 to 42 days), mixed with broiler feed. To determine the composition of the microbiota, five samples of ileal digesta were collected from 42-day-old chickens of each experimental group. The alpha and beta diversity of the ileal microbiota showed differences between the groups. MCSPs presented greater richness and uniformity compared to the positive control, negative control, and NCSSPs treatments, while the negative control exhibited greater homogeneity among samples than NCSSPs. MCSPs also showed a higher abundance of the genus Enterococcus. There were differences between the groups for low-abundance taxa (<0.5%), with NAGF showing higher levels of Delftia, Brevibacterium, and Bulleidia. In contrast, NCSSPs had a higher abundance of Ochrobactrum, Rhodoplanes, and Nitrospira. It was concluded that the treatments analyzed in this study induced modulations in the ileal microbiota of the chickens examined.
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Affiliation(s)
- Julia Marixara Sousa da Silva
- Veterinary and Animal Science School, Federal University of Goiás, Goiania 74605-080, Goiás, Brazil; (J.M.S.d.S.); (A.M.D.S.A.); (A.C.B.); (E.d.P.N.); (J.M.M.B.); (A.B.V.S.G.); (J.H.S.); (N.S.M.L.)
| | - Ana Maria De Souza Almeida
- Veterinary and Animal Science School, Federal University of Goiás, Goiania 74605-080, Goiás, Brazil; (J.M.S.d.S.); (A.M.D.S.A.); (A.C.B.); (E.d.P.N.); (J.M.M.B.); (A.B.V.S.G.); (J.H.S.); (N.S.M.L.)
| | - Ana Carolina Borsanelli
- Veterinary and Animal Science School, Federal University of Goiás, Goiania 74605-080, Goiás, Brazil; (J.M.S.d.S.); (A.M.D.S.A.); (A.C.B.); (E.d.P.N.); (J.M.M.B.); (A.B.V.S.G.); (J.H.S.); (N.S.M.L.)
| | | | - Eduardo de Paula Nascente
- Veterinary and Animal Science School, Federal University of Goiás, Goiania 74605-080, Goiás, Brazil; (J.M.S.d.S.); (A.M.D.S.A.); (A.C.B.); (E.d.P.N.); (J.M.M.B.); (A.B.V.S.G.); (J.H.S.); (N.S.M.L.)
| | - João Marcos Monteiro Batista
- Veterinary and Animal Science School, Federal University of Goiás, Goiania 74605-080, Goiás, Brazil; (J.M.S.d.S.); (A.M.D.S.A.); (A.C.B.); (E.d.P.N.); (J.M.M.B.); (A.B.V.S.G.); (J.H.S.); (N.S.M.L.)
| | - Alison Batista Vieira Silva Gouveia
- Veterinary and Animal Science School, Federal University of Goiás, Goiania 74605-080, Goiás, Brazil; (J.M.S.d.S.); (A.M.D.S.A.); (A.C.B.); (E.d.P.N.); (J.M.M.B.); (A.B.V.S.G.); (J.H.S.); (N.S.M.L.)
| | - José Henrique Stringhini
- Veterinary and Animal Science School, Federal University of Goiás, Goiania 74605-080, Goiás, Brazil; (J.M.S.d.S.); (A.M.D.S.A.); (A.C.B.); (E.d.P.N.); (J.M.M.B.); (A.B.V.S.G.); (J.H.S.); (N.S.M.L.)
| | - Nadja Susana Mogyca Leandro
- Veterinary and Animal Science School, Federal University of Goiás, Goiania 74605-080, Goiás, Brazil; (J.M.S.d.S.); (A.M.D.S.A.); (A.C.B.); (E.d.P.N.); (J.M.M.B.); (A.B.V.S.G.); (J.H.S.); (N.S.M.L.)
| | - Marcos Barcellos Café
- Veterinary and Animal Science School, Federal University of Goiás, Goiania 74605-080, Goiás, Brazil; (J.M.S.d.S.); (A.M.D.S.A.); (A.C.B.); (E.d.P.N.); (J.M.M.B.); (A.B.V.S.G.); (J.H.S.); (N.S.M.L.)
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Nouri A. Age-dependent development trends (models) of intestinal significant microbiota species and Eimeria oocysts in coccidia-challenged broiler chickens as affected by dietary encapsulated organic acids and anticoccidial drugs. Avian Pathol 2024; 53:264-284. [PMID: 38349388 DOI: 10.1080/03079457.2024.2319284] [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: 06/26/2023] [Accepted: 09/20/2023] [Indexed: 03/12/2024]
Abstract
ABSTRACTThe study was conducted to investigate the effect of dietary encapsulated organic acids (EOAs) and anticoccidials on the age-dependent development trend of intestinal Lactobacillus, E. coli, coliforms, and Eimeria in Eimeria spp.-infected broiler chickens from reused litter. In total, 525 mixed-sex 1-day-old broiler chickens were used in an uninfected/un-supplemented control plus a 2 (no EOA or 0.1% EOA) × 3 (no anticoccidial, 0.05% maduramicin, and 0.02% diclazuril) factorial arrangement of treatments as a completely randomized design with five replicates of 15 chickens. Results indicated that the cubic model is the best model for explaining the development trends of the intestinal microbial population in uninfected and infected chickens (affected by the EOAs and anticoccidials). Based on the cubic models, the microbial populations had development trends with a decreasing slope from 1-day-old until the early or middle finisher period. EOAs and anticoccidials, especially their simultaneous usage, improved (P < 0.05) the linear and cubic models' slope (affected negatively by Eimeria infection). A polynomial model (order = 6) was determined as the best model for explaining the EOAs and anticoccidial effects on the trend of intestinal Eimeria oocysts in infected chickens. The infection peak (which happened at 25 days) was reduced by EOAs and anticoccidials, especially their simultaneous usage. In conclusion, cubic and polynomial (order = 6) regressions are the best models fitted for explaining the microbiota and Eimeria oocysts trends, respectively. EOAs and anticoccidials, especially their simultaneous usage, had beneficial effects on the microbiota and Eimeria development trends and gastrointestinal health in coccidia-infected broiler chickens.RESEARCH HIGHLIGHTSCubic regression is the best model for explaining intestinal microbiota development.Polynomial regression is the best model for intestinal Eimeria oocysts development.Age-development trends are affected by dietary encapsulated organic acids and anticoccidials.
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Affiliation(s)
- Ali Nouri
- Department of Animal Science, Garmsar Branch, Islamic Azad University, Garmsar, Iran
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Xiong X, Lan Y, Wang Z, Xu J, Gong J, Chai X. Bacteroidales reduces growth rate through serum metabolites and cytokines in Chinese Ningdu yellow chickens. Poult Sci 2024; 103:103905. [PMID: 38870614 PMCID: PMC11225896 DOI: 10.1016/j.psj.2024.103905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/15/2024] Open
Abstract
Increasing evidence has indicated that the gut microbiome plays an important role in chicken growth traits. However, the cecal microbial taxa associated with the growth rates of the Chinese Ningdu yellow chickens are unknown. In this study, shotgun metagenomic sequencing was used to identify cecal bacterial species associated with the growth rate of the Chinese Ningdu yellow chickens. We found that nine cecal bacterial species differed significantly between high and low growth rate chickens, including three species (Succinatimonas hippei, Phocaeicola massiliensis, and Parabacteroides sp. ZJ-118) that were significantly enriched in high growth rate chickens. We identified six Bacteroidales that were significantly enriched in low growth rate chickens, including Barnesiella sp. An22, Barnesiella sp. ET7, and Bacteroidales bacterium which were key biomarkers in differentiating high and low growth rate chickens and were associated with alterations in the functional taxa of the cecal microbiome. Untargeted serum metabolome analysis revealed that 8 metabolites showing distinct enrichment patterns between high and low growth rate chickens, including triacetate lactone and N-acetyl-a-neuraminic acid, which were at higher concentrations in low growth rate chickens and were positively and significantly correlated with Barnesiella sp. An22, Barnesiella sp. ET7, and Bacteroidales bacterium. Furthermore, the results suggest that serum cytokines, such as IL-5, may reduce growth rate and are related to changes in serum metabolites and gut microbes (e.g., Barnesiella sp. An22 and Barnesiella sp. ET7). These results provide important insights into the effects of the cecal microbiome, serum metabolism and cytokines in Ningdu yellow chickens.
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Affiliation(s)
- Xinwei Xiong
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi 330032, China.
| | - Yuehang Lan
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi 330032, China
| | - Zhangfeng Wang
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi 330032, China
| | - Jiguo Xu
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi 330032, China
| | - Jishang Gong
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi 330032, China
| | - Xuewen Chai
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi 330032, China
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Riva F, McGuinness DH, McKeegan DEF, Peinado-Izaguerri J, Bruggeman G, Hermans D, Eckersall PD, McLaughlin M, Bain M. Measuring the impact of dietary supplementation with citrus or cucumber extract on chicken gut microbiota using 16s rRNA gene sequencing. Vet Res Commun 2024; 48:2369-2384. [PMID: 38780824 PMCID: PMC11315731 DOI: 10.1007/s11259-024-10417-w] [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: 02/11/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
This study investigated the effects of dietary supplements, citrus (CTS) and cucumber (CMB), on the jejunum and cecum microbiota of 14- and 28-days old broiler chickens to evaluate their impact on the gut health and assess their role as alternatives to antibiotic growth promoters (ABGPs). 16SrRNA gene sequencing revealed the overall bacterial microbiota composition was significantly affected by the gut site (p?0.001) but not by either of the dietary supplements, CTS and CMB, at both 14 and 28 days of age. However, as a result of Linear discriminant analysis (LDA) effect size (LEfSE), CTS dietary supplements significantly increased the counts of Lactobacillus (p?0.01) and decreased the counts of Enterococcus (p?0.01) and Clostridium (p?0.05) in the jejunum, whereas the counts of Blautia were increased (p?0.01) and Enterococcus were decreased (p?0.05) in the cecum at both ages. Only minor CMB effects were identified in the cecum and non in the jejunum. The use of CTS dietary supplements has been shown to be associated to the reduction of potentially pathogenic bacteria (Enterococcus and Clostridium) and to the growth of beneficial bacteria (Lactobacillus and Blautia) which are known to have positive effects on chicken health in terms of nutrients absorption, stimulation and production of short chain fatty acids (SCFAs). Therefore, this study suggests that the use of a CTS supplemented diet could promote gut health while no clear advantages have been identified with the use of CMB as a dietary supplement.
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Affiliation(s)
- Francesca Riva
- School of Health and Life Sciences, University of the West of Scotland, High St, PA1 2BE, Paisley, UK
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Bearsden Rd, G61 1QH, Glasgow, UK
- Faculty of Veterinary Medicine, University of Zagreb, Radoslava Cimermana, 10000, Zagreb, Croatia
| | - David H McGuinness
- Glasgow Polyomics, University of Glasgow, Switchback Rd, G61 1BD, Bearsden, Glasgow, UK
| | - Dorothy E F McKeegan
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Bearsden Rd, G61 1QH, Glasgow, UK
| | - Jorge Peinado-Izaguerri
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Bearsden Rd, G61 1QH, Glasgow, UK
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Ko?ice, Komensk?ho, 041 81, Ko?ice, Slovakia
- School of Biological Sciences, The University of Manchester, Oxford Rd, M13 9PT, Manchester, UK
| | | | - David Hermans
- Nutrition Sciences N. V, B-9031, Booiebos, Ghent, Belgium
| | - Peter D Eckersall
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Bearsden Rd, G61 1QH, Glasgow, UK
| | - Mark McLaughlin
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Bearsden Rd, G61 1QH, Glasgow, UK.
| | - Maureen Bain
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Bearsden Rd, G61 1QH, Glasgow, UK
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Glendinning L, Jia X, Kebede A, Oyola SO, Park JE, Park W, Assiri A, Holm JB, Kristiansen K, Han J, Hanotte O. Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia. MICROBIOME 2024; 12:138. [PMID: 39044244 PMCID: PMC11267795 DOI: 10.1186/s40168-024-01847-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 05/28/2024] [Indexed: 07/25/2024]
Abstract
BACKGROUND Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies. RESULTS Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into three enterotypes, with one particularly enriched at high altitudes. We assembled 9977 taxonomically and functionally diverse metagenome-assembled genomes. The vast majority of these were not found in a dataset of previously published chicken microbes or in the Genome Taxonomy Database. CONCLUSIONS The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argue for further discoveries in other agro-ecologies. Video Abstract.
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Affiliation(s)
- Laura Glendinning
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK.
| | - Xinzheng Jia
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Sciences and Engineering, Foshan University, Foshan, People's Republic of China.
| | - Adebabay Kebede
- CTLGH - LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
| | - Samuel O Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Jong-Eun Park
- Department of Animal Biotechnology, Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University, 63243, Jeju, Republic of Korea
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, 55365, Wanju, Republic of Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, 55365, Wanju, Republic of Korea
| | - Abdulwahab Assiri
- School of Life Sciences, the University of Nottingham, University Park, Nottingham, UK
- Department of Animal and Fisheries Production, King Faisal University, Al-Hofuf, Saudi Arabia
| | - Jacob Bak Holm
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Clinical Microbiomics, Copenhagen, Denmark
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, People's Republic of China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, People's Republic of China
| | - Olivier Hanotte
- CTLGH - LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.
- School of Life Sciences, the University of Nottingham, University Park, Nottingham, UK.
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Li X, Li J, Yuan H, Chen Y, Li S, Jiang S, Zha Xi Y, Zhang G, Lu J. Effect of supplementation with Glycyrrhiza uralensis extract and Lactobacillus acidophilus on growth performance and intestinal health in broiler chickens. Front Vet Sci 2024; 11:1436807. [PMID: 39091388 PMCID: PMC11291472 DOI: 10.3389/fvets.2024.1436807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 07/08/2024] [Indexed: 08/04/2024] Open
Abstract
Intestinal microbiota community is an important factor affecting the nutritional and health status of poultry, and its balance is crucial for improving the overall health of poultry. The study aimed to investigate the effect of dietary supplementation with Glycyrrhiza uralensis extract (GUE), Lactobacillus acidophilus (Lac) and their combination (GL) on growth performance and intestinal health in broilers in an 84-day feeding experiment. Supplementary 0.1% GUE and 4.5×107 CFU/g Lac significantly increased average daily gain (ADG), and GL (0.1% GUE and 4.5×107 CFU/g Lac) increased ADG and average daily feed intake (ADFI), and decreased feed conversion rate (FCR) in broilers aged 29 to 84 d and 1 to 84 d. Dietary GUE, Lac and GL increased the superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX) activity and decreased Malondialdehyde (MDA) content in the jejunum mucosa of broilers, and increased secretory IgA (sIgA) content in broilers at 84 d. Moreover, GUE, Lac and GL increased cecal microbial richness and diversity, and modulated microbial community composition. Both GUE and Lac reduced the harmful bacteria Epsilonbacteraeota, Helicobacter, and H. pullorum at 28 d and Proteobacteria, Escherichia, and E. coli at 84 d, while Lac and GL increased beneficial bacteria Lactobacillus and L. gallinarum at 28 d. Compared with individual supplementation, GL markedly increased the SOD activity and the sIgA content, and reduced Helicobacter and Helicobacter pullorum. In conclusion, GUE and Lactobacillus acidophilus as feed additives benefit growth performance and intestinal health, and their combined use shows an even more positive effect in broilers.
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Affiliation(s)
- Ximei Li
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
| | - Jiawei Li
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
| | - Haotian Yuan
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
| | - Yan Chen
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
| | - Shuaibing Li
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
| | - Susu Jiang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
- Department of Animal Science and Technology, Gansu Agriculture Technology College, Lanzhou, China
| | - Yingpai Zha Xi
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
| | - Guohua Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
| | - Jianxiong Lu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
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Stege PB, Schokker D, Harders F, Kar SK, Stockhofe N, Perricone V, Rebel JMJ, de Jong IC, Bossers A. Diet-induced changes in the jejunal microbiota of developing broilers reduce the abundance of Enterococcus hirae and Enterococcus faecium. BMC Genomics 2024; 25:627. [PMID: 38910254 PMCID: PMC11193906 DOI: 10.1186/s12864-024-10496-8] [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: 02/12/2024] [Accepted: 06/05/2024] [Indexed: 06/25/2024] Open
Abstract
Modern broiler breeds allow for high feed efficiency and rapid growth, which come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are affected by the composition of the gut microbiota, which in turn is influenced by diet. In this study, we therefore assessed how diet composition can affect the broiler jejunal gut microbiota. A total of 96 broiler chickens were divided into four diet groups: control, coated butyrate supplementation, medium-chain fatty acid supplementation, or a high-fibre low-protein content. Diet groups were sub-divided into age groups (4, 12 and 33 days of age) resulting in groups of 8 broilers per diet per age. The jejunum content was used for metagenomic shotgun sequencing to determine the microbiota taxonomic composition at species level. The composed diets resulted in a total of 104 differentially abundant bacterial species. Most notably were the butyrate-induced changes in the jejunal microbiota of broilers 4 days post-hatch, resulting in the reduced relative abundance of mainly Enterococcus faecium (-1.8 l2fc, Padj = 9.9E-05) and the opportunistic pathogen Enterococcus hirae (-2.9 l2fc, Padj = 2.7E-08), when compared to the control diet. This effect takes place during early broiler development, which is critical for broiler health, thus exemplifying the importance of how diet can influence the microbiota composition in relation to broiler health. Future studies should therefore elucidate how diet can be used to promote a beneficial microbiota in the early stages of broiler development.
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Affiliation(s)
- Paul B Stege
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands.
| | - Dirkjan Schokker
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Frank Harders
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Soumya K Kar
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Norbert Stockhofe
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Vera Perricone
- Department of Veterinary Medicine and Animal Science, University of Milan, Milan, Italy
| | - Johanna M J Rebel
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Ingrid C de Jong
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Alex Bossers
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
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10
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Stefanello TB, Cardinal KM, Orso C, Franceschi CH, Silva JP, Mann MB, Frazzon J, Moraes PO, Ribeiro AML. The impact of different levels of functional oil supplementation in combination with salinomycin on growth performance and intestinal microbiota of broilers undergoing Eimeria challenge: An analysis of dynamics. Res Vet Sci 2024; 172:105249. [PMID: 38579633 DOI: 10.1016/j.rvsc.2024.105249] [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: 01/25/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/07/2024]
Abstract
The effect of salinomycin sodium alone and in combination with functional oils on performance and microbiota of broiler infected Eimeria were evaluated. 512 broilers were randomly assigned to 4 treatments (8 replicates, 16 birds/pen): a Control group (any additives); Ionophore group: salinomycin supplementation at 66 ppm (SS66); Ionophore +0.075% Functional oil (FO) group (SS66 + FO supplementation at 750 ppm); and Ionophore +0.10% FO group (SS66 + FO supplementation at 1000 ppm). At 14 days of age, birds were gavaged with 1 mL of a saline solution containing sporulated oocysts of E. tenella, E. acervulina and E. maxima. Performance indices were measured weekly. At 28 days, intestinal content was collected for microbiota analysis. Broilers of Control group presented the worst performance indices. Broilers of Ionophore + FO (0.075% and 0.10%) groups exhibited a higher BW at 28 days of age. The supplementation of Ionophore +0.075% FO resulted in a higher relative proportion of Firmicutes and a lower proportion of Actinobacteria in the ileum-jejunum. Lactobacillaceae was the dominant family in the jejunal, and ileal microbiotas of broilers fed diets supplemented with Ionophore, Ionophore +0.075% FO and Ionophore +0.10% FO. The supplementation of ionophore yielded higher numbers of Lactobacillaceae, Enterobactereaceae and Cloritridiaceae in the cecal. Ionophore associated with FO controlled the Lactobacillaceae, Enterobactereaceae and Cloritridiaceae families present in the cecum. Therefore, the combination of salinomycin with functional oil showed synergistic effect on performance and modulation of intestinal microbiota of broilers challenged with Eimeria.
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Affiliation(s)
- Thaís Bastos Stefanello
- Department of Animal Science, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Kátia Maria Cardinal
- Department of Animal Science, Instituto Federal Farroupilha, Alegrete, RS, Brazil
| | - Catiane Orso
- Department of Animal Science, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Jéssica Pereira Silva
- Department of Animal Science, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Micheli Bertoni Mann
- Institute of Food Science and Technology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Jeverzon Frazzon
- Institute of Food Science and Technology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Priscila Oliveira Moraes
- Department of Animal Science and Rural Development, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
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11
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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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12
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Duangnumsawang Y, Zentek J, Vahjen W, Tarradas J, Boroojeni FG. Impact of feed additives and host-related factors on bacterial metabolites, mucosal integrity and immune response in the ileum of broilers. Vet Res Commun 2023; 47:1861-1878. [PMID: 37160636 DOI: 10.1007/s11259-023-10135-9] [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: 01/18/2023] [Accepted: 04/30/2023] [Indexed: 05/11/2023]
Abstract
The present study aimed to investigate the effect of age, breed, and sex of broilers, as well as a probiotic or phytobiotic product on mucosal morphology, bacterial metabolites, and immune traits in the ileum of broilers. A total of 2,880 one-day-old male and female broiler chicks from two breeds (Ross308® and Cobb500®) were randomly assigned to 72 pens. Broilers were offered a wheat-soybean diet without (CO), or with either a probiotic (PO; 2.4 × 109 CFU/kg of Bacillus subtilis DSM32324 and DSM32325 and B. amyloliquefaciens DSM25840) or a phytobiotic (PY; grape extract, 165 ppm procyanidin and 585 ppm polyphenols of the diet) product. The trial was conducted with a 3 × 2 × 2 factorial arrangement of diet, breed, and sex in a completely randomized design (6 replicate-pens per treatment). At day 7, 21, and 35, one chicken per pen was slaughtered for collecting ileal tissue to evaluate of histomorphology and mRNA expression, as well as ileal digesta to measure bacterial metabolites. Data were subjected to ANOVA (the main factors; age, diet, breed, and sex) and Four-Way ANOVA (interactions) using GLM procedure. Overall, the concentration of acetate and total short chain fatty acids reached the peak and lactate decreased to its lowest on day 21, but their concentrations at day 7 and 35 were similar (p > 0.05). Spermine, spermidine, and ammonia decreased after day 7, while putrescine and cadaverine increased after day 21 (p < 0.05). mRNA expression of cytokines, mucin 2 (MUC2) and claudin 5 (CLDN5) was similar; increased from day 7 to 21 and decreased afterward (p < 0.05). Villus height, crypt depth and villus surface area increased with age (p < 0.05). Acidic goblet cells (GC) number and density increased after day 21 (p < 0.05). Ross broilers showed higher D-lactate concentration and IFN-γ expression, while Cobb broilers had greater IL-4, IL-6 and TNF-α expression and higher total GC number (p < 0.05). Female displayed higher villus height and GC number and density (mixed and total GC) than male (p < 0.05). The effect of dietary treatment was not found on any investigated variables (p > 0.05). In conclusion, aging of broilers affected ileal histomorphology, cytokine expression, and barrier integrity, as well as bacterial activity. These observed impacts could be attributed to host-microbiota interaction and the direct effects of bacterial metabolites on intestinal cells and immune system.
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Affiliation(s)
- Yada Duangnumsawang
- Institute of Animal Nutrition, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Faculty of Veterinary Science, Prince of Songkla University, Hatyai, Songkhla, Thailand
| | - Jürgen Zentek
- Institute of Animal Nutrition, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Wilfried Vahjen
- Institute of Animal Nutrition, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Joan Tarradas
- ‡Institute for Food and Agricultural Research and Technology IRTA, Constantí, Spain
| | - Farshad Goodarzi Boroojeni
- Institute of Animal Nutrition, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.
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13
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Ayalew H, Wang J, Wu S, Qiu K, Tekeste A, Xu C, Lamesgen D, Cao S, Qi G, Zhang H. Biophysiology of in ovo administered bioactive substances to improve gastrointestinal tract development, mucosal immunity, and microbiota in broiler chicks. Poult Sci 2023; 102:103130. [PMID: 37926011 PMCID: PMC10633051 DOI: 10.1016/j.psj.2023.103130] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 11/07/2023] Open
Abstract
Early embryonic exogenous feeding of bioactive substances is a topic of interest in poultry production, potentially improving gastrointestinal tract (GIT) development, stimulating immunization, and maximizing the protection capability of newly hatched chicks. However, the biophysiological actions and effects of in ovo administered bioactive substances are inconsistent or not fully understood. Thus, this paper summarizes the functional effects of bioactive substances and their interaction merits to augment GIT development, the immune system, and microbial homeostasis in newly hatched chicks. Prebiotics, probiotics, and synbiotics are potential bioactive substances that have been administered in embryonic eggs. Their biological effects are enhanced by a variety of mechanisms, including the production of antimicrobial peptides and antibiotic responses, regulation of T lymphocyte numbers and immune-related genes in either up- or downregulation fashion, and enhancement of macrophage phagocytic capacity. These actions occur directly through the interaction with immune cell receptors, stimulation of endocytosis, and phagocytosis. The underlying mechanisms of bioactive substance activity are multifaceted, enhancing GIT development, and improving both the innate and adaptive immune systems. Thus summarizing these modes of action of prebiotics, probiotics and synbiotics can result in more informed decisions and also provides baseline for further research.
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Affiliation(s)
- Habtamu Ayalew
- Laboratory of Quality and Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Jing Wang
- Laboratory of Quality and Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shugeng Wu
- Laboratory of Quality and Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kai Qiu
- Laboratory of Quality and Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ayalsew Tekeste
- College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Changchun Xu
- Laboratory of Quality and Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dessalegn Lamesgen
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Sumei Cao
- Laboratory of Quality and Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guanghai Qi
- Laboratory of Quality and Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haijun Zhang
- Laboratory of Quality and Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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14
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Huang T, Han J, Liu Y, Fei M, Du X, He K, Zhao A. Dynamic distribution of gut microbiota in posthatching chicks and its relationship with average daily gain. Poult Sci 2023; 102:103008. [PMID: 37598556 PMCID: PMC10462888 DOI: 10.1016/j.psj.2023.103008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/30/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023] Open
Abstract
The colonization and development of gut microbiota are essential for the health and growth of chicks after hatching. However, the colonization and prevalence of gut microbiota have not been well characterized, and knowledge of which microbes and their relationship with average daily gain in chicks is still limited. This study characterized the dynamic succession of microbiota in the intestinal tract of chicks and investigated its relationship with daily weight gain. A total of 121 fecal samples across 7 time points from d 0 to 10 posthatching were collected from 19 chicks randomly selected from 1,950 chicks. Using 16S rRNA gene sequencing examined microbial composition of fecal samples. The observed species index of alpha diversity increased with age, gradually achieving stability at 3 d of age. The microbiota of chicks after hatching was primarily Clostridium_sensu_stricto_1 (34.49%), and its relative abundance diminishes with age. In contrast, Lactobacillus had a low relative abundance in the first 2 d after hatching and gradually increased with age. Predicted functional capacities found that the microbiota of early-stage posthatching (d 0 and 1 after hatching) was involved in metabolism, including amino acid metabolism, metabolism of cofactors and vitamins, and nitrogen metabolism. However, at the later stage posthatching (from d 3-10 after hatching), the intestinal microbial function was involved in carbohydrate metabolism, amino acid metabolism, cell growth and death, and methane metabolism. It was identified that 47 operational taxonomic units were associated with average daily gain of chicks, 12 of which were annotated with Lactobacillus and significantly positive associated with average daily gain. In addition, Clostridium_sensu_stricto_1 was significantly negatively associated with average daily gain. Taken together, we characterized the dynamic successions of intestinal microbiota in hatching chicks. The intestinal microbiota of chicks has an impact on the host average daily gain. Our findings should be instrumental in improving local chick production.
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Affiliation(s)
- Tao Huang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jie Han
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yongqi Liu
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, China
| | - Meina Fei
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xue Du
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, China
| | - Ke He
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, China
| | - Ayong Zhao
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, China.
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15
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Kim JE, Tun HM, Bennett DC, Leung FC, Cheng KM. Microbial diversity and metabolic function in duodenum, jejunum and ileum of emu (Dromaius novaehollandiae). Sci Rep 2023; 13:4488. [PMID: 36934111 PMCID: PMC10024708 DOI: 10.1038/s41598-023-31684-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/15/2023] [Indexed: 03/20/2023] Open
Abstract
Emus (Dromaius novaehollandiae), a large flightless omnivorous ratite, are farmed for their fat and meat. Emu fat can be rendered into oil for therapeutic and cosmetic use. They are capable of gaining a significant portion of its daily energy requirement from the digestion of plant fibre. Despite of its large body size and low metabolic rate, emus have a relatively simple gastroinstetinal (GI) tract with a short mean digesta retention time. However, little is known about the GI microbial diversity of emus. The objective of this study was to characterize the intraluminal intestinal bacterial community in the different segments of small intestine (duodenum, jejunum, and ileum) using pyrotag sequencing and compare that with the ceca. Gut content samples were collected from each of four adult emus (2 males, 2 females; 5-6 years old) that were free ranged but supplemented with a barley-alfalfa-canola based diet. We amplified the V3-V5 region of 16S rRNA gene to identify the bacterial community using Roche 454 Junior system. After quality trimming, a total of 165,585 sequence reads were obtained from different segments of the small intestine (SI). A total of 701 operational taxonomic units (OTUs) were identified in the different segments of small intestine. Firmicutes (14-99%) and Proteobacteria (0.5-76%) were the most predominant bacterial phyla in the small intestine. Based on species richness estimation (Chao1 index), the average number of estimated OTUs in the small intestinal compartments were 148 in Duodenum, 167 in Jejunum, and 85 in Ileum, respectively. Low number of core OTUs identified in each compartment of small intestine across individual birds (Duodenum: 13 OTUs, Jejunum: 2 OTUs, Ileum: 14 OTUs) indicated unique bacterial community in each bird. Moreover, only 2 OTUs (Escherichia and Sinobacteraceae) were identified as core bacteria along the whole small intestine. PICRUSt analysis has indicated that the detoxification of plant material and environmental chemicals seem to be performed by SI microbiota, especially those in the jejunum. The emu cecal microbiome has more genes than SI segments involving in protective or immune response to enteric pathogens. Microbial digestion and fermentation is mostly in the jejunum and ceca. This is the first study to characterize the microbiota of different compartments of the emu intestines via gut samples and not fecal samples. Results from this study allow us to further investigate the influence of the seasonal and physiological changes of intestinal microbiota on the nutrition of emus and indirectly influence the fatty acid composition of emu fat.
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Affiliation(s)
- Ji Eun Kim
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Hein M Tun
- School of Public Health, Li Ka Shing, Faculty of Medicine, HKU-Pasteur Research Pole, University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- JC School of Public Health and Primary Care, Faculty of Medicine, Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Darin C Bennett
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Animal Science Department, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Frederick C Leung
- School of Biological Sciences, Faculty of Science, University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Kimberly M Cheng
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
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16
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Pottenger S, Watts A, Wedley A, Jopson S, Darby AC, Wigley P. Timing and delivery route effects of cecal microbiome transplants on Salmonella Typhimurium infections in chickens: potential for in-hatchery delivery of microbial interventions. Anim Microbiome 2023; 5:11. [PMID: 36788638 PMCID: PMC9926694 DOI: 10.1186/s42523-023-00232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND Exposure to microbes early in life has long-lasting effects on microbial community structure and function of the microbiome. However, in commercial poultry settings chicks are reared as a single-age cohort with no exposure to adult birds which can have profound effects on microbiota development and subsequent pathogen challenge. Microbiota manipulation is a proven and promising strategy to help reduce pathogen load and transmission within broiler flocks. However, administration of microbiota transplant products in a hatchery setting may prove challenging. Effective administration strategies are dependent on key factors, such as; the age of chicks receiving interventions and mode of delivery. This study aimed to assess these two aspects to provide supporting evidence towards microbiome manipulation strategies for use in commercial hatcheries. RESULTS Manipulation of the microbiota between 4 and 72 h of hatch markedly reduced faecal shedding and colonisation with the foodborne pathogen Salmonella enterica serovar Typhimurium (ST4/74). Administration of transplant material via spray or gel drop delivery systems had minimal effect on the protection conferred with fewer birds in transplant groups shown to shed ST4/74 in the faeces compared to PBS-gavaged control birds. Analysis of the microbiome following transplantation demonstrated that all transplant groups had higher diversity and species richness than non-transplant groups during the first week of life and the early stages of infection with ST47/4.The relative abundance of the bacterium Faecalibacterium prausnitzii was significantly higher in CMT groups compared to PBS controls. The presence of F. prausnitzii was also shown to increase in PBS-challenged birds compared to unchallenged birds potentially indicating a role of this bacterium in limiting Salmonella infections. CONCLUSIONS This study demonstrated that administration of microbiome transplants, using methods that would align with hatchery practices, effectively reduced colonisation and shedding of Salmonella in chickens. Age of chicks at microbiome administration had limited effect on the diversity and composition of the microbiome and conferred protection against Salmonella infections. Traditional hatchery delivery systems, such as spray or gel-drop, are sufficient to transfer donor material, alter the microbiome and confer protection against Salmonella. This study helps highlight the opportunity for use of microbiome modification methods within the hatchery.
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Affiliation(s)
- Sian Pottenger
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
| | - Amyleigh Watts
- grid.10025.360000 0004 1936 8470Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Amy Wedley
- grid.10025.360000 0004 1936 8470Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Sue Jopson
- grid.10025.360000 0004 1936 8470Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Alistair C. Darby
- grid.10025.360000 0004 1936 8470Centre for Genomic Research, University of Liverpool, Liverpool, UK
| | - Paul Wigley
- grid.10025.360000 0004 1936 8470Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK ,grid.5337.20000 0004 1936 7603School of Veterinary Sciences, University of Bristol, Bristol, UK
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17
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Rychlik I, Karasova D, Crhanova M. Microbiota of Chickens and Their Environment in Commercial Production. Avian Dis 2023; 67:1-9. [PMID: 37140107 DOI: 10.1637/aviandiseases-d-22-00048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 01/24/2023]
Abstract
Chickens in commercial production are subjected to constant interaction with their environment, including the exchange of microbiota. In this review, we therefore focused on microbiota composition in different niches along the whole line of chicken production. We included a comparison of microbiota of intact eggshells, eggshell waste from hatcheries, bedding, drinking water, feed, litter, poultry house air and chicken skin, trachea, crop, small intestine, and cecum. Such a comparison showed the most frequent interactions and allowed for the identification of microbiota members that are the most characteristic for each type of sample as well as those that are the most widespread in chicken production. Not surprisingly, Escherichia coli was the most widely distributed species in chicken production, although its dominance was in the external aerobic environment and not in the intestinal tract. Other broadly distributed species included Ruminococcus torque, Clostridium disporicum, and different Lactobacillus species. The consequence and meaning of these and other observations are evaluated and discussed.
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Affiliation(s)
- Ivan Rychlik
- Veterinary Research Institute, Brno 621 00, Czech Republic
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18
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Cardoso Dal Pont G, Lee A, Bortoluzzi C, Farnell YZ, Gougoulias C, Kogut MH. Novel model for chronic intestinal inflammation in chickens: (2) Immunologic mechanism behind the inflammatory response. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 138:104524. [PMID: 36067905 DOI: 10.1016/j.dci.2022.104524] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Intestinal inflammation in poultry is a complex response that involves immune and intestinal cells which is still not fully understood. Thus, to better understand the mechanisms that drive the chronic intestinal inflammation in fowl we conducted an experiment applying a previously established nutritional model of low-grade chronic intestinal inflammation to evaluate cytokine and chemokine profiles in the chicken intestine. For this, we placed 90 one-day chickens into two treatments: (1) a control group (CNT) fed a corn-soybean diet, and (2) a group fed a diet high in non-starch polysaccharides (NSP). At days 14, 22, 28 and 36 of age, 6 birds from each treatment were euthanized, jejunal and ileal samples were collected for histological examination and cytokine measurements. The cytokines interferon-alpha (IFN-α), IFN-γ, interleukin-16 (IL-16), IL-10, IL-21, IL-6, macrophage-colony stimulating factor (M-CSF), chemokine C-C motif ligand 20 (CCL20), CCL4, CCL5 and vascular endothelial growth factor (VEGF) were quantified in the intestinal tissue. Histologically, both jejunum and ileum of broilers fed NSP diet showed marked infiltration of mononuclear immune cells into the villi. Further, these birds exhibited a significant (P < 0.05) increase in CCL20 concentration in the jejunum at 14d, but a dramatic reduction of M-CSF at 14 and 21d. Later at 28d and 36d, birds fed the NSP diet exhibited increased IL-16 concentration in the jejunum. Since M-CSF is a monocyte stimulatory cytokine and CCL20 a chemokine of T-cells, the reduced M-CSF and increased production of CCL20 may indicate the involvement of the adaptive immune response, specifically driven by T-cells, occurring around the third week of age in the NSP model. Lastly, as a result of the mononuclear cell infiltration and activation of T-cells, IL-16, a pro-inflammatory T-cell cytokine, increased. Therefore, the current work indicates the importance of adaptive immune cells, especially T-cells, in the chronic intestinal inflammation in broiler chicken.
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Affiliation(s)
- Gabriela Cardoso Dal Pont
- Department of Poultry Science, Texas A&M AgriLife Research, Texas A&M University, College Station, TX, USA.
| | - A Lee
- Department of Poultry Science, Texas A&M AgriLife Research, Texas A&M University, College Station, TX, USA
| | - C Bortoluzzi
- Department of Poultry Science, Texas A&M AgriLife Research, Texas A&M University, College Station, TX, USA
| | - Y Z Farnell
- Department of Poultry Science, Texas A&M AgriLife Research, Texas A&M University, College Station, TX, USA
| | - C Gougoulias
- Innovad NV/SA, Postbaan 69, 2910, Essen, Belgium
| | - M H Kogut
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, USA.
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19
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Wang L, Zhang F, Li H, Yang S, Chen X, Long S, Yang S, Yang Y, Wang Z. Metabolic and inflammatory linkage of the chicken cecal microbiome to growth performance. Front Microbiol 2023; 14:1060458. [PMID: 36910194 PMCID: PMC9995838 DOI: 10.3389/fmicb.2023.1060458] [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: 10/03/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction Chinese indigenous chicken breeds are widely used as food in China but their slow growth rate and long farming cycle has limited their industrial production. Methods In the current study we examined whether the market weights of native chicken breeds were related to specific cecal bacteria, serum metabolites and inflammatory cytokines. We examined cecal bacterial taxa using 16S rDNA analysis along with untargeted serum metabolites and serum inflammatory cytokines. Results We found that the cecal microbiota could explain 10.1% of the individual differences in chicken weights and identified key cecal bacterial genera that influenced this phenotype. The presence of Sphaerochaeta spp. improved growth performance via bovinic acid metabolism. In contrast, Synergistes and norank_f_Desulfovibrionaceae had a negative effect on growth by inducing expression of the inflammatory cytokine IL-6. Discussion We were able to link specific bacterial genera with growth promotion in chickens and this study will allow further development of their use as probiotics in these animals.
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Affiliation(s)
- Liqi Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Fuping Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Hui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Shenglin Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Xiang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Shuihua Long
- School of Public Health, Xinyu University, Xinyu, Jiangxi, China
| | - Shenghong Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Yongxian Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Zhong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
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20
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Campos PM, Miska KB, Jenkins MC, Yan X, Proszkowiec-Weglarz M. Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the duodenum and jejunum in broiler chickens. Front Microbiol 2023; 14:1147579. [PMID: 37020716 PMCID: PMC10067739 DOI: 10.3389/fmicb.2023.1147579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/27/2023] [Indexed: 04/07/2023] Open
Abstract
The intestinal disease coccidiosis, caused by Eimeria parasites, impacts nutrient absorption in broiler chickens, leading to weight gain depression and major losses in the poultry industry. To develop alternatives to antibiotics for treating infected chickens, the gut microbiota has been researched because of its association with health factors such as nutrient exchange, immune system modulation, digestive system physiology, and pathogen exclusion. The aim of this study was to determine the effect of Eimeria acervulina infection on the luminal and mucosal microbiota of both the duodenum (DuoL and DuoM) and jejunum (JejL and JejM) at multiple time points (days 3, 5, 7, 10, and 14) post-infection. 16S rRNA amplicon sequencing was utilized to characterize the microbiota and analyze differences in alpha and beta diversity between infected (IF) and control (C) birds at each time point. Alpha diversity differed between IF and C birds in DuoM and JejM microbiota. Combined with beta diversity results, DuoM microbiota appeared to be affected by infection in the longer-term, while JejM microbiota were affected in the shorter-term. Relative abundances of bacterial taxa known for short-chain fatty acid (SCFA) production, such as Lachnospiraceae, Subdoligranulum, and Peptostreptococcaceae, tended to be lower in IF birds for all four microbiota. Moreover, predicted functional abundances showed MetaCyc pathways related to SCFA production, especially butyrate, may be influenced by these differences in bacterial relative abundance. Our findings expand understanding of how Eimeria infection affects luminal and mucosal microbiota in the duodenum and jejunum, and further research on metagenomic function may provide insights on the degree of influence duodenal and jejunal bacteria have on chicken health.
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Affiliation(s)
- Philip M. Campos
- USDA-ARS Research Participation Program, Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, United States
- USDA-ARS, NEA Bioinformatics, Statistics Group, Beltsville, MD, United States
- Animal Biosciences and Biotechnology Laboratory, USDA-ARS, NEA, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Katarzyna B. Miska
- Animal Biosciences and Biotechnology Laboratory, USDA-ARS, NEA, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Mark C. Jenkins
- Animal Parasitic Diseases Laboratory, USDA-ARS, NEA, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Xianghe Yan
- Environmental Microbial and Food Safety Laboratory, USDA-ARS, NEA, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Monika Proszkowiec-Weglarz
- Animal Biosciences and Biotechnology Laboratory, USDA-ARS, NEA, Beltsville Agricultural Research Center, Beltsville, MD, United States
- *Correspondence: Monika Proszkowiec-Weglarz,
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21
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Leigh RJ, Corrigan A, Murphy RA, Walsh F. Effect of Mannan-rich fraction supplementation on commercial broiler intestinum tenue and cecum microbiota. Anim Microbiome 2022; 4:66. [PMID: 36536475 PMCID: PMC9762088 DOI: 10.1186/s42523-022-00208-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 10/15/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The broiler gastrointestinal microbiome is a potent flock performance modulator yet may also serve as a reservoir for pathogen entry into the food chain. The goal of this project was to characterise the effect of mannan rich fraction (MRF) supplementation on microbiome diversity and composition of the intestinum tenue and cecum of commercial broilers. This study also aimed to address some of the intrinsic biases that exist in microbiome studies which arise due to the extensive disparity in 16S rRNA gene copy numbers between bacterial species and due to large intersample variation. RESULTS We observed a divergent yet rich microbiome structure between different anatomical sites and observed the explicit effect MRF supplementation had on community structure, diversity, and pathogen modulation. Birds supplemented with MRF displayed significantly higher species richness in the cecum and significantly different bacterial community composition in each gastrointestinal (GI) tract section. Supplemented birds had lower levels of the zoonotic pathogens Escherichia coli and Clostridioides difficile across all three intestinum tenue sites highlighting the potential of MRF supplementation in maintaining food chain integrity. Higher levels of probiotic genera (eg. Lactobacillus and Blautia) were also noted in the MRF supplemented birds. Following MRF supplementation, the cecum displayed higher relative abundances of both short chain fatty acid (SFCA) synthesising bacteria and SCFA concentrations. CONCLUSIONS Mannan rich fraction addition has been observed to reduce the bioburden of pathogens in broilers and to promote greater intestinal tract microbial biodiversity. This study is the first, to our knowledge, to investigate the effect of mannan-rich fraction supplementation on the microbiome associated with different GI tract anatomical geographies. In addition to this novelty, this study also exploited machine learning and biostatistical techniques to correct the intrinsic biases associated with microbiome community studies to enable a more robust understanding of community structure.
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Affiliation(s)
- Robert J. Leigh
- grid.95004.380000 0000 9331 9029Antimicrobial Resistance and Microbiome Research Group, Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - Aoife Corrigan
- grid.496915.6Alltech Inc. (Alltech European Bioscience Centre), Summerhill Road, Sarney, Dunboyne, Co. Meath, Ireland
| | - Richard A. Murphy
- grid.496915.6Alltech Inc. (Alltech European Bioscience Centre), Summerhill Road, Sarney, Dunboyne, Co. Meath, Ireland
| | - Fiona Walsh
- grid.95004.380000 0000 9331 9029Antimicrobial Resistance and Microbiome Research Group, Department of Biology, Maynooth University, Co. Kildare, Ireland
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22
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Alvarenga BO, Paiva JB, Souza AI, Rodrigues DR, Tizioto PC, Ferreira AJP. Metagenomics analysis of the morphological aspects and bacterial composition of broiler feces. Poult Sci 2022; 102:102401. [PMID: 36565637 PMCID: PMC9800314 DOI: 10.1016/j.psj.2022.102401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/11/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
In this descriptive study, we used metagenomics to analyze the relationship between the morphological aspects of chicken feces and its respective bacterial compositions. The microbiota composition was determined by sequencing the V4 region of the 16S rRNA genes collected from fresh broiler feces at 19 d old. In total, 48 samples were collected and divided into 8 groups of 6 samples each. The morphological changes studied were feed passage (FP) and reddish mucus (RM). Each was classified into 3 levels of intensity: 1 (slight), 2 (moderate), or 3 (intense). Thus, the 8 groups studied were feed passage (FP-1; FP-2; FP-3), reddish mucus (RM-1; RM-2; RM-3), normal ileal feces (NIF), and cecal discharge (CD). The alpha diversity (Shannon's index) revealed that the CD group showed greater diversity, and was significantly different from FP-2, FP-3, and RM-1. The beta diversity showed that the CD group samples were more homogeneous than the ileal feces groups. The relative abundance analysis revealed that Firmicutes and Proteobacteria were the most abundant phyla in the ileal feces groups. In CD, Firmicutes and Bacteroidetes were the most abundant. The relative abundance at the genus level revealed 136 different bacterial genera. In the ileal feces groups, the two most abundant genera were Lactobacillus and Escherichia/Shigella, except in the FP-1 and RM-2 groups, which had the opposite order. Unlike the others, the CD group had a higher abundance of Bacteroides and Faecalibacterium. When comparing the NIF group with the others, significant changes were found in the fecal microbiota, with nine genera for the FP groups, 19 for the RM groups, and 61 when compared to CD. The results of the present study suggest that evaluation of fecal morphology is a fundamental task that makes it possible to act quickly and assertively, as the morphological aspects of the feces may be related to the composition and structure of fecal microbiota.
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Affiliation(s)
| | | | | | - Denise R. Rodrigues
- Department of Inspection of Animal Products, Ministry of Agriculture, Livestock and Food Supply (MAPA), Brasília, Brazil
| | | | - Antonio J. Piantino Ferreira
- School of Veterinary Medicine and Animal Science of University of São Paulo, São Paulo, Brazil,Corresponding author:
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23
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A new monocomponent xylanase improves performance, ileal digestibility of energy and nutrients, intestinal morphology, and intestinal microbiota in young broilers. J APPL POULTRY RES 2022. [DOI: 10.1016/j.japr.2022.100301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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24
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Duangnumsawang Y, Zentek J, Vahjen W, Tarradas J, Goodarzi Boroojeni F. Alterations in bacterial metabolites, cytokines, and mucosal integrity in the caecum of broilers caused by feed additives and host-related factors. Front Physiol 2022; 13:935870. [PMID: 36171972 PMCID: PMC9512067 DOI: 10.3389/fphys.2022.935870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022] Open
Abstract
A total of 2,880 one-day-old male and female broiler chicks from two breeds, Ross308 and Cobb500 were randomly assigned to 72 pens. Broilers were offered three diets: a wheat-soybean diet without (CO), or with either a probiotic (probiotic; 2.4 x 109 CFU/kg diet of Bacillus subtilis DSM32324 and DSM32325 and B. amyloliquefaciens DSM25840) or a phytobiotic (phytobiotic; grape extract with 165 ppm procyanidin and 585 ppm polyphenol) product. The trial was conducted with a 3 × 2 × 2 factorial arrangement of diet, breed and sex in a completely randomized design and consisted of 6 replicate-pens per treatment (40 birds per pen). At day 7, 21, and 35, one chicken per pen was slaughtered for caecal sampling to quantify bacterial metabolites (digesta) as well as evaluate mRNA abundance and histomorphology (tissue). Data were subjected to ANOVA using GLM procedure to evaluate age, diet, breed and sex and their interactions. Spearman’s correlation (r) was analyzed between metabolite concentration and mRNA abundance. Overall, the concentration of short chain fatty acids increased with age, while lactate decreased from day 7 to 21 (p < 0.05). The mRNA abundance of IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-17α, IL-18, IFN-γ and TGF-β2 increased with age but IL-1β and TNF-α increased in abundance from day 7 to 21 and then decreased (p < 0.05). Abundance of MUC2 and CLDN5 increased after day 21 (p < 0.05). Caecal crypt depth increased with age (p < 0.05). Acidic goblet cell (GC) number peaked at day 21 (p < 0.05), while mixed GC number was not affected by age. A few impacts of breed, diet and interactions on the investigated variables showed no meaningful biological pattern. Propionate positively correlated with all cytokines investigated (r = 0.150–0.548), except TNF-α. Lactate negatively correlated with pro-inflammatory cytokines like IL-1β (r = −0.324). Aging affected caecal histomorphology, bacterial activity and genes responsible for barrier integrity and inflammatory response. This effect could be attributed to the interaction between gut microbiota and immune system as well as the direct effect of metabolites on gut histomorphology and cytokine mRNA abundance.
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Affiliation(s)
- Yada Duangnumsawang
- Institute of Animal Nutrition, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Faculty of Veterinary Science, Prince of Songkla University, Hatyai, Songkhla, Thailand
| | - Jürgen Zentek
- Institute of Animal Nutrition, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Wilfried Vahjen
- Institute of Animal Nutrition, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Joan Tarradas
- Animal nutrition, Institute of Agrifood Research and Technology IRTA, Constantí, Spain
| | - Farshad Goodarzi Boroojeni
- Institute of Animal Nutrition, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- *Correspondence: Farshad Goodarzi Boroojeni,
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25
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Greene G, Koolman L, Whyte P, Burgess C, Lynch H, Coffey A, Lucey B, O’Connor L, Bolton D. Effect of Doxycycline Use in the Early Broiler Production Cycle on the Microbiome. Front Microbiol 2022; 13:885862. [PMID: 35875529 PMCID: PMC9301238 DOI: 10.3389/fmicb.2022.885862] [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: 02/28/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
16S rRNA amplicon sequencing was used to investigate changes in the broiler gastrointestinal tract (GIT) microbiota throughout the rearing period and in combination with antibiotic treatment. Thirty birds (from a commercial flock) were removed at multiple points throughout the rearing period on days 13, 27, and 33, euthanised, and their GIT aseptically removed and divided into upper (the crop, proventriculus, and the gizzard), middle (the duodenum, jejunum, and ileum) and lower (the large intestine, the caeca, and the cloaca) sections. In a separate commercial flock, on the same farm with similar husbandry practices and feed, doxycycline (100 mg/ml per kg body weight) was administered in drinking water between day 8 and 12 (inclusive) of the production cycle. Birds were removed on days, 13, 27, and 33 and GIT samples prepared as above. The contents of three merged samples from each GIT section were pooled (n = 60), the DNA extracted and analysed by 16S rRNA amplicon metagenomic sequencing and analysed. Major changes in the broiler microbiota were observed as the birds aged particularly with the Firmicutes/Bacteroidetes ratio (F:B) of the lower GIT. Moreover, Chao1, ACE, and Shannon indices showed the antibiotic treatment significantly altered the microbiota, and this change persisted throughout the rearing period. Further research is required to investigate the effect of these changes on bird performance, susceptibility to infections and Campylobacter carriage.
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Affiliation(s)
- Genevieve Greene
- Teagasc Food Research Centre, Dublin, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | | | - Paul Whyte
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | | | - Helen Lynch
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Department of Agriculture, Food and the Marine, Backweston, Ireland
| | - Aidan Coffey
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | | | - Declan Bolton
- Teagasc Food Research Centre, Dublin, Ireland
- *Correspondence: Declan Bolton,
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26
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Farkas V, Csitári G, Menyhárt L, Such N, Pál L, Husvéth F, Rawash MA, Mezőlaki Á, Dublecz K. Microbiota Composition of Mucosa and Interactions between the Microbes of the Different Gut Segments Could Be a Factor to Modulate the Growth Rate of Broiler Chickens. Animals (Basel) 2022; 12:ani12101296. [PMID: 35625142 PMCID: PMC9137591 DOI: 10.3390/ani12101296] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/05/2022] [Accepted: 05/16/2022] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The microbial communities inhabiting the gastrointestinal tract (GIT) of chickens are essential for the gut homeostasis, metabolism, and health status of the host animal. Previous studies exploring the relationship between chicken growth performance and gut microbiota focused mostly on gut content and excreta samples, neglecting the mucosa that promotes colonisation by distinct groups of microorganisms. These observations emphasised the importance of studying the variations between the bacterial communities of the lumen and mucosa throughout the different sections of the GIT. The novelty of this study is that we have evaluated the microbial communities of the jejunum chymus, jejunum mucosa, and caecum chymus of broiler chickens with different growth rates. Besides the bacteriota composition, the interactions between the bacteria were also evaluated. We have confirmed that the microbiota composition is influenced mostly by the sampling place. However, some body weight (BW)-related changes and interactions have also been found. In these cases, the mucosa seems to play a crucial role. Abstract The study reported here aimed to determine whether correlations can be found between the intestinal segment-related microbiota composition and the different growing intensities of broiler chickens. The bacterial community structures of three intestinal segments (jejunum chymus—JC, jejunum mucosa—JM, caecum chymus—CC) from broiler chickens with low body weight (LBW) and high body weight (HBW) were investigated. Similar to the previous results in most cases, significant differences were found in the bacteriota diversity and composition between the different sampling places. However, fewer body weight (BW)-related differences were detected. In the JM of the HBW birds, the Bacteroidetes/Firmicutes ratio (B/F) was also higher. At the genus level significant differences were observed between the BW groups in the relative abundance of Enterococcus, mainly in the JC; Bacteroides and Ruminococcaceae UCG-010, mainly in the JM; and Ruminococcaceae UCG-013, Negativibacillus, and Alistipes in the CC. These genera and others (e.g., Parabacteroides and Fournierella in the JM; Butyricoccus, Ruminiclostridium-9, and Bilophila in the CC) showed a close correlation with BW. The co-occurrence interaction results in the JC revealed a correlation between the genera of Actinobacteria (mainly with Corynebacterium) and Firmicutes Bacilli classes with different patterns in the two BW groups. In the JM of LBW birds, two co-occurring communities were found that were not identifiable in HBW chickens and their members belonged to the families of Ruminococcaceae and Lachnospiraceae. In the frame of the co-occurrence evaluation between the jejunal content and mucosa, the two genera (Trichococcus and Oligella) in the JC were found to have a significant positive correlation with other genera of the JM only in LBW chickens.
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Affiliation(s)
- Valéria Farkas
- Institute of Physiology and Nutrition, Department of Animal Nutrition and Nutritional Physiology, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary; (V.F.); (G.C.); (N.S.); (L.P.); (F.H.); (M.A.R.)
| | - Gábor Csitári
- Institute of Physiology and Nutrition, Department of Animal Nutrition and Nutritional Physiology, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary; (V.F.); (G.C.); (N.S.); (L.P.); (F.H.); (M.A.R.)
| | - László Menyhárt
- Institute of Mathematics and Basic Science, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary;
| | - Nikoletta Such
- Institute of Physiology and Nutrition, Department of Animal Nutrition and Nutritional Physiology, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary; (V.F.); (G.C.); (N.S.); (L.P.); (F.H.); (M.A.R.)
| | - László Pál
- Institute of Physiology and Nutrition, Department of Animal Nutrition and Nutritional Physiology, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary; (V.F.); (G.C.); (N.S.); (L.P.); (F.H.); (M.A.R.)
| | - Ferenc Husvéth
- Institute of Physiology and Nutrition, Department of Animal Nutrition and Nutritional Physiology, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary; (V.F.); (G.C.); (N.S.); (L.P.); (F.H.); (M.A.R.)
| | - Mohamed Ali Rawash
- Institute of Physiology and Nutrition, Department of Animal Nutrition and Nutritional Physiology, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary; (V.F.); (G.C.); (N.S.); (L.P.); (F.H.); (M.A.R.)
| | - Ákos Mezőlaki
- Agrofeed Ltd., Duna Kapu Square 10, 9022 Győr, Hungary;
| | - Károly Dublecz
- Institute of Physiology and Nutrition, Department of Animal Nutrition and Nutritional Physiology, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary; (V.F.); (G.C.); (N.S.); (L.P.); (F.H.); (M.A.R.)
- Correspondence: ; Tel.: +36-30-6418597
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Jia L, Hsu CY, Zhang X, Li X, Schilling MW, Peebles ED, Kiess AS, Zhang L. Effects of dietary bacitracin or Bacillus subtilis on the woody breast myopathy-associated gut microbiome of Eimeria spp. challenged and unchallenged broilers. Poult Sci 2022; 101:101960. [PMID: 35690000 PMCID: PMC9192972 DOI: 10.1016/j.psj.2022.101960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/26/2022] Open
Abstract
Study suggested that dysbiosis of the gut microbiota may affect the etiology of woody breast (WB). In the current study, the cecal microbiota and WB in chickens fed three different diets were investigated. A total of 504 male chicks were used in a randomized complete block design with a 3 (Diet) × 2 (Challenge) factorial arrangement of treatments with 6 replicates per treatment, 6 treatments per block, and 14 birds per treatment. The experimental diets were a control diet (corn-soybean meal basal diet), an antibiotic diet (basal diet + 6.075 mg bacitracin/kg feed), and a probiotic diet (basal diet + 2.2 × 108 CFU Bacillus subtilis PB6/kg feed). On d 14, birds that were assigned to the challenge treatment received a 20 × live cocci vaccine. On d 41, breast muscle hardness in live birds was palpated and grouped into normal (NB) and WB phenotypes. Cecal contents were collected and their bacterial compositions were analyzed and compared. The genomic DNA of the cecal contents was extracted and the V3 and V4 regions of 16S rRNA gene were amplified and sequenced via an Illumina MiSeq platform. There were no differences (P > 0.05) in Shannon and Chao 1 indexes between the challenges, diets, and phenotypes (NB vs. WB). However, there was a difference (P = 0.001) in the beta diversity of the samples between the challenged and nonchallenged groups. Relative bacterial abundance differed (false discovery rate, FDR < 0.05) between the challenge treatments, but there were no significant differences (FDR > 0.05) among the three diets or two phenotypes. Predicted energy metabolism, nucleotide metabolism, and amino acid and coenzyme biosynthesis activities only differed (q-value < 0.05) between challenged and nonchallenged groups. The cocci challenge altered the gut microbial composition on Butyricicoccus pullicaecorum, Sporobacter termitidis, and Subdoligranulum variabile, but the dietary antibiotic and probiotic treatments did not impact gut microbial composition. No strong association was found between WB myopathy and gut microbial composition in this study.
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Microbiota and Transcriptomic Effects of an Essential Oil Blend and Its Delivery Route Compared to an Antibiotic Growth Promoter in Broiler Chickens. Microorganisms 2022; 10:microorganisms10050861. [PMID: 35630307 PMCID: PMC9147064 DOI: 10.3390/microorganisms10050861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022] Open
Abstract
This study evaluated the effect of the delivery of a commercial essential oil blend containing the phytonutrients star anise, cinnamon, rosemary, and thyme oil (via different routes) on broiler chickens’ ileal and ceca microbiota and liver transcriptome compared to an antibiotic growth promoter. Eggs were incubated and allocated into three groups: non-injected, in ovo saline, and in ovo essential oil. On day 18 of incubation, 0.2 mL of essential oil in saline (dilution ratio of 2:1) or saline alone was injected into the amnion. At hatch, chicks were assigned to post-hatch treatment combinations: (A) a negative control (corn-wheat-soybean diet), (B) in-feed antibiotics, (C) in-water essential oil (250 mL/1000 L of drinking water), (D) in ovo saline, (E) in ovo essential oil, and (F) in ovo essential oil plus in-water essential oil in eight replicate cages (six birds/cage) and raised for 28 days. On days 21 and 28, one and two birds per cage were slaughtered, respectively, to collect gut content and liver tissues for further analysis. Alpha and beta diversity differed significantly between ileal and ceca samples but not between treatment groups. In-feed antibiotic treatment significantly increased the proportion of specific bacteria in the family Lachnospiraceae while reducing the proportion of bacteria in the genus Christensenellaceae in the ceca, compared to other treatments. Sex-controlled differential expression of genes related to cell signaling and tight junctions were recorded. This study provides data that could guide the use of these feed additives and a foundation for further research.
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Kairmi SH, Taha-Abdelaziz K, Yitbarek A, Sargolzaei M, Spahany H, Astill J, Shojadoost B, Alizadeh M, Kulkarni RR, Parkinson J, Sharif S. Effects of therapeutic levels of dietary antibiotics on the cecal microbiome composition of broiler chickens. Poult Sci 2022; 101:101864. [PMID: 35477134 PMCID: PMC9061639 DOI: 10.1016/j.psj.2022.101864] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 12/11/2022] Open
Abstract
Dietary antibiotics, including antibiotic growth promoters (AGPs), have been commonly used to improve health and growth of poultry. The present study investigated the effects of therapeutic doses of dietary antibiotics, including bacitracin methylene disalicylate (BMD), penicillin G potassium (PP) and an ionophore (salinomycin, SA), on the cecal microbiome of chickens. BMD and SA treatments were given as dietary supplements from d 1 to 35 of age. The SAPP (salinomycin+ penicillin G potassium) group was given SA as a dietary supplement from d 1 to 35 of age and PP was added to drinking water from d 19 to 24 of age to simulate common practices for control of necrotic enteritis in broilers. The cecal contents were collected from all treatment groups on d 10, 24, and 35 of age and DNA was extracted for metagenomic analysis of the cecal microbiome. The results revealed that dietary or water supplementation of therapeutic levels of antibiotics and ionophores to chickens significantly altered the cecal microbial homeostasis during different stages of the chicken life. The alpha diversity analysis showed that BMD, SA, and SAPP treatments decreased diversity and evenness of the cecal microbiome of treated chickens on d 10 of age. Species richness was also reduced on d 35 following treatment with BMD. Beta diversity analyses revealed that SAPP and BMD induced significant changes in the relative abundance of Gram-positive and -negative bacteria on d 10, while no significant differences were observed on d 24. On d 35, the non-treated control group had higher relative abundance of unclassified Gram-positive and -negative bacteria compared to SA, SAPP, and BMD treatment groups. Overall, despite their beneficial role in controlling necrotic enteritis outbreaks, the findings of this study highlight the potential negative effects of dietary supplementation of therapeutic levels of antibiotics on the gut microbiome and suggest that adjusting gut bacteria may be required to restore microbial richness and diversity of the gut microbiome following treatment with these antibiotics.
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Glendinning L, Chintoan-Uta C, Stevens MP, Watson M. Effect of cecal microbiota transplantation between different broiler breeds on the chick flora in the first week of life. Poult Sci 2021; 101:101624. [PMID: 34936955 PMCID: PMC8704443 DOI: 10.1016/j.psj.2021.101624] [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: 09/15/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/30/2022] Open
Abstract
The cecal microbiota plays numerous roles in chicken health and nutrition. Where such microbiota differs between lines exhibiting distinct phenotypes, microbiota transplantation offers scope to dissect the role of gut microbial communities in those traits. However, the composition and stability of transplants over time is relatively ill-defined and varying levels of success have been reported. In this study, we transplanted cecal contents from adult Roslin broilers into chicks from a different broiler line. Within <12 h posthatch, Ross 308 chicks received an oral gavage of cecal contents (n = 26) or a PBS control (n = 24). Cecal contents samples were collected postmortem from birds on d 1, 2, 3, 4, and 7 posthatch. DNA was extracted from these samples and the transplant inoculum and the V4 region of the 16S rRNA gene was amplified and sequenced. The cecal microbiota of chickens receiving the microbiota transplant was significantly different in composition and significantly richer and more diverse, in comparison to control birds. At the final timepoint (d 7), of the 150 Operational Taxonomic Units (OTUs) that were >0.1% abundant (average) in the donor sample, 137 were detected in the treated group (75 were >0.1% abundant (average)) while only 88 were detected in the control group (29 were >0.1% abundant (average)). Our data therefore suggests that stable transplantation of the cecal microbiota between lines is achievable using the methods described in this paper.
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Affiliation(s)
- Laura Glendinning
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom.
| | - Cosmin Chintoan-Uta
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - Mark P Stevens
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
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Schokker D, Visscher J, Woelders H. Changes in Blood Metabolites, Intestinal Microbiota Composition and Gene Expression of 95 Weeks Old Laying Hens Differing in Egg Production and Egg Breaking Strength. Animals (Basel) 2021; 11:ani11113012. [PMID: 34827745 PMCID: PMC8614445 DOI: 10.3390/ani11113012] [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: 09/15/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The average cycle of laying hens is prolonged by improving one or more aspects, including genetics, nutrition, and management. Yet, this prolongation needs to go hand-in-hand with laying hens staying vital. Our objective was to explore hen vitality at an age of 95 weeks in association with performance parameters (egg production and breaking strength). To this end, we measured metabolism and disease indicators in blood, microbiota composition and diversity in different gut segments, and the biological activity of the small intestine. We observed that 12% of the hens developed certain aberrations. Additionally, five metabolites were significantly associated to these aberrations, and two metabolites to the performance parameters. In the small intestine we observed that in the production groups the physical barrier function was affected, whereas in the breaking strength group the immune function was affected. Taken together, these data show that hen vitality at later ages can still be improved and we provided data on a molecular level that could be used in future endeavors to improve animal health and welfare. Abstract Herein, we investigated to what extent molecular phenotypes of the systemic level (blood) and local (intestine) are associated with the performance of laying hens at 95 weeks of age. After the trial had run for 95 weeks, two performance groups were generated, i.e., egg production (PROD) and egg breaking strength (BS). A subset of 21 cages, 116 hens, was measured to indicate the metabolism and disease status. Additionally, a focus group (four cages) was made to perform molecular phenotyping in the intestine. A notifiable observation made during the post-mortem dissection was that approximately 12% of the birds at 95 weeks had developed certain aberrations and/or impairments (denoted as organ morbidity). At the systemic level, we observed five metabolites (γGT, triglycerides, HDL, glucose, and cholesterol) significantly associated to organ morbidity, and only two metabolites (urea and aspartate aminotransferase) to the performance phenotypes. At the local level, when comparing high PROD vs. low PROD, we observed differentially expressed genes involved in cell cycle processes and the extracellular matrix. When comparing high BS vs. low BS differentially, expressed genes were observed mainly involved in immune and cell cycle-related processes. This knowledge is crucial for developing novel strategies of keeping laying hens vital.
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Affiliation(s)
- Dirkjan Schokker
- Wageningen Livestock Research, 6708 PB Wageningen, The Netherlands
| | - Jeroen Visscher
- Hendrix Genetics Research, Technology & Services B.V., 5831 CK Boxmeer, The Netherlands
| | - Henri Woelders
- Wageningen Livestock Research, 6708 PB Wageningen, The Netherlands
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Stamilla A, Ruiz-Ruiz S, Artacho A, Pons J, Messina A, Lucia Randazzo C, Caggia C, Lanza M, Moya A. Analysis of the Microbial Intestinal Tract in Broiler Chickens during the Rearing Period. BIOLOGY 2021; 10:biology10090942. [PMID: 34571819 PMCID: PMC8469170 DOI: 10.3390/biology10090942] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 02/07/2023]
Abstract
Gut microbiota contributes to animal health. However, identifying which microorganisms or associated functions are involved remains, still, difficult to assess. In the present study, the microbiota of healthy broiler chickens, under controlled diet and farm conditions, was investigated by 16S rRNA gene sequencing in four intestine segments and at four ages. In detail, 210 Ross-308 male chickens were raised according to the EU guidelines and fed on a commercial diet. The duodenum, jejunum, ileum, and caecum microbiota were analyzed at 11, 24, 35, and 46 days of life. Although the microbial composition was revealed as homogeneous 11 days after chicks hatched, it was found to be similar in the proximal intestine segments and different in ileum and caecum, where almost the same genera and species were detected with different relative abundances. Although changes during the later growth stage were revealed, each genus remained relatively unchanged. Lactobacillus mostly colonized the upper tract of the intestine, whereas the Escherichia/Shigella genus the ileum. Clostridium and Bacteroides genera were predominant in the caecum, where the highest richness of bacterial taxa was observed. We also analyze and discuss the predicted role of the microbiota for each intestine segment and its potential involvement in nutrient digestion and absorption.
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Affiliation(s)
- Alessandro Stamilla
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), University of Catania, 95123 Catania, Italy; (A.S.); (C.L.R.); (C.C.); (M.L.)
| | - Susana Ruiz-Ruiz
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), 46020 València, Spain; (A.A.); (J.P.)
- Correspondence: (S.R.-R.); (A.M.)
| | - Alejandro Artacho
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), 46020 València, Spain; (A.A.); (J.P.)
| | - Javier Pons
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), 46020 València, Spain; (A.A.); (J.P.)
| | | | - Cinzia Lucia Randazzo
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), University of Catania, 95123 Catania, Italy; (A.S.); (C.L.R.); (C.C.); (M.L.)
| | - Cinzia Caggia
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), University of Catania, 95123 Catania, Italy; (A.S.); (C.L.R.); (C.C.); (M.L.)
| | - Massimiliano Lanza
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), University of Catania, 95123 Catania, Italy; (A.S.); (C.L.R.); (C.C.); (M.L.)
| | - Andrés Moya
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), 46020 València, Spain; (A.A.); (J.P.)
- Instituto de Biología Integrativa de Sistemas (I2Sysbio), Universitat de València and Consejo Superior de Investigaciones Científicas (CSIC), 46980 València, Spain
- Correspondence: (S.R.-R.); (A.M.)
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Zhou Q, Lan F, Li X, Yan W, Sun C, Li J, Yang N, Wen C. The Spatial and Temporal Characterization of Gut Microbiota in Broilers. Front Vet Sci 2021; 8:712226. [PMID: 34527716 PMCID: PMC8435590 DOI: 10.3389/fvets.2021.712226] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/03/2021] [Indexed: 01/01/2023] Open
Abstract
The gut microbiota of chickens plays an important role in host physiology. However, the colonization and prevalence of gut microbiota have not been well-characterized. Here, we performed 16S rRNA gene sequencing on the duodenal, cecal and fecal microbiota of broilers at 1, 7, 21, and 35 days of age and characterized the dynamic succession of microbiota across the intestinal tract. Our results showed that Firmicutes was the most abundant phylum detected in each gut site at various ages, while the microbial diversity and composition varied among the duodenum, cecum, and feces at different ages. The microbial diversity and complexity of the cecal microbiota increased with age, gradually achieving stability at 21 days of age. As a specific genus in the cecum, Clostridium_sensu_stricto_1 accounted for 83.50% of the total abundance at 1 day of age, but its relative abundance diminished with age. Regarding the feces, the highest alpha diversity was observed at 1 day of age, significantly separated from the alpha diversity of other ages. In addition, no significant differences were observed in the alpha diversity of duodenal samples among 7, 21, and 35 days of age. The predominant bacterium, Lactobacillus, was relatively low (0.68–6.04%) in the intestinal tract of 1-day-old chicks, whereas its abundance increased substantially at 7 days of age and was higher in the duodenum and feces. Escherichia-Shigella, another predominant bacterium in the chicken intestinal tract, was also found to be highly abundant in fecal samples, and the age-associated dynamic trend coincided with that of Lactobacillus. In addition, several genera, including Blautia, Ruminiclostridium_5, Ruminococcaceae_UCG-014, and [Ruminococcus]_torques_group, which are related to the production of short-chain fatty acids, were identified as biomarker bacteria of the cecum after 21 days of age. These findings shed direct light on the temporal and spatial dynamics of intestinal microbiota and provide new opportunities for the improvement of poultry health and production.
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Affiliation(s)
- Qianqian Zhou
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Fangren Lan
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Xiaochang Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Wei Yan
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Chaoliang Wen
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
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Such N, Farkas V, Csitári G, Pál L, Márton A, Menyhárt L, Dublecz K. Relative Effects of Dietary Administration of a Competitive Exclusion Culture and a Synbiotic Product, Age and Sampling Site on Intestinal Microbiota Maturation in Broiler Chickens. Vet Sci 2021; 8:vetsci8090187. [PMID: 34564581 PMCID: PMC8472864 DOI: 10.3390/vetsci8090187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 01/01/2023] Open
Abstract
In this research, the effects of early post-hatch inoculation of a competitive exclusion product (Br) and the continuous feeding of a synbiotic supplement (Sy) containing probiotic bacteria, yeast, and inulin on the production traits and composition of ileal chymus (IC), ileal mucosa (IM), and caecal chymus (CC) microbiota of broiler chickens were evaluated. The dietary treatments had no significant effects on the pattern of intestinal microbiota or production traits. The digestive tract bacteriota composition was affected mostly by the sampling place and age of birds. The dominant family of IC was Lactobacillaceae, without change with the age. The abundance of the two other major families, Enterococcaceae and Lachnospiraceae decreased with the age of birds. In the IM, Clostridiaceae was the main family in the first three weeks. Its ratio decreased later and Lactobacillaceae became the dominant family. In the CC, Ruminococcaceae and Lachnospiraceae were the main families with decreasing tendency in the age. In IC, Br treatment decreased the abundance of genus Lactobacillus, and both Br and Sy increased the ratio of Enterococcus at day 7. In all gut segments, a negative correlation was found between the IBD antibody titer levels and the ratio of genus Leuconostoc in the first three weeks, and a positive correlation was found in the case of Bifidobacterium, Rombutsia, and Turicibacter between day 21 and 40.
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Affiliation(s)
- Nikoletta Such
- Institute of Physiology and Nutrition, Department of Animal Nutrition and Nutritional Physiology, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary; (N.S.); (V.F.); (G.C.); (L.P.); (A.M.)
| | - Valéria Farkas
- Institute of Physiology and Nutrition, Department of Animal Nutrition and Nutritional Physiology, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary; (N.S.); (V.F.); (G.C.); (L.P.); (A.M.)
| | - Gábor Csitári
- Institute of Physiology and Nutrition, Department of Animal Nutrition and Nutritional Physiology, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary; (N.S.); (V.F.); (G.C.); (L.P.); (A.M.)
| | - László Pál
- Institute of Physiology and Nutrition, Department of Animal Nutrition and Nutritional Physiology, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary; (N.S.); (V.F.); (G.C.); (L.P.); (A.M.)
| | - Aliz Márton
- Institute of Physiology and Nutrition, Department of Animal Nutrition and Nutritional Physiology, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary; (N.S.); (V.F.); (G.C.); (L.P.); (A.M.)
| | - László Menyhárt
- Institute of Technology, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary;
| | - Károly Dublecz
- Institute of Physiology and Nutrition, Department of Animal Nutrition and Nutritional Physiology, Georgikon Campus, Deák Ferenc Street 16, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary; (N.S.); (V.F.); (G.C.); (L.P.); (A.M.)
- Correspondence: ; Tel.: +36-30-6418597
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Yang C, Diarra MS, Choi J, Rodas-Gonzalez A, Lepp D, Liu S, Lu P, Mogire M, Gong J, Wang Q, Yang C. Effects of encapsulated cinnamaldehyde on growth performance, intestinal digestive and absorptive functions, meat quality and gut microbiota in broiler chickens. Transl Anim Sci 2021; 5:txab099. [PMID: 34222827 PMCID: PMC8252029 DOI: 10.1093/tas/txab099] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023] Open
Abstract
Essential oils are potential antimicrobial alternatives and their applications in animal feeds are limited due to their fast absorption in the upper gastrointestinal tract. This study investigated the effects of encapsulated cinnamaldehyde (CIN) at 50 mg/kg or 100 mg/kg on the growth performance, organ weights, meat quality, intestinal morphology, jejunal gene expression, nutrient digestibility, and ileal and cecal microbiota. A total of 320 male day-old broiler Cobb-500 chicks were randomly allocated to four treatments with eight pens per treatment (10 birds per pen): 1) basal diet (negative control, NC); 2) basal diet supplemented with 30 mg/kg avilamycin premix (positive control, PC); 3) basal diet with 50 mg/kg encapsulated CIN (EOL); 4) basal diet with 100 mg/kg encapsulated CIN (EOH). Despite birds fed EOH tended to increase (P = 0.05) meat pH at 24 h, all pH values were normal. Similar to PC group, meats from birds fed EOL and EOH showed a reduced (P < 0.05) Warner-Bratzler force shear (WBFS) compared to the NC group. The highest villus to crypt ratios (VH/CD; P < 0.05) were observed in broilers fed either EOL or EOH, with an average of 14.67% and 15.13% in the duodenum and 15.13% and 13.58% in the jejunum, respectively. For jejunal gene expressions, only six out of the 11 studied genes showed statistically significant differences among the dietary treatments. Gene expressions of cationic amino acid transporter 1 (CAT-1) and neutral amino acid transporter 1 (B0AT-1) were upregulated in EOH-fed birds compared to PC and NC-fed birds (P < 0.05), respectively; while the expression of proliferating cell nuclear antigen (PCNA) was downregulated in EOL-fed birds when compared to NC birds (P < 0.05). Nonetheless, the expressions of cadherin 1 (CDH-1), zonula occludens 1 (ZO-1), and maltase-glucoamylase (MG) were all upregulated (P < 0.05) in EOH-fed birds compared to PC-fed birds. The apparent ileal digestibility (AID) of dry matter, crude protein, crude fat and of all 18 tested amino acids increased in EOL-fed birds (P < 0.01). Additionally, relative abundances (%) of ileal Proteobacteria decreased, while ileal and cecal Lactobacillus increased in EOH-fed birds (P < 0.05). In conclusion, dietary encapsulated CIN improved meat quality and gut health by reducing meat WBFS, increasing VH/CD in intestines, jejunal gene expressions, AID of nutrients and beneficial ileal and cecal microbiota composition.
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Affiliation(s)
- Chongwu Yang
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- Guelph Research and Development Centre, Agriculture Agri-Food Canada, Guelph, Ontario N1G 5C9, Canada
| | - Moussa S Diarra
- Guelph Research and Development Centre, Agriculture Agri-Food Canada, Guelph, Ontario N1G 5C9, Canada
| | - Janghan Choi
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Argenis Rodas-Gonzalez
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Dion Lepp
- Guelph Research and Development Centre, Agriculture Agri-Food Canada, Guelph, Ontario N1G 5C9, Canada
| | - Shangxi Liu
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Peng Lu
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Marion Mogire
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Joshua Gong
- Guelph Research and Development Centre, Agriculture Agri-Food Canada, Guelph, Ontario N1G 5C9, Canada
| | - Qi Wang
- Guelph Research and Development Centre, Agriculture Agri-Food Canada, Guelph, Ontario N1G 5C9, Canada
| | - Chengbo Yang
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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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: 29] [Impact Index Per Article: 9.7] [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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16S rRNA Sequencing Analysis of the Gut Microbiota in Broiler Chickens Prophylactically Administered with Antimicrobial Agents. Antibiotics (Basel) 2021; 10:antibiotics10020146. [PMID: 33540533 PMCID: PMC7912790 DOI: 10.3390/antibiotics10020146] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/12/2022] Open
Abstract
In poultry production, gut microbiota (GM) plays a pivotal role and influences different host functions related to the efficiency of production performances. Antimicrobial (AM) use is one of the main factors affecting GM composition and functions. Although several studies have focused their attention on the role of AMs as growth promoters in the modulation of GM in broilers, the consequences of higher AM concentrations administered during prophylactic treatments need to be better elucidated. For this purpose, 16S rRNA gene sequencing was performed to evaluate the impact of different prophylactic AM protocols on the composition and diversity of the broiler GM. Diversity analysis has shown that AM treatment significantly affects alpha diversity in ileum and beta diversity in both ileum and caecum. In ileal samples, the Enterobacteriaceae family has been shown to be particularly affected by AM treatments. AMs have been demonstrated to affect GM composition in broiler. These findings indicate that withdrawal periods were not enough for the restoral of the original GM. Further studies are needed for a better elucidation of the negative effects caused by an altered GM in broilers.
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Pollock J, Low AS, McHugh RE, Muwonge A, Stevens MP, Corbishley A, Gally DL. Alternatives to antibiotics in a One Health context and the role genomics can play in reducing antimicrobial use. Clin Microbiol Infect 2020; 26:1617-1621. [PMID: 32220638 DOI: 10.1016/j.cmi.2020.02.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/19/2020] [Accepted: 02/22/2020] [Indexed: 01/16/2023]
Abstract
BACKGROUND This review follows on from the International Conference on One Health Antimicrobial Resistance (ICOHAR 2019), where strategies to improve the fundamental understanding and management of antimicrobial resistance at the interface between humans, animals and the environment were discussed. OBJECTIVE This review identifies alternatives to antimicrobials in a One Health context, noting how advances in genomic technologies are assisting their development and enabling more targeted use of antimicrobials. SOURCES Key articles on the use of microbiota modulation, livestock breeding and gene editing, vaccination, antivirulence strategies and bacteriophage therapy are discussed. CONTENT Antimicrobials are central for disease control, but reducing their use is paramount as a result of the rise of transmissible antimicrobial resistance. This review discusses antimicrobial alternatives in the context of improved understanding of fundamental host-pathogen and microbiota interactions using genomic tools. IMPLICATIONS Host and microbial genomics and other novel technologies play an important role in devising disease control strategies for healthier animals and humans that in turn reduce our reliance on antimicrobials.
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Affiliation(s)
- J Pollock
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | - A S Low
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | - R E McHugh
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, Scotland, UK; Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - A Muwonge
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | - M P Stevens
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | - A Corbishley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | - D L Gally
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK.
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Maki JJ, Bobeck EA, Sylte MJ, Looft T. Eggshell and environmental bacteria contribute to the intestinal microbiota of growing chickens. J Anim Sci Biotechnol 2020; 11:60. [PMID: 32537141 PMCID: PMC7288515 DOI: 10.1186/s40104-020-00459-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/08/2020] [Indexed: 12/14/2022] Open
Abstract
Background The initial intestinal microbiota acquired from different sources has profound impacts on animal health and productivity. In modern poultry production practices, the source(s) of the establishing microbes and their overall contribution during development of gastrointestinal tract communities are still unclear. Using fertilized eggs from two independent sources, we assessed the impact of eggshell- and environmental-associated microbial communities on the successional processes and bacterial community structure throughout the intestinal tract of chickens for up to 6 weeks post-hatch. Results Culturing and sequencing techniques identified a viable, highly diverse population of anaerobic bacteria on the eggshell. The jejunal, ileal, and cecal microbial communities for the egg-only, environment-only, and conventionally raised birds generally displayed similar successional patterns characterized by increasing community richness and evenness over time, with strains of Enterococcus, Romboutsia, and unclassified Lachnospiraceae abundant for all three input groups in both trials. Bacterial community structures differed significantly based on trial and microbiota input with the exception of the egg-exposed and conventional birds in the jejunum at week 1 and the ileum at week 6. Cecal community structures were different based on trial and microbiota input source, and cecal short-chain fatty acid profiles at week 6 highlighted functional differences as well. Conclusion We identified distinct intestinal microbial communities and differing cecal short-chain fatty acid profiles between birds exposed to the microbiota associated with either the eggshell or environment, and those of conventionally hatched birds. Our data suggest the eggshell plays an appreciable role in the development of the chicken intestinal microbiota, especially in the jejunum and ileum where the community structure of the eggshell-only birds was similar to the structure of conventionally hatched birds. Our data identify a complex interplay between the eggshell and environmental microbiota during establishment and succession within the chicken gut. Further studies should explore the ability of eggshell- and environment-derived microbes to shape the dynamics of succession and how these communities can be targeted through interventions to promote gut health and mitigate food-borne pathogen colonization in poultry.
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Affiliation(s)
- Joel J Maki
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, US Department of Agriculture, 1920 Dayton Ave, Ames, IA 50010 USA.,Interdepartmental Microbiology Graduate Program, Iowa State University
- , Ames, IA 50011 USA.,Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN 37830 USA
| | | | - Matthew J Sylte
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, US Department of Agriculture, 1920 Dayton Ave, Ames, IA 50010 USA
| | - Torey Looft
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, US Department of Agriculture, 1920 Dayton Ave, Ames, IA 50010 USA
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Williams T, Athrey G. Cloacal Swabs Are Unreliable Sources for Estimating Lower Gastro-Intestinal Tract Microbiota Membership and Structure in Broiler Chickens. Microorganisms 2020; 8:E718. [PMID: 32408567 PMCID: PMC7285018 DOI: 10.3390/microorganisms8050718] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/22/2020] [Accepted: 05/09/2020] [Indexed: 01/04/2023] Open
Abstract
The gastrointestinal microbiota of chickens plays a central role in health and performance. Cloacal swabs, due to their proximity to the ceca (a vital site of functional activity), are an alternative, non-invasive method used for assaying microbial communities and might be a viable option for longitudinal studies. In this study, the microbiota of twenty paired cecal content and cloacal swab samples representing two dietary treatments was assessed using 16S rRNA V4 hypervariable region sequencing and was analyzed using the MOTHUR pipeline, Phyloseq, and Vegan packages. Paired t-test and Wilcoxon signed-rank tests showed significant differences in the Chao1 index (p-value <0.0001 and p-value <0.0001, respectively) but not in the Inverse Simpson species diversity estimator (p-value = 0.06763 and p-value = 0.06021, respectively) between the cecal content and cloacal swabs. β-diversity between the cloacal swabs and cecal microbiota also showed significant differences using PERMANOVA, HOMOVA, and weighted UniFrac testing (p-values < 0.001). Based on a paired sample analysis, this study provided evidence of the high inter-individual variation and randomness of cloacal microbiota, in contrast to cecal microbiota. Our findings indicated that cloacal swabs do not approximate the α or β diversity of cecal samples and are not suitable for longitudinal studies of gut microbiota.
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Affiliation(s)
- Travis Williams
- Department of Poultry Science, Texas A&M University, 101 Kleberg Center, 2472 TAMU, College Station, TX 77843-2472, USA;
| | - Giridhar Athrey
- Department of Poultry Science, Texas A&M University, 101 Kleberg Center, 2472 TAMU, College Station, TX 77843-2472, USA;
- Faculty of Ecology and Evolutionary Biology, Texas A&M University, 101 Kleberg Center, 2472 TAMU, College Station, TX 77843-2472, USA
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