201
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Jacobs L, McMahon BH, Berendzen J, Longmire J, Gleasner C, Hengartner NW, Vuyisich M, Cohn JR, Jenkins M, Bartlow AW, Fair JM. California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals. PLoS One 2019; 14:e0225858. [PMID: 31825977 PMCID: PMC6905524 DOI: 10.1371/journal.pone.0225858] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/13/2019] [Indexed: 12/02/2022] Open
Abstract
Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to deal with higher amounts of bacteria in their primary diet of carcasses in varying levels of decay. These observations motivate us to present an analysis of captive and healthy California condor (Gymnogyps californianus) microbiomes to characterize a population raised together under similar conditions. Shotgun metagenomic DNA sequences were analyzed from fecal and cloacal samples of captive birds. Classification of shotgun DNA sequence data with peptide signatures using the Sequedex package provided both phylogenetic and functional profiles, as well as individually annotated reads for targeted confirmatory analysis. We observed bacterial species previously associated with birds and gut microbiomes, including both virulent and opportunistic pathogens such as Clostridium perfringens, Propionibacterium acnes, Shigella flexneri, and Fusobacterium mortiferum, common flora such as Lactobacillus johnsonii, Lactobacillus ruminus, and Bacteroides vulgatus, and mucosal microbes such as Delftia acidovorans, Stenotrophomonas maltophilia, and Corynebacterium falsnii. Classification using shotgun metagenomic reads from phylogenetic marker genes was consistent with, and more specific than, analysis based on 16S rDNA data. Classification of samples based on either phylogenetic or functional profiles of genomic fragments differentiated three types of samples: fecal, mature cloacal and immature cloacal, with immature birds having approximately 40% higher diversity of microbes.
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Affiliation(s)
- Lindsey Jacobs
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Benjamin H. McMahon
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Joel Berendzen
- GenerisBio, Santa Fe, New Mexico, United States of America
| | - Jonathan Longmire
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Cheryl Gleasner
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | | | | | - Judith R. Cohn
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Marti Jenkins
- The Peregrine Fund, Boise, Idaho, United States of America
| | - Andrew W. Bartlow
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jeanne M. Fair
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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202
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Shi S, Qi Z, Gu B, Cheng B, Tu J, Song X, Shao Y, Liu H, Qi K, Li S. Analysis of high-throughput sequencing for cecal microbiota diversity and function in hens under different rearing systems. 3 Biotech 2019; 9:438. [PMID: 31750036 DOI: 10.1007/s13205-019-1970-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/23/2019] [Indexed: 01/16/2023] Open
Abstract
Rearing systems play an important role in animal welfare, health and the composition of the gut microbiome. Therefore, the purpose of this study was to investigate the effects of different rearing systems on the composition and function of cecal microbiota in chickens. The 120-day-old Lohmann hens of cage rearing systems (CRS) and free-range systems (FRS) were studied. The cecal bacterial populations of hens were surveyed by high-throughput sequencing (HTS) of the bacterial 16S rRNA hypervariable region V3-V4 combined with metagenomic sequencing analysis. The 16S rRNA sequencing analysis showed that the cecal microbiota differed between the FRS and CRS. The three most abundant bacteria phyla in the two systems were the Bacteroidetes (> 48%), Firmicutes (> 37%), and Proteobacteria (> 6%), the Deferribacteres (> 2.4%) were found in FRS and almost absent in CRS (< 0.01%). The three most abundant genera were the Bacteroides, Rikenellaceae_RC9, and Faecalibacterium, and we found relative abundance of the Parabacteroides (P < 0.05), Prevotellaceae_Ga6A1 (P < 0.01), unclassified Proteobacteria (P < 0.05), and unclassified Spirochaetaceae (P < 0.01) was greater in FRS, whereas abundance of Faecalibacterium, Ruminococcaceae, and Helicobacter was greater in CRS (P < 0.05). Functional gene classification of metagenomic sequencing suggested that energy production and conversion, carbohydrate transport and metabolism, as well as amino acid transport and metabolism were significantly more abundant in FRS, and we identified a range of antibiotic resistance categories in gut microbes of hens reared under both systems. We confirmed differences in microbe gut composition and function in hens reared using two contrasting systems, and ARGs were also identified in the microbiota of these hens. This work has produced new data for laying hens in different production systems and increased the understanding of intestinal microorganisms in laying hens.
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Affiliation(s)
- Shuiqin Shi
- 1Present Address: Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science 11 and Technology, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui People's Republic of China
| | - Zhao Qi
- 2School of Information and Computer, Anhui Agricultural University, Hefei, 230036 People's Republic of China
| | - Bintao Gu
- 1Present Address: Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science 11 and Technology, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui People's Republic of China
| | - Baoyan Cheng
- 1Present Address: Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science 11 and Technology, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui People's Republic of China
| | - Jian Tu
- 1Present Address: Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science 11 and Technology, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui People's Republic of China
| | - Xiangjun Song
- 1Present Address: Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science 11 and Technology, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui People's Republic of China
| | - Yin Shao
- 1Present Address: Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science 11 and Technology, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui People's Republic of China
| | - Hongmei Liu
- 1Present Address: Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science 11 and Technology, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui People's Republic of China
| | - Kezong Qi
- 1Present Address: Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science 11 and Technology, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui People's Republic of China
| | - Shaowen Li
- 2School of Information and Computer, Anhui Agricultural University, Hefei, 230036 People's Republic of China
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203
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Kothari D, Lee WD, Niu KM, Kim SK. The Genus Allium as Poultry Feed Additive: A Review. Animals (Basel) 2019; 9:E1032. [PMID: 31779230 PMCID: PMC6940947 DOI: 10.3390/ani9121032] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 01/01/2023] Open
Abstract
The genus Allium, belonging to the family Amaryllidaceae has been known since ancient times for their therapeutic potentials. As the number of multi-drug resistant infections has increased due to in-feed antibiotic usage in poultry, the relevance of alliums as feed additives has been critically assessed. Garlic and the other Allium species, such as onions, leek, shallot, scallion, and chives, have been characterized to contain a plethora of bioactive compounds such as organosulfur compounds, polyphenols, saponins, fructans, and fructo-oligosaccharides. Consequently, alliums have been validated to confer antioxidant, antibacterial, antiviral, immunostimulatory, gut homeostasis, and lipid- as well as cholesterol-lowering properties in poultry. This review intends to summarize recent progress on the use of edible alliums as poultry feed additives, their beneficial effects, and the underlying mechanisms of their involvement in poultry nutrition. Perspectives for future research and limitations are also briefly discussed.
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Affiliation(s)
- Damini Kothari
- Department of Animal Science and Technology, Konkuk University, Seoul 05029, Korea
| | - Woo-Do Lee
- Department of Animal Science and Technology, Konkuk University, Seoul 05029, Korea
| | - Kai-Min Niu
- Institute of Biological Resource, Jiangxi Academy of Sciences, Nanchang 330029, China
| | - Soo-Ki Kim
- Department of Animal Science and Technology, Konkuk University, Seoul 05029, Korea
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204
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De Maesschalck C, Eeckhaut V, Maertens L, De Lange L, Marchal L, Daube G, Dewulf J, Haesebrouck F, Ducatelle R, Taminau B, Van Immerseel F. Amorphous cellulose feed supplement alters the broiler caecal microbiome. Poult Sci 2019; 98:3811-3817. [PMID: 31065709 DOI: 10.3382/ps/pez090] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/23/2019] [Indexed: 12/12/2022] Open
Abstract
The grains that form the basis of most commercial chicken diets are rich in cellulose, an unbranched β-1,4-linked D-glucopyranose polymer, used as a structural molecule in plants. Although it is a predominant polysaccharide in cereal hulls, it is considered an inert non-fermentable fiber. The aim of the current study was to analyze the effect of in-feed supplementation of cellulose on the gut microbiota composition of broilers. Administration of cellulose to chickens, on top of a wheat-based diet, changed the caecal microbiota composition, as determined using pyrosequencing of the 16S rRNA gene. At day 26, a significantly (P < 0.01) higher relative abundance of the Alistipes genus was observed in the caeca of broilers fed the cellulose-supplemented diet, compared to animals fed the control diet. An in vitro batch fermentation assay showed a significant (P < 0.01) growth stimulation of Alistipes finegoldii in the presence of cellulose. In conclusion, in-feed supplementation of cellulose alters the microbiota composition at the level of the phylum Bacteroidetes, specifically the Alistipes genus. This suggests that cellulose is not essentially inert but can alter the gut micro-environment.
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Affiliation(s)
- Celine De Maesschalck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - Venessa Eeckhaut
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - Luc Maertens
- Animal Science Unit, Institute for Agricultural and Fisheries Research, Scheldeweg 68, B-9090 Melle, Belgium
| | - Loek De Lange
- Schothorst Feed Research, Meerkoetenweg 26, NL-8200 AM Lelystad, The Netherlands
| | - Leon Marchal
- ForFarmers BV, Kwinkweerd 12, NL-7241 CW Lochem, The Netherlands
| | - Georges Daube
- Laboratory of Food Microbiology, Department of Food Sciences, Fundamental and Applied Research for Animal and Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Quartier vallée 2, Avenue de Cureghem 10, B-4000 Liège, Belgium
| | - Jeroen Dewulf
- Veterinary Epidemiology Unit, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 13, B-9820 Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - Richard Ducatelle
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - Bernard Taminau
- Laboratory of Food Microbiology, Department of Food Sciences, Fundamental and Applied Research for Animal and Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Quartier vallée 2, Avenue de Cureghem 10, B-4000 Liège, Belgium
| | - Filip Van Immerseel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
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205
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Islam MR, Lepp D, Godfrey DV, Orban S, Ross K, Delaquis P, Diarra MS. Effects of wild blueberry (Vaccinium angustifolium) pomace feeding on gut microbiota and blood metabolites in free-range pastured broiler chickens. Poult Sci 2019; 98:3739-3755. [PMID: 30918964 DOI: 10.3382/ps/pez062] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 03/18/2019] [Indexed: 12/19/2022] Open
Abstract
There is a need to develop cost-effective approaches to modulate gut microbiota, promote bird health, and prevent infections in pasture-raised broiler chickens. The present study evaluated the efficacy of organic wild blueberry (Vaccinium angustifolium) also called low-bush blueberry pomace (LBBP)-supplemented feed to modulate the chicken gut microbiota, and blood metabolites in order to improve bird health and productivity. Slow-growing broiler chickens were reared on pasture up to 64 D for sampling after 2 wk of treatment during brooding with 0, 1, and 2% LBBP in feed. Intestinal samples were collected at different time-points throughout the trial for bacterial culture and microbial community analysis by 16S rRNA gene sequencing using Illumina MiSeq. Blood sera were also analyzed for metabolites at each sampling time. Of the 14 bacterial phyla, the predominant taxa across all sampling time-points were Firmicutes, Proteobacteria, Bacteroidetes, and Tenericutes, representing >97% of all sequences. Bacteroidetes seemed to be replacing Firmicutes by LBBP supplementation, with the most noticeable effect at day 64 with 1% LBBP. LBBP inclusion enriched Lactobacillus, Bacteroides, and Bifidobacterium, while Escherichia coli, Clostridium_Clostridiaceae, Helicobacter, and Enterococcus showed higher abundances in control birds at the end of trial. Principal co-ordinate analysis showed a clear clustering of the intestinal samples from control and LBBP-treated groups at day 29. Application of LBBP resulted in a decrease (P < 0.05) in cholesterol at day 21, and an increase (P < 0.05) in high-density lipoprotein cholesterol in 14-day-old broilers. Higher (P < 0.05) levels of phosphorus, magnesium, and globulin at day 21 as well as iron and albumin at day 36 were also observed in 1% LBBP-fed birds. Despite limitations consisting essentially of low sampled birds for measurements, this study indicated that dietary supplementation of LBBP could positively influence gut microbiota and blood metabolites that may contribute to the overall health of pasture-raised broiler chickens.
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Affiliation(s)
- Md Rashedul Islam
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, Canada
| | - Dion Lepp
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, Canada
| | - David V Godfrey
- Summerland Research and Development Centre, AAFC, Summerland, BC V0H 1Z0, Canada
| | - Steve Orban
- Summerland Research and Development Centre, AAFC, Summerland, BC V0H 1Z0, Canada
| | - Kelly Ross
- Summerland Research and Development Centre, AAFC, Summerland, BC V0H 1Z0, Canada
| | - Pascal Delaquis
- Summerland Research and Development Centre, AAFC, Summerland, BC V0H 1Z0, Canada
| | - Moussa S Diarra
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, Canada
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206
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Hong Y, Cheng Y, Li Y, Li X, Zhou Z, Shi D, Li Z, Xiao Y. Preliminary Study on the Effect of Bacillus amyloliquefaciens TL on Cecal Bacterial Community Structure of Broiler Chickens. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5431354. [PMID: 31687392 PMCID: PMC6794981 DOI: 10.1155/2019/5431354] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/11/2019] [Indexed: 02/01/2023]
Abstract
Probiotics can promote the health and growth performance of animals through modulation of intestinal microbiota. When used as a feed additive, they have the potential to minimize or abolish the use of antibiotics. In this study, we investigated the effect of the probiotic strain Bacillus amyloliquefaciens TL on the growth performance and cecum microflora composition in Cobb 500 broiler chickens. In total, 180 broilers were randomly divided into three groups-each group comprised 4 pens, and each pen contained 15 chickens. The three groups were fed either a control diet, or a diet supplemented with either the antibiotic chlortetracycline or B. amyloliquefaciens TL. Broilers were weighed, and cecum contents were collected on days 7, 14, 21, and 35, respectively. The broilers in both the antibiotic and probiotic groups exhibited significant weight gain compared with controls, exhibiting increases of 16.02% and 13.40%, respectively, after 35 days (P < 0.01). Similarly, the feed conversion ratio (FCR, 1-35 days) of broilers in the chlortetracycline and B. amyloliquefaciens TL groups was lower than that of the controls. HiSeq high-throughput sequencing of 16S rRNA of the cecal microbiota was performed on days 7, 14, 21, and 35, respectively. The Firmicutes/Bacteroidetes ratio was higher in the chlortetracycline and B. amyloliquefaciens TL groups than in the control group on days 14, 21, and 35, and especially on day 21. The prevalence of genera Oscillospira, Ruminococcus, Butyricicoccus, and Faecalibacterium (Firmicutes) was higher in the antibiotic and probiotic groups, while that of Bacteroides, Parabacteroides (Bacteroidetes), and Lactobacillus was higher in the control group. In this study, the changes in the microbiota of the probiotic group were similar to those in the antibiotic group. These results suggest that the probiotic strain B. amyloliquefaciens TL can modulate the cecal microbiota of broilers similar to chlortetracycline.
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Affiliation(s)
- Yuxuan Hong
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yingxian Cheng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yanjuan Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Xiaowen Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Zutao Zhou
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Deshi Shi
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Zili Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yuncai Xiao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
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207
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Antibiotic Resistance of Escherichia Coli Isolated from Broiler Chickens. FOLIA VETERINARIA 2019. [DOI: 10.2478/fv-2019-0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
The purpose of this study was to detect the antibiotic resistance of forty-one Escherichia coli isolates from the intestinal contents of slaughtered broiler chickens using the disk diffusion method according to Kirby-Bauer. Mueller-Hinton agar plates were inoculated with 0.1 ml overnight broth cultures of individual E. coli isolates and the disks with the following concentrations of antibiotics were applied onto them: ampicillin (10 μg), cefotaxime (30 μg), gentamicin (10 μg), streptomycin (10 μg), azithromycin (15 μg), tetracycline (30 μg), ciprofloxacin (30 μg) and levofloxacin (3 μg). After the incubation at 37 °C for 16—18 hours, the inhibition zones were measured and interpreted in accordance with the Clinical and Laboratory Standard Institute (CLSI) zone diameter breakpoints. Almost all E. coli isolates showed resistance to tetracycline (92.68 %), most of them were resistant to gentamicin (75.61 %) and levofloxacine (70.73 %). Phenotypic resistance to tetracycline was further confirmed with the help of the Polymerase Chain Reaction (PCR) procedure focused on the presence of specific tet(A) and tet(B) genes. These genes were detected in all 41 E. coli isolates. On the contrary, E. coli isolates were highly susceptible to both azithromycin and streptomycin. In conclusion, the study highlighted the role of commensal E. coli bacteria isolated from the intestines of broiler chickens as an important reservoir of tetracycline resistance genes.
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208
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Yan W, Sun C, Zheng J, Wen C, Ji C, Zhang D, Chen Y, Hou Z, Yang N. Efficacy of Fecal Sampling as a Gut Proxy in the Study of Chicken Gut Microbiota. Front Microbiol 2019; 10:2126. [PMID: 31572332 PMCID: PMC6753641 DOI: 10.3389/fmicb.2019.02126] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 08/29/2019] [Indexed: 12/31/2022] Open
Abstract
Despite the convenience and non-invasiveness of fecal sampling, the fecal microbiota does not fully represent that of the gastrointestinal (GI) tract, and the efficacy of fecal sampling to accurately represent the gut microbiota in birds is poorly understood. In this study, we aim to identify the efficacy of feces as a gut proxy in birds using chickens as a model. We collected 1,026 samples from 206 chickens, including duodenum, jejunum, ileum, cecum, and feces samples, for 16S rRNA amplicon sequencing analyses. In this study, the efficacy of feces as a gut proxy was partitioned to microbial community membership and community structure. Most taxa in the small intestine (84.11-87.28%) and ceca (99.39%) could be identified in feces. Microbial community membership was reflected with a gut anatomic feature, but community structure was not. Excluding shared microbes, the small intestine and ceca contributed 34.12 and 5.83% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria members in the ceca could be well mirrored by the observations in fecal samples (ρ = 0.54-0.71 and 0.71-0.78, respectively, P < 0.001). However, there were few significant correlations for each genus between feces and each of the four gut segments, and these correlations were not high (ρ = -0.2-0.4, P < 0.05) for most genera. Our results suggest that fecal microbial community has a good potential to identify most taxa in the chicken gut and could moderately mirror the microbial structure in the intestine at the microbial population level with phylum specificity. However, it should be interpreted with caution by using feces as a proxy to study associations for microbial structure at individual microorganism level.
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Affiliation(s)
- Wei Yan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiangxia Zheng
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chaoliang Wen
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Congliang Ji
- Wen’s sNanfang Poultry Breeding Co. Ltd., Yunfu, China
| | - Dexiang Zhang
- Wen’s sNanfang Poultry Breeding Co. Ltd., Yunfu, China
| | - Yonghua Chen
- Wen’s sNanfang Poultry Breeding Co. Ltd., Yunfu, China
| | - Zhuocheng Hou
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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209
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Crippen TL, Sheffield CL, Singh B, Byrd JA, Beier RC. How Management Practices Within a Poultry House During Successive Flock Rotations Change the Structure of the Soil Microbiome. Front Microbiol 2019; 10:2100. [PMID: 31572320 PMCID: PMC6753631 DOI: 10.3389/fmicb.2019.02100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/26/2019] [Indexed: 01/21/2023] Open
Abstract
The microbiome within a poultry production house influences the attainment of physiologically strong birds and thus food safety and public health. Yet little is known about the microbial communities within the house and the effects on the soil microbes onto which the houses are placed; nor the effects of management practices on their equilibrium. This study looked at the soil bacterial microbiome before a broiler house was constructed, then through 11 flock rotations (2.5 years) that included a partial clean-out and a total clean-out within the management regimen. Major shifts were observed, occurring at the taxonomic class level, related to the introduction of bedding and birds on top of the soil. The partial clean-out of litter did not change the soil bacterial community in any substantial way, only prompting a temporary increase in some genera; however, the total litter clean-out caused a major increase in a cohort of Actinobacteria. The underlying soil contained bacteria beneficial for poultry metabolism, such as Lactobacillus, Faecalibacterium, Bacteriodes, and Ruminococcus. Additionally, management practices affected the class structure of the soil bacterial community beneath the poultry house. The scheduling of these practices should be leveraged to exploit maintenance of beneficial bacteria that maximize microbiome contributions to bird production processes, while minimizing possible antibiotic-resistant bacteria and environmental effects.
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Affiliation(s)
- Tawni L. Crippen
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States
| | - Cynthia L. Sheffield
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States
| | - Baneshwar Singh
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, United States
| | - J. Allen Byrd
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States
| | - Ross C. Beier
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States
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210
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Kers JG, Velkers FC, Fischer EAJ, Hermes GDA, Lamot DM, Stegeman JA, Smidt H. Take care of the environment: housing conditions affect the interplay of nutritional interventions and intestinal microbiota in broiler chickens. Anim Microbiome 2019; 1:10. [PMID: 33499936 PMCID: PMC7807522 DOI: 10.1186/s42523-019-0009-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
Background The intestinal microbiota is shaped by many interactions between microorganisms, host, diet, and the environment. Exposure to microorganisms present in the environment, and exchange of microorganisms between hosts sharing the same environment, can influence intestinal microbiota of individuals, but how this affects microbiota studies is poorly understood. We investigated the effects of experimental housing circumstances on intestinal microbiota composition in broiler chickens, and how these effects may influence the capacity to determine diet related effects in a nutrition experiment. A cross-sectional experiment was conducted simultaneously in a feed research facility with mesh panels between pens (Housing condition 1, H1), in an extensively cleaned stable with floor pens with solid wooden panels (H2), and in isolators (H3). In H1 and H2 different distances between pens were created to assess gut microbiota exchange between pens. Feed with and without a blend of medium-chain fatty acids (MCFA) was used to create differences in cecal microbiota between pens or isolators within the same housing condition. Male one-day-old Ross broiler chickens (n = 370) were randomly distributed across H1, H2, and H3. After 35 days cecal microbiota composition was assessed by 16S ribosomal RNA gene amplicon sequencing. Metabolic functioning of cecal content was assessed based on high-performance liquid chromatography. Results Microbial alpha diversity was not affected in broilers fed +MCFA in H1 but was increased in H2 and H3. Based on weighted UniFrac distances, the nutritional intervention explained 10%, whereas housing condition explained 28% of cecal microbiota variation between all broilers. The effect size of the nutritional intervention varied within housing conditions between 11, 27, and 13% for H1, H2, and H3. Furthermore, performance and metabolic output were significantly different between housing conditions. The distance between pens within H1 and H2 did not influence the percentage of shared genera or operational taxonomic units (OTUs). Conclusions The cecal microbiota of broilers was modifiable by a nutritional intervention, but the housing condition affected microbiota composition and functionality stronger than the diet intervention. Consequently, for interpretation of intestinal microbiota studies in poultry it is essential to be aware of the potentially large impact of housing conditions on the obtained results. Electronic supplementary material The online version of this article (10.1186/s42523-019-0009-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jannigje G Kers
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, Utrecht, the Netherlands. .,Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands.
| | - Francisca C Velkers
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, Utrecht, the Netherlands
| | - Egil A J Fischer
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, Utrecht, the Netherlands
| | - Gerben D A Hermes
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - David M Lamot
- Cargill Animal Nutrition Innovation Center, Velddriel, the Netherlands
| | - J Arjan Stegeman
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, Utrecht, the Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
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211
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Tong Q, Liu XN, Hu ZF, Ding JF, Bie J, Wang HB, Zhang JT. Effects of Captivity and Season on the Gut Microbiota of the Brown Frog ( Rana dybowskii). Front Microbiol 2019; 10:1912. [PMID: 31507549 PMCID: PMC6716059 DOI: 10.3389/fmicb.2019.01912] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/05/2019] [Indexed: 12/14/2022] Open
Abstract
The gut microbiota of amphibians is affected by exogenous and endogenous factors. We performed a comprehensive analysis using high-throughput sequencing technology and functional predictions and observed general changes in the gut microbiota of frogs in different growth stages, seasons, and growth environments. There were no significant differences in microbial richness and diversity between juvenile and adult wild frogs, between the summer and autumn groups of captive frogs, or between wild and captive frogs. There were significant differences in the gut microbiota community structure of Rana dybowskii between the summer and autumn groups of captive frogs and between wild and captive R. dybowskii, whereas the differences between juvenile and adult wild frogs were not significant. The dominant gut bacterial phyla in frogs from both captive and wild environments included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Linear discriminant effect size (LEfSe) analysis showed that Bacteroidetes and Firmicutes were significantly enriched in captive and wild R. dybowskii, respectively linear discriminant analysis (LDA > 4). The core operational taxonomical units (OTUs) that were found in >90% of all frogs tested encompassed 15 core OTUs. The captive frogs exhibited 15 core OTUs in addition to the above overall core microbiota, whereas the wild frogs exhibited 19 core OTUs in addition to the above overall core microbiota. Predictions made using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that eleven KEGG pathways, such as infectious diseases, immune system diseases, metabolism, metabolism of other amino acids, metabolism of cofactors and vitamins, metabolism of terpenoids and polyketides, neurodegenerative diseases, and transport and catabolism, were enriched in captive frogs. The relative abundance of several red-leg-syndrome-related pathogens increased significantly in captive frogs compared with that in wild frogs. To our knowledge, this is the first study on the effects of individual seasons and captivity on the gut microbiota of frogs.
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Affiliation(s)
- Qing Tong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xiao-Ning Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Zong-Fu Hu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jia-Feng Ding
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jia Bie
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Hong-Bin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jian-Tao Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
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212
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Laviad-Shitrit S, Izhaki I, Lalzar M, Halpern M. Comparative Analysis of Intestine Microbiota of Four Wild Waterbird Species. Front Microbiol 2019; 10:1911. [PMID: 31481943 PMCID: PMC6711360 DOI: 10.3389/fmicb.2019.01911] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/05/2019] [Indexed: 01/07/2023] Open
Abstract
Waterbirds are ubiquitous and globally distributed. Yet, studies on wild waterbirds' gut microbiota are still rare. Our aim was to explore and compare the gut microbial community composition of wild waterbird species. Four wild waterbird species that are either wintering or all-year residents in Israel were studied: great cormorants, little egrets, black-crowned night herons and black-headed gulls. For each bird, three intestinal sections were sampled; anterior, middle and posterior. No significant differences were found among the microbiota compositions in the three intestine sections of each individual bird. Each waterbird species had a unique microbial composition. The gut microbiota of the black-headed gulls' fundamentally deviated from that of the other bird species, probably due to a very high abundance (58.8%) of the genus Catellicoccus (Firmicutes). Our results suggest a correlation between the waterbird species' phylogeny and their intestine microbial community hierarchical tree, which evinced phylosymbiosis. This recent coinage stands for eco-evolutionary patterns between the host phylogeny and its microbiota composition. We conclude that eco-evolutionary processes termed phylosymbiosis may occur between wild waterbird species and their gut microbial community composition.
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Affiliation(s)
- Sivan Laviad-Shitrit
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Ido Izhaki
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Maya Lalzar
- Bioinformatics Service Unit, University of Haifa, Haifa, Israel
| | - Malka Halpern
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel.,Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa at Oranim, Tivon, Israel
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213
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Hidalgo-Cantabrana C, Goh YJ, Pan M, Sanozky-Dawes R, Barrangou R. Genome editing using the endogenous type I CRISPR-Cas system in Lactobacillus crispatus. Proc Natl Acad Sci U S A 2019; 116:15774-15783. [PMID: 31341082 PMCID: PMC6690032 DOI: 10.1073/pnas.1905421116] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems are now widely used for genome editing and transcriptional regulation in diverse organisms. The compact and portable nature of class 2 single effector nucleases, such as Cas9 or Cas12, has facilitated directed genome modifications in plants, animals, and microbes. However, most CRISPR-Cas systems belong to the more prevalent class 1 category, which hinges on multiprotein effector complexes. In the present study, we detail how the native type I-E CRISPR-Cas system, with a 5'-AAA-3' protospacer adjacent motif (PAM) and a 61-nucleotide guide CRISPR RNA (crRNA) can be repurposed for efficient chromosomal targeting and genome editing in Lactobacillus crispatus, an important commensal and beneficial microbe in the vaginal and intestinal tracts. Specifically, we generated diverse mutations encompassing a 643-base pair (bp) deletion (100% efficiency), a stop codon insertion (36%), and a single nucleotide substitution (19%) in the exopolysaccharide priming-glycosyl transferase (p-gtf). Additional genetic targets included a 308-bp deletion (20%) in the prophage DNA packaging Nu1 and a 730-bp insertion of the green fluorescent protein gene downstream of enolase (23%). This approach enables flexible alteration of the formerly genetically recalcitrant species L. crispatus, with potential for probiotic enhancement, biotherapeutic engineering, and mucosal vaccine delivery. These results also provide a framework for repurposing endogenous CRISPR-Cas systems for flexible genome targeting and editing, while expanding the toolbox to include one of the most abundant and diverse systems found in nature.
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Affiliation(s)
- Claudio Hidalgo-Cantabrana
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695
| | - Yong Jun Goh
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695
| | - Meichen Pan
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695
| | - Rosemary Sanozky-Dawes
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695
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214
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Alrubaye B, Abraha M, Almansour A, Bansal M, Wang H, Kwon YM, Huang Y, Hargis B, Sun X. Microbial metabolite deoxycholic acid shapes microbiota against Campylobacter jejuni chicken colonization. PLoS One 2019; 14:e0214705. [PMID: 31276498 PMCID: PMC6611565 DOI: 10.1371/journal.pone.0214705] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/13/2019] [Indexed: 12/14/2022] Open
Abstract
Despite reducing the prevalent foodborne pathogen Campylobacter jejuni in chickens decreases campylobacteriosis, few effective approaches are available. The aim of this study was to use microbial metabolic product bile acids to reduce C. jejuni chicken colonization. Broiler chicks were fed with deoxycholic acid (DCA), lithocholic acid (LCA), or ursodeoxycholic acid (UDCA). The birds were also transplanted with DCA modulated anaerobes (DCA-Anaero) or aerobes (DCA-Aero). The birds were infected with human clinical isolate C. jejuni 81-176 or chicken isolate C. jejuni AR101. Notably, C. jejuni 81-176 was readily colonized intestinal tract at d16 and reached an almost plateau at d21. Remarkably, DCA excluded C. jejuni cecal colonization below the limit of detection at 16 and 28 days of age. Neither chicken ages of infection nor LCA or UDCA altered C. jejuni AR101 chicken colonization level, while DCA reduced 91% of the bacterium in chickens at d28. Notably, DCA diet reduced phylum Firmicutes but increased Bacteroidetes compared to infected control birds. Importantly, DCA-Anaero attenuated 93% of C. jejuni colonization at d28 compared to control infected birds. In conclusion, DCA shapes microbiota composition against C. jejuni colonization in chickens, suggesting a bidirectional interaction between microbiota and microbial metabolites.
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Affiliation(s)
- Bilal Alrubaye
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Mussie Abraha
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Ayidh Almansour
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Mohit Bansal
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Hong Wang
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Young Min Kwon
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Yan Huang
- Department of Animal Science, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Billy Hargis
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Xiaolun Sun
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, Arkansas, United States of America
- * E-mail:
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215
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Gangadoo S, Bauer BW, Bajagai YS, Van TTH, Moore RJ, Stanley D. In vitro growth of gut microbiota with selenium nanoparticles. ACTA ACUST UNITED AC 2019; 5:424-431. [PMID: 31890921 PMCID: PMC6920403 DOI: 10.1016/j.aninu.2019.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/20/2019] [Accepted: 06/04/2019] [Indexed: 12/26/2022]
Abstract
The application of nanoparticles rose steeply in the last decade, where they have become a common ingredient used in processed human food, improving food properties such as shelf life and appearance. Nanoparticles have also attracted considerable interest to the livestock industry, due to their efficacy in intestinal pathogen control, with the regulatory and consumer driven push for the removal of antibiotic growth promoters. The influence of selenium (Se) nanoparticles was investigated on a diverse and mature broiler caecal microbiota using in vitro culturing and 16S rRNA gene sequencing methods for microbiota characterisation. Caecal microbiota was collected from 4 traditionally grown heritage roosters and grown for 48 h, in the presence and absence of Se nanoparticles, with 2 technical replicates each. The effect of rooster as a biological variable strongly overpowered the effects of nano-Se in the media, resulting in moderate effects on the structure and diversity of the caecal microbial community. However the nanoparticles showed a significant reduction (P < 0.05) in the abundance of an emerging poultry pathogen, Enterococcus cecorum identical operational taxonomic units (OTU), which could be of notable interest in poultry production for targeted E. cecorum control without significant disturbance to the total microbial community.
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Affiliation(s)
- Sheeana Gangadoo
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, Queensland, 4702, Australia
- Poultry Cooperative Research Centre, University of New England Armidale, New South Wales, 2315, Australia
- School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, Queensland, 4702, Australia
- Corresponding author.
| | - Benjamin W. Bauer
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, Queensland, 4702, Australia
- Poultry Cooperative Research Centre, University of New England Armidale, New South Wales, 2315, Australia
- School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, Queensland, 4702, Australia
| | - Yadav S. Bajagai
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, Queensland, 4702, Australia
| | - Thi Thu Hao Van
- RMIT University, School of Science, Bundoora, Victoria, 3083, Australia
| | - Robert J. Moore
- Poultry Cooperative Research Centre, University of New England Armidale, New South Wales, 2315, Australia
- RMIT University, School of Science, Bundoora, Victoria, 3083, Australia
| | - Dragana Stanley
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, Queensland, 4702, Australia
- Poultry Cooperative Research Centre, University of New England Armidale, New South Wales, 2315, Australia
- School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, Queensland, 4702, Australia
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216
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Micciche A, Rothrock MJ, Yang Y, Ricke SC. Essential Oils as an Intervention Strategy to Reduce Campylobacter in Poultry Production: A Review. Front Microbiol 2019; 10:1058. [PMID: 31139172 PMCID: PMC6527745 DOI: 10.3389/fmicb.2019.01058] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/26/2019] [Indexed: 12/19/2022] Open
Abstract
Campylobacter is a major foodborne pathogen and can be acquired through consumption of poultry products. With 1.3 million United States cases a year, the high prevalence of Campylobacter within the poultry gastrointestinal tract is a public health concern and thus a target for the development of intervention strategies. Increasing demand for antibiotic-free products has led to the promotion of various alternative pathogen control measures both at the farm and processing level. One such measure includes utilizing essential oils in both pre- and post-harvest settings. Essential oils are derived from plant-based extracts, and there are currently over 300 commercially available compounds. They have been proposed to control Campylobacter in the gastrointestinal tract of broilers. When used in concentrations low enough to not influence sensory characteristics, essential oils have also been proposed to decrease bacterial contamination of the poultry product during processing. This review explores the use of essential oils, particularly thymol, carvacrol, and cinnamaldehyde, and their role in reducing Campylobacter concentrations both pre- and post-harvest. This review also details the suggested mechanisms of action of essential oils on Campylobacter.
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Affiliation(s)
- Andrew Micciche
- Center of Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR, United States
| | - Michael J. Rothrock
- United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - Yichao Yang
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Center of Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR, United States
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217
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Xi Y, Shuling N, Kunyuan T, Qiuyang Z, Hewen D, ChenCheng G, Tianhe Y, Liancheng L, Xin F. Characteristics of the intestinal flora of specific pathogen free chickens with age. Microb Pathog 2019; 132:325-334. [PMID: 31082529 DOI: 10.1016/j.micpath.2019.05.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/08/2019] [Accepted: 05/09/2019] [Indexed: 02/06/2023]
Abstract
Specific pathogen-free (SPF) experimental animals are recognized as standard laboratory animals in the fields of biomedical, animal husbandry and veterinary research and production. Intestinal flora plays a critical role in nutrient absorption, improving health and protecting the host from pathogens. We therefore explored the variation and maintenance of intestinal flora in SPF chicks in order to better understand the composition of intestinal microflorain SPF chickens, and provide reference for the study of intestinal flora of SPF experimental animals. Five chicks were randomly selected at each of 14, 28, and 42 days, and ceca were removed for DNA extraction. The Illumina Miseq platform was used for microbiome analysis of the V3-V4 region of the 16S rRNA gene. During the course of chick gut microbiome development, we observed major changes in diversity, especially between day 14 and day 28. Firmicutes, Proteobacteria, and Bacteroidetes were the main bacterial taxa, and Firmicutes increased significantly with age. The genus with the highest relative abundance was Lactobacillus, followed by Faecalibacterium. In addition, while abundance of Ruminococcaceae spp., Ruminococcus, and Blautia increased with age, Lactobacillus, Enterobacteriaceae spp., and Oscillospira decreased with age. Interestingly, the abundance of Faecalibacterium first increased and then decreased over time. The characteristics of SPF chicken gut flora at different ages establish a basis for the regulation of intestinal flora in the early stage of brooding, and also provide a theoretical foundation for controlling and preventing infections and poultry diseases in newborn chickens.
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Affiliation(s)
- Yu Xi
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China
| | - Niu Shuling
- College of Animal Science and Technology, Changchun Sci-Tech University, Shuangyang, Jilin Province, 130600, China
| | - Tie Kunyuan
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China
| | - Zhang Qiuyang
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China
| | - Deng Hewen
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China
| | - Gao ChenCheng
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China
| | - Yu Tianhe
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China
| | - Lei Liancheng
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China
| | - Feng Xin
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China.
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218
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Biasato I, Ferrocino I, Grego E, Dabbou S, Gai F, Gasco L, Cocolin L, Capucchio MT, Schiavone A. Gut Microbiota and Mucin Composition in Female Broiler Chickens Fed Diets including Yellow Mealworm ( Tenebrio molitor, L.). Animals (Basel) 2019; 9:ani9050213. [PMID: 31058804 PMCID: PMC6562683 DOI: 10.3390/ani9050213] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/23/2019] [Accepted: 04/29/2019] [Indexed: 12/19/2022] Open
Abstract
A total of 160 female broiler chickens were divided into four dietary treatments (control feed [C] and 5, 10 and 15% TM meal inclusion, respectively, with five replicate pens/treatment and eight birds/pen) to investigate the effects of Tenebrio molitor (TM) meal utilization on poultry gut microbiota and mucin composition. The cecal microbiota assessment displayed a shift in the beta diversity in chickens fed TM-based diets. The TM10 and TM15 birds showed a significant decrease in the relative abundance of Firmicutes phylum and lower Firmicutes:Bacteroidetes ratios (False Discovery Rate [FDR] < 0.05), respectively, than the TM5 group. The relative abundance of Clostridium, Alistipes and Sutterella genera significantly increased in TM chickens (FDR < 0.05), while birds fed TM-based diets displayed a significant decrease in the relative abundance of Ruminococcus genus in comparison with the C group (FDR < 0.05). Gut mucin composition evaluation revealed higher mucin staining intensity in the intestinal villi of TM5 birds than the other TM groups, as well as mucin reduction in the intestinal villi of TM10 birds when compared to the C group (p < 0.05). In conclusion, dietary TM meal utilization (especially the 10-15% inclusion levels) may negatively influence either the cecal microbiota or the intestinal mucin dynamics of broiler chickens.
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Affiliation(s)
- Ilaria Biasato
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy.
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy.
| | - Elena Grego
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy.
| | - Sihem Dabbou
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy.
| | - Francesco Gai
- Institute of Science of Food Production, National Research Council, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy.
| | - Laura Gasco
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy.
| | - Luca Cocolin
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy.
| | - Maria Teresa Capucchio
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy.
- Institute of Science of Food Production, National Research Council, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy.
| | - Achille Schiavone
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy.
- Institute of Science of Food Production, National Research Council, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy.
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219
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Functioning of the Intestinal Ecosystem: From New Technologies in Microbial Research to Practical Poultry Feeding – A Review. ANNALS OF ANIMAL SCIENCE 2019. [DOI: 10.2478/aoas-2019-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
Unlike classical microbiology which focuses on bacteria capable of growing in vitro, metagenomics is a study of genetic information originating from microflora which aims to characterise the microbiome, namely the common genome of bacteria, archaea, fungi, protozoa and viruses living in the host. Metagenomics relies on next-generation sequencing (NGS), a large-scale sequencing technique which allows millions of sequential reactions to be carried out in parallel to decode entire communities of microorganisms. Metagenomic analyses support taxonomic analyses (involving gene fragments encoding ribosomal RNAs 5S and 16S in bacteria) or functional analyses for identifying genes encoding proteins that participate in the regulation of metabolic pathways in the body. New metagenomics technologies expand our knowledge of the phylogenetic structure of microflora in the gastrointestinal tract of poultry, and they support the identification of previously unknown groups of microbiota, mainly those occurring in small numbers. Next-generation sequencing also provides indirect information about the quantitative structure of the genes of gut microorganisms, but microbial activity and changes in the proportions of microbial metabolites that affect the host’s intestinal integrity and metabolism remain insufficiently investigated. Therefore, research studies are undertaken to investigate the proportions of the key microbial metabolites in the intestinal contents of poultry relative to changes in the population size of the most important bacterial groups, including those determined by cheaper techniques.
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220
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Proctor A, Phillips GJ. Differential Effects of Bacitracin Methylene Disalicylate (BMD) on the Distal Colon and Cecal Microbiota of Young Broiler Chickens. Front Vet Sci 2019; 6:114. [PMID: 31058171 PMCID: PMC6478705 DOI: 10.3389/fvets.2019.00114] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 03/27/2019] [Indexed: 02/01/2023] Open
Abstract
Antibiotics have been used extensively for growth promotion in poultry, along with other food production animals, as well as therapeutically to treat infectious diseases. However, with concerns over selection for drug antibiotic resistant bacteria the practice of using subtherapeutic doses of antibiotics is under increased scrutiny. Consequently, we assessed the impact of the commonly used antibiotic bacitracin methylene disalicylate (BMD) on the gastrointestinal microbiota of chickens. For this we administered therapeutic doses of BMD as a feed additive and 16s rRNA gene amplicon sequencing to measure changes in taxonomic abundance on the distal colon and cecal microbiota of young broiler chickens. While BMD treatment was found to impact the abundance of selected taxa and overall beta diversity, significant changes were, in general, limited to the colon of the treated birds. Selected taxa at the phylum, class, and genus levels that were most impacted were identified. The composition of the cecum remained relatively stable in BMD-treated animals. As poultry production practices seek alternatives to growth promoting antibiotic feed additives, manipulation of the gastrointestinal microbiota holds promise. These results suggest that targeting the cecum may offer a means to promote changes to the microbiota that maximize the benefits for the hosts.
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Affiliation(s)
| | - Gregory J. Phillips
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
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Saeed M, Yatao X, Tiantian Z, Qian R, Chao S. 16S ribosomal RNA sequencing reveals a modulation of intestinal microbiome and immune response by dietary L-theanine supplementation in broiler chickens. Poult Sci 2019; 98:842-854. [PMID: 30169691 PMCID: PMC7107316 DOI: 10.3382/ps/pey394] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/03/2018] [Indexed: 01/01/2023] Open
Abstract
Despite the availability of abundant literature on green tea, studies on the use of L-theanine (an amino acid found only in green tea) as a feed additive in poultry especially broiler are limited. So, this study was conducted to explore the effects of L-theanine on the intestinal microbiome and immune response in a broiler. A total of 400-d-old chicks were randomly divided into four treatment groups (A, B, C, and D) using a complete randomized design. Treatments were as follows: A, control (basal diet); B, basal diet + 100 mg L-theanine/kg diet; C, basal diet + 200 mg L-theanine/kg diet; and D, basal diet + 300 mg L-theanine/kg diet. Mucosal samples from ileum and jejunum of broiler chicken were extracted at 21 and 42 d of age. Extraction of genomic DNA was followed by amplification of V3 and V4 hypervariable regions of 16S ribosomal RNA. After Illumina sequencing, results revealed that treatment with L-theanine significantly increased the population of Lactobacillus in ileum and jejunum as compared to a control group, but the higher population was observed in jejunum at both 21 and 42 d of age. The overall diversity of the jejunum microbiome in the treatment group was significantly lower than that of the ileum and control group (P < 0.05). Results of this study revealed that mRNA expression of TLRs (TLR-2 and TLR-4) and cytokines (TNF-α, IFN-γ, and IL-2) was decreased in response to treatment with L-theanine. Moreover, the negative correlation of abundance of Lactobacillus was observed with expression of IL-2 and IFN-γ in the intestine and these effects were highly significant (P < 0.01). In summary, our finding revealed that dietary supplementation of L-theanine exhibited a positive influence on intestinal bacteria by supporting beneficial microbes like Lactobacillus while decreasing harmful microbes like Clostridium.
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Affiliation(s)
- Muhammad Saeed
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, 712100, P.R China
| | - Xu Yatao
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, 712100, P.R China
| | - Zhang Tiantian
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, 712100, P.R China
| | - Ren Qian
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, 712100, P.R China
| | - Sun Chao
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, 712100, P.R China
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223
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Rubio LA. Possibilities of early life programming in broiler chickens via intestinal microbiota modulation. Poult Sci 2019; 98:695-706. [PMID: 30247675 DOI: 10.3382/ps/pey416] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/29/2018] [Indexed: 01/03/2023] Open
Abstract
The strong selection in search for a higher growth rate in broilers has resulted in adverse effects such as metabolic disorders, low responsiveness of the immune system, and decreased resistance to pathogens. On the other hand, newly hatched chicks rely mostly on innate immune responses until their gut gets colonized with microbiota. In consequence, early access to active substances or bacteria (pre- and post-hatch) is particularly relevant here because in broilers much of the immune system development occurs early in life. Therefore, early stimulation of beneficial microflora is critical, as it affects, to a great extent, the entire life-span of an individual, and also because the nutritional manipulations of the gastrointestinal tract (GIT) microbiome to enhance productivity and health are rather limited by the resilience of the ecosystem once established in the chicken´s gut. Early life or developmental programming is based on the assumption that the development of diseases later in life can be modulated by perturbations or environmental exposures during critical pre- or early post-natal life. Substances such as plant derivatives, Na butyrate, pre- and probiotics, and β-glucans have been shown to induce beneficial microbiological and immunological changes within the GIT, and therefore are potential candidates to be used as tools to manipulate GIT functionality in the young chicken. Accordingly, substances as these might represent promising candidates to study intestinal microbiota/immune system modulation in broilers´ early stages of breeding. In ovo-delivered prebiotics and synbiotics have been shown to have no adverse effect on the development of the immune system in exposed chickens, while being able to affect lymphoid-organs' morphology in chickens. In ovo procedures have also been proposed as means of promoting a healthy microflora in embryonic guts and stimulating maturation of the cellular and humoral immune responses in central and peripheral immune organs, including those in the GIT. The purpose of this presentation is to discuss the potential usefulness of the instruments currently available to induce early life programming in broilers.
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Affiliation(s)
- Luis A Rubio
- Physiology and Biochemistry of Animal Nutrition (EEZ, CSIC), Granada 18008, Spain
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SORESCU IONUT, DUMITRU MIHAELA, CIURESCU GEORGETA. Lactobacillus spp. and Enterococcus faecium strains isolation, identification, preservation and quantitative determinations from turkey gut content. ROMANIAN BIOTECHNOLOGICAL LETTERS 2019. [DOI: 10.25083/rbl/24.1/41.49] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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225
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Slawinska A, Dunislawska A, Plowiec A, Radomska M, Lachmanska J, Siwek M, Tavaniello S, Maiorano G. Modulation of microbial communities and mucosal gene expression in chicken intestines after galactooligosaccharides delivery In Ovo. PLoS One 2019; 14:e0212318. [PMID: 30811518 PMCID: PMC6392319 DOI: 10.1371/journal.pone.0212318] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 01/31/2019] [Indexed: 12/21/2022] Open
Abstract
Intestinal mucosa is the interface between the microbial content of the gut and the host's milieu. The goal of this study was to modulate chicken intestinal microflora by in ovo stimulation with galactooligosaccharides (GOS) prebiotic and to demonstrate the molecular responses of the host. The animal trial was performed on meat-type chickens (Ross 308). GOS was delivered by in ovo injection performed into the air cell on day 12 of egg incubation. Analysis of microbial communities and mucosal gene expression was performed at slaughter (day 42 post-hatching). Chyme (for DNA isolation) and intestinal mucosa (for RNA isolation) from four distinct intestinal segments (duodenum, jejunum, ileum, and caecum) was sampled. The relative abundance of Bifidobacterium spp. and Lactobacillus spp. in DNA isolated from chyme samples was determined using qPCR. On the host side, the mRNA expression of 13 genes grouped into two panels was analysed with RT-qPCR. Panel (1) included genes related to intestinal innate immune responses (IL-1β, IL-10 and IL-12p40, AvBD1 and CATHL2). Panel (2) contained genes involved in intestinal barrier function (MUC6, CLDN1 and TJAP1) and nutrients sensing (FFAR2 and FFAR4, GLUT1, GLUT2 and GLUT5). GOS increased the relative abundance of Bifidobacterium in caecum (from 1.3% to 3.9%). Distinct effects of GOS on gene expression were manifested in jejunum and caecum. Cytokine genes (IL-1β, IL-10 and IL-12p40) were up-regulated in the jejunum and caecum of the GOS-treated group. Host defence peptides (AvBD1 and CATHL2) were up-regulated in the caecum of the GOS-treated group. Free fatty acid receptors (FFAR2 and FFAR4) were up-regulated in all three compartments of the intestine (except the duodenum). Glucose transporters were down-regulated in duodenum (GLUT2 and GLUT5) but up-regulated in the hindgut (GLUT1 and GLUT2). In conclusion, GOS delivered in ovo had a bifidogenic effect in adult chickens. It also modulated gene expression related to intestinal immune responses, gut barrier function, and nutrient sensing.
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Affiliation(s)
- Anna Slawinska
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Bydgoszcz, Poland
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso, Italy
| | - Aleksandra Dunislawska
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Bydgoszcz, Poland
| | - Arkadiusz Plowiec
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Bydgoszcz, Poland
| | - Malgorzata Radomska
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Bydgoszcz, Poland
| | - Jagoda Lachmanska
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Bydgoszcz, Poland
| | - Maria Siwek
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Bydgoszcz, Poland
| | - Siria Tavaniello
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso, Italy
| | - Giuseppe Maiorano
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso, Italy
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226
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Ocejo M, Oporto B, Hurtado A. 16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan. Sci Rep 2019; 9:2506. [PMID: 30792439 PMCID: PMC6385345 DOI: 10.1038/s41598-019-39323-x] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/21/2019] [Indexed: 01/27/2023] Open
Abstract
Gut microbiota affects health, metabolism and immunity of the host, and in the case of livestock, also food-safety. Here, 16S rRNA gene high-throughput Illumina sequencing was used to describe the microbiome of chicken caeca in two different breeds and management systems throughout their whole productive lifespan. Broilers (Ross-308), as a fast-growing breed reared in an intensive system for 42-days, and a slow-growing breed of chicken (Sasso-T451A) reared in an extensive farming system with outdoor access for 86-days, were compared. The core microbiome and differentially abundant taxa, as well as taxa associated with age were identified. Age was identified as the strongest influencing factor in caecal microbiota composition, and, in general, each age-group showed an age-associated community profile, with a transition period at the middle of their lifespan. However, substantial differences were observed in the composition of caecal microbiota of both chicken breeds, microbiota being richer and more complex in free-range chicken than in broilers. Several taxa positively/negatively correlated with Campylobacter relative abundance were also identified. Especially noteworthy was the identification by microbial community comparison of microbiota profiles suggestive of dysbiosis in several free-range chickens, probably associated to the typhlitis observed in the lumen of their caeca.
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Affiliation(s)
- Medelin Ocejo
- NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Animal Health Department, Derio, 48160, Spain
| | - Beatriz Oporto
- NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Animal Health Department, Derio, 48160, Spain
| | - Ana Hurtado
- NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Animal Health Department, Derio, 48160, Spain.
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227
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Zhang HL, Wei JK, Wang QH, Yang R, Gao XJ, Sang YX, Cai PP, Zhang GQ, Chen QJ. Lignocellulose utilization and bacterial communities of millet straw based mushroom (Agaricus bisporus) production. Sci Rep 2019; 9:1151. [PMID: 30718596 PMCID: PMC6362146 DOI: 10.1038/s41598-018-37681-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 12/10/2018] [Indexed: 12/17/2022] Open
Abstract
Agaricus bisporus is in general cultivated on wheat and rice straw in China. However, millet straw is a potential alternative resource for Agaricus bisporus cultivation, but this has hardly been studied. In the present study, the feasibility of millet straw based mushroom production was analyzed by three successive trials. Mature compost demonstrated high quality with total nitrogen, pH, and C/N ratio of 2.0%, 7.5, and 18:1 respectively, which was suitable for mushroom mycelia growth. During composting, 47–50% of cellulose, 63–65% of hemicellulose, and 8–17% lignin were degraded, while 22–27% of cellulose, 14–16% of hemicellulose, and 15–21% of lignin were consumed by A. bisporus mycelia during cultivation. The highest FPUase and CMCase were observed during mushroom flushes. Endo-xylanase had the key role in hemicellulose degradation with high enzyme activity during cultivation stages. Laccase participated in lignin degradation with the highest enzyme activity in Pinning stage followed by a sharp decline at the first flush. Yield was up to 20 kg/m2, as this is similar to growth on wheat straw, this shows that millet straw is an effective resource for mushroom cultivation. Actinobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Firmicutes, and Proteobacteria were the dominant phyla, based on 16S rRNA gene sequencing during composting. The key environmental factors dominating bacterial communities of the samples were determined to be pH value, cellulose content, and hemicellulose content for prewetting and premixed phase of basic mixture (P0); moisture content for phase I (PI); and nitrogen content, lignin content, and ash content for phase II (PII), respectively.
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Affiliation(s)
- Hao-Lin Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.,College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Jin-Kang Wei
- Beijing Agricultural Technology Extension Station, Beijing, 100029, China
| | - Qing-Hui Wang
- Chengde Xingchunhe Agricultural Co. Ltd., Chengde, 067000, China
| | - Rui Yang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Xiao-Jing Gao
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Yu-Xi Sang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Pan-Pan Cai
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Guo-Qing Zhang
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, College of Biological Science and Engineering, Beijing University of Agriculture, Beijing, 102206, China.
| | - Qing-Jun Chen
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.
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228
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Microbiota of eggs revealed by 16S rRNA-based sequencing: From raw materials produced by different suppliers to chilled pasteurized liquid products. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.09.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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229
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Li CL, Wang J, Zhang HJ, Wu SG, Hui QR, Yang CB, Fang RJ, Qi GH. Intestinal Morphologic and Microbiota Responses to Dietary Bacillus spp. in a Broiler Chicken Model. Front Physiol 2019; 9:1968. [PMID: 30705639 PMCID: PMC6344408 DOI: 10.3389/fphys.2018.01968] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/31/2018] [Indexed: 12/12/2022] Open
Abstract
Dietary inclusion of probiotic Bacillus spp. beneficially affect the broiler chickens by balancing the properties of the indigenous microbiota causing better growth performance. The effects of three Bacillus spp. on the growth performance, intestinal morphology and the compositions of jejunal microflora were investigated in broiler chickens. A total of 480 1-day-old male Arbor Acres broilers were randomly divided into four groups. All groups had six replicates and 20 birds were included in each replicate. The control birds were fed with a corn-soybean basal diet, while three treatment diets were supplemented with Bacillus coagulans TBC169, B. subtilis PB6, and B. subtilis DSM32315 with a dosage of 1 × 109 cfu/kg, respectively. The experiment lasted for 42 days. The compositions and diversity of jejunal microflora were analyzed by MiSeq high-throughput sequencing. The B. coagulans TBC169 group showed marked improvements of growth performance, nutrient digestibility and intestinal morphology compared with the other B. subtilis treatments. B. coagulans TBC169 supplementation improved the average body weight (BW), average daily weight gain (ADG), total tract apparent digestibility of crude protein and gross energy (GE), and reduced feed conversion rate (FCR) compared with the control group (P < 0.05). The villus height to crypt depth ratio (VH/CD) of jejunum and duodenum was increased in the birds fed with B. coagulans TBC169 compared with the control group (P < 0.05). However, two B. subtilis treatments presented more positive variation of the jejunum microflora of chickens than that in the B. coagulans TBC169 group. B. subtilis PB6 and B. subtilis DSM32315 treatments improved the diversity of jejunal microbiota on day 21 compared with the control (P < 0.05), while which were decreased on day 42 (P < 0.05). The supplementation with B. coagulans TBC169 significantly improved the proportion of Firmicutes, otherwise two B. subtilis significantly improved the proportion of Proteobacteria, Bacteroidetes, Actinobacteria, and Acidobacteria at the phylum level during starter phase and decreased the proportion of Bacteroidetes during growing phase compared with the control. The supplementation with B.subtilis DSM32315 significantly improved the proportion of Clostridiales during starter phase, whereas two B. subtilis significantly improved the proportion of Pseudomonas, Burkholderia, Prevotella, DA101 during growing phase at the genus level compared with the control. In conclusion, the dietary supplementation with probiotic Bacillus spp. strains improved body weight and intestinal morphology in broiler chickens, which might be associated with the gut microbiota.
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Affiliation(s)
- Cheng-liang Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Wang
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hai-jun Zhang
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shu-geng Wu
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qian-ru Hui
- Department of Animal Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Cheng-bo Yang
- Department of Animal Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Re-jun Fang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Guang-hai Qi
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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230
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Yang G, Zhang P, Liu H, Zhu X, Dong W. Spatial variations in intestinal skatole production and microbial composition in broilers. Anim Sci J 2019; 90:412-422. [PMID: 30656801 DOI: 10.1111/asj.13164] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/17/2018] [Accepted: 11/27/2018] [Indexed: 11/28/2022]
Abstract
Spatial variations in intestinal skatole production and microbial composition in broilers were evaluated. Fifteen 42-day-old broilers were slaughtered. Samples were taken from the broilers' ileum, cecum, and rectum and analyzed for skatole levels. Denaturing gradient gel electrophoresis (DGGE) technique was used to analyze the microbial community from the intestinal digesta. The skatole levels could be arranged in decreasing order: cecum > rectum > ileum. Cecal lactate and acetate levels were higher than those of ileum and rectum (p < 0.01). Cecal microbial diversity and richness were higher than those of ileum (p < 0.05). One specific DGGE band was found in cecal sample and is closely related to Bacteroides uniformis. Cecum and rectum samples consisted of three coexistence bands, the related bacteria included Lactobacillus vaginalis and two members of Candidatus Arthromitus. The total bacterial population in cecum was higher than that in ileum and rectum (p < 0.05). Skatole levels were positively correlated with microbial Shannon-Wiener index, richness, total bacteria (p < 0.01) and Lactobacilli and Bifidobacterium (p < 0.05) populations. These results suggest that the variations in fermentation patterns are more likely to explain differences in intestinal skatole level. Bacteroides uniformis may play a role in the production of skatole.
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Affiliation(s)
- Guiqin Yang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Pei Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Haiying Liu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Xin Zhu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Weiguo Dong
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
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231
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Yadav S, Jha R. Strategies to modulate the intestinal microbiota and their effects on nutrient utilization, performance, and health of poultry. J Anim Sci Biotechnol 2019; 10:2. [PMID: 30651986 PMCID: PMC6332572 DOI: 10.1186/s40104-018-0310-9] [Citation(s) in RCA: 272] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/27/2018] [Indexed: 12/12/2022] Open
Abstract
Poultry is widely produced and consumed meat globally. Its demand is expected to continue increasing to meet the animal protein requirement for ever-increasing human population. Thus, the challenge that poultry scientists and industry face are to produce sufficient amount of poultry meat in the most efficient way. In the past, using antibiotics to promote the growth of poultry and manage gut microbiota was a norm. However, due to concerns over potential fatalistic impacts on food animals and indirectly to humans, their use as feed additives are banned or regulated in several jurisdictions. In this changed context, several alternative strategies have been proposed with some success that mimics the functions of antibiotics as growth promoters and modulate gut microbiota for their beneficial roles. These include the use of probiotics, prebiotics, organic acids, and exogenous enzyme, among others. Gut microbiota and their metabolic products improve nutrient digestion, absorption, metabolism, and overall health and growth performance of poultry. This paper reviews the available information on the effect of feed additives used to modulate intestinal microbiota of poultry and their effects on overall health and growth performance. Understanding these functions and interactions will help to develop new dietary and managerial strategies that will ultimately lead to enhanced feed utilization and improved growth performance of poultry. This review will help future researchers and industry to identify alternative feed ingredients having properties like prebiotics, probiotics, organic acids, and exogenous enzymes.
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Affiliation(s)
- Sudhir Yadav
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, 1955 East-West Rd, Honolulu, HI 96822 USA
| | - Rajesh Jha
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, 1955 East-West Rd, Honolulu, HI 96822 USA
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232
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Chen WL, Tang SGH, Jahromi MF, Candyrine SCL, Idrus Z, Abdullah N, Liang JB. Metagenomics analysis reveals significant modulation of cecal microbiota of broilers fed palm kernel expeller diets. Poult Sci 2019; 98:56-68. [DOI: 10.3382/ps/pey366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 07/18/2018] [Indexed: 12/12/2022] Open
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233
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Siwek M, Slawinska A, Stadnicka K, Bogucka J, Dunislawska A, Bednarczyk M. Prebiotics and synbiotics - in ovo delivery for improved lifespan condition in chicken. BMC Vet Res 2018; 14:402. [PMID: 30558599 PMCID: PMC6296066 DOI: 10.1186/s12917-018-1738-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 12/05/2018] [Indexed: 02/06/2023] Open
Abstract
Commercially produced chickens have become key food-producing animals in the global food system. The scale of production in industrial settings has changed management systems to a point now very far from traditional methods. During the perinatal period, newly hatched chicks undergo processing, vaccination and transportation, which introduces a gap in access to feed and water. This gap, referred to as the hatching window, dampens the potential for microflora inoculation and as such, prevents proper microbiome, gastrointestinal system and innate immunity development. As a consequence, the industrial production of chickens with a poor microbial profile leads to enteric microbial infestation and infectious disease outbreaks, which became even more prevalent after the withdrawal of antibiotic growth promoters on many world markets (e.g., the EU).This review presents the rationale, methodology and life-long effects of in ovo stimulation of chicken microflora. In ovo stimulation provides efficient embryonic microbiome colonization with commensal microflora during the perinatal period. A carefully selected bioactive formulation (prebiotics, probiotics alone or combined into synbiotics) is delivered into the air cell of the egg on day 12 of egg incubation. The prebiotic penetrates the outer and inner egg membranes and stimulates development on the innate microflora in the embryonic guts. Probiotics are available after the mechanical breakage of the shell membranes by the chick's beak at the beginning of hatching (day 19). The intestinal microflora after in ovo stimulation is potent enough for competitive exclusion and programs the lifespan condition. We present the effects of different combinations of prebiotic and probiotic delivered in ovo on day 12 of egg incubation on microflora, growth traits, feed efficiency, intestinal morphology, meat microstructure and quality, immune system development, physiological characteristics and the transcriptome of the broiler chickens.We discuss the differences between in ovo stimulation (day 12 of egg incubation) and in ovo feeding (days 17-18 of egg incubation) and speculate about possible future developments in this field. In summary, decades of research on in ovo stimulation and the lifelong effects support this method as efficient programming of lifespan conditions in commercially raised chickens.
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Affiliation(s)
- M. Siwek
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Mazowiecka, 28 85-084 Bydgoszcz, Poland
| | - A. Slawinska
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Mazowiecka, 28 85-084 Bydgoszcz, Poland
| | - K. Stadnicka
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Mazowiecka, 28 85-084 Bydgoszcz, Poland
| | - J. Bogucka
- Department of Animal Physiology, Physiotherapy and Nutrition, UTP University of Science and Technology, Mazowiecka, 28 85-084 Bydgoszcz, Poland
| | - A. Dunislawska
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Mazowiecka, 28 85-084 Bydgoszcz, Poland
| | - M. Bednarczyk
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Mazowiecka, 28 85-084 Bydgoszcz, Poland
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234
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Dias DM, Kolba N, Binyamin D, Ziv O, Regini Nutti M, Martino HSD, Glahn RP, Koren O, Tako E. Iron Biofortified Carioca Bean ( Phaseolus vulgaris L.)-Based Brazilian Diet Delivers More Absorbable Iron and Affects the Gut Microbiota In Vivo ( Gallus gallus). Nutrients 2018; 10:E1970. [PMID: 30551574 PMCID: PMC6316146 DOI: 10.3390/nu10121970] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/04/2018] [Accepted: 12/09/2018] [Indexed: 12/22/2022] Open
Abstract
Biofortification aims to improve the micronutrient concentration and bioavailability in staple food crops. Unlike other strategies utilized to alleviate Fe deficiency, studies of the gut microbiota in the context of Fe biofortification are scarce. In this study, we performed a 6-week feeding trial in Gallus gallus (n = 15), aimed to investigate the Fe status and the alterations in the gut microbiome following the administration of Fe-biofortified carioca bean based diet (BC) versus a Fe-standard carioca bean based diet (SC). The tested diets were designed based on the Brazilian food consumption survey. Two primary outcomes were observed: (1) a significant increase in total body Hb-Fe values in the group receiving the Fe-biofortified carioca bean based diet; and (2) changes in the gut microbiome composition and function were observed, specifically, significant changes in phylogenetic diversity between treatment groups, as there was increased abundance of bacteria linked to phenolic catabolism, and increased abundance of beneficial SCFA-producing bacteria in the BC group. The BC group also presented a higher intestinal villi height compared to the SC group. Our results demonstrate that the Fe-biofortified carioca bean variety was able to moderately improve Fe status and to positively affect the intestinal functionality and bacterial populations.
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Affiliation(s)
- Desirrê Morais Dias
- Department of Nutrition and Health, Federal University of Viçosa, 36570000 Viçosa, Minas Gerais, Brazil.
- Department of Food Science and Technology, Cornell University, Ithaca, NY 14850, USA.
| | - Nikolai Kolba
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14850, USA.
| | - Dana Binyamin
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel.
| | - Oren Ziv
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel.
| | | | | | - Raymond P Glahn
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14850, USA.
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel.
| | - Elad Tako
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14850, USA.
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235
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Biasato I, Ferrocino I, Biasibetti E, Grego E, Dabbou S, Sereno A, Gai F, Gasco L, Schiavone A, Cocolin L, Capucchio MT. Modulation of intestinal microbiota, morphology and mucin composition by dietary insect meal inclusion in free-range chickens. BMC Vet Res 2018; 14:383. [PMID: 30514391 PMCID: PMC6278000 DOI: 10.1186/s12917-018-1690-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 11/09/2018] [Indexed: 11/19/2022] Open
Abstract
Background Gut health in poultry depends on the balance between the host, intestinal microbiota, intestinal microscopic features and diet. The effects of insect meal (a promising alternative protein source for poultry feed) on chicken gut morphology have recently been reported, but no data about intestinal microbiota and mucin composition modulation are available. The present study evaluated the effects of dietary Tenebrio molitor (TM) meal inclusion on gut health of free-range chickens by intestinal microbiota, morphology and mucin composition characterization. Results One hundred forty female medium-growing hybrids were divided into 2 dietary treatments (control feed [C] and 7.5% TM inclusion, with 5 replicate pens/treatment and 14 birds/pen) and slaughtered at 97 days of age (2 birds/pen for a total of 10 chickens/diet). The gut microbiota assessment on cecal content samples by 16S rRNA amplicon based sequencing showed higher alpha (Shannon, P < 0.05) and beta (Adonis and ANOSIM, P < 0.001) diversity in birds fed TM diet than C. In comparison with C group, TM birds displayed significant increase and decrease, respectively, of the relative abundances of Firmicutes and Bacteroidetes phyla, with higher Firmicutes:Bacteroidetes ratios (False Discovery Rate [FDR] < 0.05). The relative abundance of Clostridium, Oscillospira, Ruminococcus, Coprococcus and Sutterella genera was higher in TM chickens than C (FDR < 0.05). On the contrary, TM birds displayed significant decrease of the relative abundance of Bacteroides genus compared to the C group (FDR < 0.05). Gut morphology evaluation by morphometric analysis on small intestine revealed similar villus height, crypt depth and villus height to crypt depth ratio between C and TM birds. Characterization of gut mucin composition by periodic-acid Schiff, Alcian Blue pH 2.5 and high iron diamine staining on small and large intestine showed unaffected mucin staining intensity in TM chickens when compared to C group. Conclusions Dietary TM meal inclusion may positively modulate the gut microbiota of the free-range chickens without influencing the intestinal morphology and mucin composition. Since the rapid growth of chickens directly depends on morphological and functional integrity of the digestive tract, the gut health assessment by a post mortem multidisciplinary approach appears to be fundamental. Electronic supplementary material The online version of this article (10.1186/s12917-018-1690-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ilaria Biasato
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Elena Biasibetti
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Elena Grego
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Sihem Dabbou
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Alessandra Sereno
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Francesco Gai
- Institute of Science of Food Production, National Research Council, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Laura Gasco
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy.,Institute of Science of Food Production, National Research Council, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Achille Schiavone
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy. .,Institute of Multidisciplinary Research on Sustainability, University of Turin, Via Accademia Albertina 13, 10100, Turin, Italy.
| | - Luca Cocolin
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Maria Teresa Capucchio
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
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236
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Community-Level Physiological Profiling for Microbial Community Function in Broiler Ceca. Curr Microbiol 2018; 76:173-177. [PMID: 30488164 DOI: 10.1007/s00284-018-1602-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/20/2018] [Indexed: 10/27/2022]
Abstract
Poultry production is a major agricultural output worldwide. It is known that the gut health of broilers is essential for their growth and for providing wholesome products for human consumption. Previously, the microbial diversity of broiler ceca was studied at the genetic level. However, the functional diversity and metabolic activity of broiler cecal bacterial communities are not fully investigated. Recently, the EcoPlates™ from Biolog, Inc. have been used for characterizing bacterial communities from various environments. In this study, we applied these plates to physiologically profile cecal bacterial communities in broilers. The ceca were aseptically excised from 6-week-old broilers, and their contents were suspended in phosphate buffered saline. The cultures in the EcoPlates™ were incubated at 42 °C for 5 days in an OmniLog® system. Responses of the bacterial communities to the various chemicals as carbon sources were measured on formazan production. The results show sigmoidal growth curves with three phases in all 12 cecal samples. Cecal bacterial communities could not use 11 carbon substrates for carbon sources; instead, they used pyruvic acid methyl ester, glycogen, glucose-1-phosphate and N-acetyl-D-glucosamine most frequently. Each bacterial community metabolized various numbers of the substrates at different rates among broilers. In the future, modification of the culture conditions to mimic the gut environment is needed. More investigations on the effects of nutrients, Salmonella or Campylobacter on physiological functions of cecal bacterial communities will provide insights into the improvement of animal well-being, saving production expenditures for producers and providing safer poultry products for human consumption.
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237
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Shang Y, Kumar S, Oakley B, Kim WK. Chicken Gut Microbiota: Importance and Detection Technology. Front Vet Sci 2018; 5:254. [PMID: 30406117 PMCID: PMC6206279 DOI: 10.3389/fvets.2018.00254] [Citation(s) in RCA: 219] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 09/24/2018] [Indexed: 12/29/2022] Open
Abstract
Sustainable poultry meat and egg production is important to provide safe and quality protein sources in human nutrition worldwide. The gastrointestinal (GI) tract of chickens harbor a diverse and complex microbiota that plays a vital role in digestion and absorption of nutrients, immune system development and pathogen exclusion. However, the integrity, functionality, and health of the chicken gut depends on many factors including the environment, feed, and the GI microbiota. The symbiotic interactions between host and microbe is fundamental to poultry health and production. The diversity of the chicken GI microbiota is largely influenced by the age of the birds, location in the digestive tract and diet. Until recently, research on the poultry GI microbiota relied on conventional microbiological techniques that can only culture a small proportion of the complex community comprising the GI microbiota. 16S rRNA based next generation sequencing is a powerful tool to investigate the biological and ecological roles of the GI microbiota in chicken. Although several challenges remain in understanding the chicken GI microbiome, optimizing the taxonomic composition and biochemical functions of the GI microbiome is an attainable goal in the post-genomic era. This article reviews the current knowledge on the chicken GI function and factors that influence the diversity of gut microbiota. Further, this review compares past and current approaches that are used in chicken GI microbiota research. A better understanding of the chicken gut function and microbiology will provide us new opportunities for the improvement of poultry health and production.
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Affiliation(s)
- Yue Shang
- St. Boniface Hospital Research Centre, Winnipeg, MB, Canada
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Sanjay Kumar
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Brian Oakley
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Woo Kyun Kim
- Department of Poultry Science, University of Georgia, Athens, GA, United States
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238
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Birkl P, Bharwani A, Kjaer JB, Kunze W, McBride P, Forsythe P, Harlander-Matauschek A. Differences in cecal microbiome of selected high and low feather-pecking laying hens. Poult Sci 2018; 97:3009-3014. [PMID: 29800328 PMCID: PMC6093748 DOI: 10.3382/ps/pey167] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/07/2018] [Indexed: 01/08/2023] Open
Abstract
In mammals, it has become increasingly clear that the gut microbiota influences not only gastrointestinal physiology but also modulates behavior. In domestic birds, ceca have the greatest gastrointestinal microbial population. Feather-pecking (FP) behavior in laying hens is one of the most important unsolved behavioral issues in modern agriculture. The aim of the present study was to assess the cecal microbial community of divergently selected high (HFP; n = 20) and low (LFP; n = 20) feather-pecking birds at 60 wk of age. The cecal samples were subjected to community profiling of 16S rRNA and in silico metagenomics using a modified bar-coded Illumina sequencing method on a MiSeq Illumina sequencer. Our results revealed that compared to HFP birds, LFP birds are characterized by an increased overall microbial diversity (beta diversity) shown by a difference in the Bray–Curtis index (R2 = 0.171, P < 0.05). Furthermore, operational taxonomic unit comparisons showed an increased presence of Clostridiae and decreased presence of Lactobaccillacae in HFP birds when compared to LFP birds (False Discovery Rate < 0.05, Mann–Whitney comparisons). Our data indicate that there may be differences in the cecal profile between these 2 lines of laying hens. More research, building on this first study using sequencing technology for profiling the chicken cecal microbiome, will be needed in order to reveal if and how there exists a functional link between the performance of FP and the cecal microbial community.
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Affiliation(s)
- P Birkl
- Department of Animal Biosciences, University of Guelph, ON N1G 2W1 Guelph, Canada
| | - A Bharwani
- Brain-Body Institute and Firestone Institute for Respiratory Health, Department of Medicine, McMaster University, 50 Carlton Avenue East, L8N 4A6 Hamilton, Canada
| | - J B Kjaer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Animal Welfare and Animal Husbandry, Doernbergstrasse 25 & 27, 29223 Celle, Germany
| | - W Kunze
- Brain-Body Institute and Firestone Institute for Respiratory Health, Department of Medicine, McMaster University, 50 Carlton Avenue East, L8N 4A6 Hamilton, Canada
| | - P McBride
- Department of Animal Biosciences, University of Guelph, ON N1G 2W1 Guelph, Canada
| | - P Forsythe
- Brain-Body Institute and Firestone Institute for Respiratory Health, Department of Medicine, McMaster University, 50 Carlton Avenue East, L8N 4A6 Hamilton, Canada
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239
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Broom LJ, Kogut MH. The role of the gut microbiome in shaping the immune system of chickens. Vet Immunol Immunopathol 2018; 204:44-51. [PMID: 30596380 DOI: 10.1016/j.vetimm.2018.10.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/14/2018] [Accepted: 10/10/2018] [Indexed: 01/01/2023]
Abstract
Most animals are colonised by at least as many microbial cells as somatic cells, potentially comprising at least 100 times more genes within just the gut microbiota than the host itself. It is, therefore, evident that such a conglomeration can have a profound effect on various bodily systems, particularly the (gut) immune system. Chickens are major providers of efficiently produced protein for humans but also harbour common foodborne pathogens and are susceptible to significant and costly diseases, making a thorough understanding of the influence of the gut microbiome on the immune system very pertinent. Major colonisation of the chicken intestine occurs after hatch and this, along with subsequent microbiota composition and activity, are influenced by numerous host and environmental factors, such that each individual has a unique microbiome signature. However, both extreme (e.g. germ free) and more subtle (e.g. diet changes) microbiome modifications can profoundly impact the development of the gut immune system, particularly adaptive immune apparatus and function. This review will consider the influence of the chicken gut microbiome on immune system development, the implications of this relationship in terms of disease susceptibility, vaccine response, optimal health and productivity, and thus exogenous approaches to positively shape microbiome-immune system interactions.
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Affiliation(s)
- Leon J Broom
- Gut Health Consultancy, Exeter, Devon, United Kingdom; Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom.
| | - Michael H Kogut
- Southern Plains Agricultural Research Center, USDA-ARS, College Station, TX, 77845, United States of America
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240
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Shang Y, Kumar S, Thippareddi H, Kim WK. Effect of Dietary Fructooligosaccharide (FOS) Supplementation on Ileal Microbiota in Broiler Chickens. Poult Sci 2018; 97:3622-3634. [DOI: 10.3382/ps/pey131] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 07/11/2018] [Indexed: 12/11/2022] Open
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241
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The use of random forests modelling to detect yeast-mannan sensitive bacterial changes in the broiler cecum. Sci Rep 2018; 8:13270. [PMID: 30185819 PMCID: PMC6125325 DOI: 10.1038/s41598-018-31438-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 08/16/2018] [Indexed: 02/08/2023] Open
Abstract
In this study, sequencing of the 16S rRNA gene targeting the V4-V6 regions was conducted to assess the cecal microbial alterations in response to dietary supplementation with a yeast derived mannan rich fraction (MRF) in standard commercial broiler production settings across four separate broiler trials. The resulting data was analysed to identify consistent changes in the bacterial community structure of the broiler cecum in response to MRF supplementation. Subsequently, the datasets from each individual trial were pooled and analysed for differences between control and MRF supplemented diets at day 35 posthatch. The results from this analysis showed that Phylum Firmicutes was decreased and Phylum Bacteroidetes was increased across all four trials at day 35 posthatch when compared to the control. An extension of the random forest bioinformatics approach to discover a highly relevant set of microbial operational taxonomic units (OTUs) which are indicative of MRF supplementation in the broiler cecum was then used. This approach has enabled the identification of a novel set of yeast-mannan sensitive bacterial OTUs in the cecal microbiome. This information will be helpful in developing potential future nutritional strategies and will be favourable to the poultry industry.
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242
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Clavijo V, Flórez MJV. The gastrointestinal microbiome and its association with the control of pathogens in broiler chicken production: A review. Poult Sci 2018; 97:1006-1021. [PMID: 29253263 PMCID: PMC5850219 DOI: 10.3382/ps/pex359] [Citation(s) in RCA: 277] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/29/2017] [Indexed: 12/23/2022] Open
Abstract
The microbiome of the broiler chicken gastrointestinal tract (GIT) has been extensively studied, and it has been amply demonstrated that it plays an important role in the health of the host, as it has a positive impact on the immune system, the physiology of the GIT, and productivity. Also, the microbiota is involved in reducing and preventing colonization by enteric pathogens through the process of competitive exclusion and the production of bacteriostatic and bactericidal substances. The taxonomic composition of the microbiota is affected by different factors, such as the organ, the age of the animal, diet and the use of antimicrobials. Different kinds of additives that regulate the microbial community in feed include probiotics (live microorganisms that when administered in adequate amounts confer a health benefit on the host), prebiotics (ingredients that stimulate increased beneficial microbial activity in the digestive system in order to improve the health of the host) and phytobiotics (primary or secondary components of plants that contain bioactive compounds that exert a positive effect on the growth and health of animals). Phages may potentially provide an integrated solution to modulate the intestinal microbiome of chicken intestines, as they reduce specific pathogenic microbial populations, permitting the proliferation of beneficial microbiota. Studies have shown that the use of cocktails of phages, especially in high concentrations and with short lapses of time between exposure to the bacteria and treatment with phages, optimize the reduction of Salmonella in chickens. Each of these technologies has demonstrable positive effects on the health of the host and the reduction of the pathogen load in controlled assays. This paper presents a comprehensive summary of the role of the microbiota in the broiler chicken gastrointestinal tract, and discusses the usefulness of different strategies for its modulation to control pathogens, with a particular emphasis on bacteriophages.
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Affiliation(s)
- Viviana Clavijo
- Department of Biological Sciences, Universidad de los Andes, Carrera 1 Este N° 19A-40, Bogotá, Colombia
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243
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Choi JH, Lee K, Kim DW, Kil DY, Kim GB, Cha CJ. Influence of dietary avilamycin on ileal and cecal microbiota in broiler chickens. Poult Sci 2018; 97:970-979. [PMID: 29253227 DOI: 10.3382/ps/pex360] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/27/2017] [Indexed: 12/20/2022] Open
Abstract
The mechanisms by which antibiotic growth promoters (AGP) enhance growth rates, feed efficiencies, and disease resistance in poultry need to be understood for designing safer and alternative strategies to replace AGP. Avilamycin has been widely used as an AGP in poultry, but its impact on the structure and function of the gut microbiome of broiler chickens has not been fully elucidated. In this study, we investigated the bacterial communities of the ileum and cecum in broiler chickens fed with an avilamycin-supplemented diet, by high-throughput sequencing of bacterial 16S rRNA genes. Alpha diversity metrics indicated that the ileal bacterial diversity was higher in avilamycin-fed chickens than in the control group, whereas the opposite was true for the cecum. Multivariate analyses revealed that the ileal microbiota of the avilamycin-fed group were clearly distinguished from those of the control group, whereas the cecal bacterial communities were apparently not influenced by feeding diets containing avilamycin. In the ilea, 2 operational taxonomic units (OTU) that matched Lactobacillus reuteri and Clostridium were enriched (P = 0.016 and P = 0.007, respectively) in the avilamycin-fed group, and an OTU belonging to Lactobacillus crispatus was decreased (P = 0.016). In the cecal microbiota showing much higher diversity with 1,286 non-singleton OTU, 12 OTU were decreased, and 3 were increased in response to avilamycin treatment (P = 0.005-0.047). Functional profiling of bacterial communities based on PICRUSt analysis revealed that 10 functional categories were enriched by avilamycin treatments, and 4 functional categories were decreased. In conclusion, our results demonstrated that the influence of avilamycin supplementation on the diversity, taxonomic composition, and functional profiles of the microbiota was evidently different in the ileum and cecum. These results further our understanding of the impact of AGP on the composition and activity of commensal bacteria in the chicken gastrointestinal tract to develop novel feeding strategies for improving animal health and performance.
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Affiliation(s)
- J-H Choi
- Department of Systems Biotechnology
| | - K Lee
- Department of Systems Biotechnology.,Center for Antibiotic Resistome
| | - D-W Kim
- Department of Systems Biotechnology.,Center for Antibiotic Resistome
| | - D Y Kil
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - G-B Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - C-J Cha
- Department of Systems Biotechnology.,Center for Antibiotic Resistome
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244
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Micciche AC, Foley SL, Pavlidis HO, McIntyre DR, Ricke SC. A Review of Prebiotics Against Salmonella in Poultry: Current and Future Potential for Microbiome Research Applications. Front Vet Sci 2018; 5:191. [PMID: 30159318 PMCID: PMC6104193 DOI: 10.3389/fvets.2018.00191] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/25/2018] [Indexed: 12/13/2022] Open
Abstract
Prebiotics are typically fermentable feed additives that can directly or indirectly support a healthy intestinal microbiota. Prebiotics have gained increasing attention in the poultry industry as wariness toward antibiotic use has grown in the face of foodborne pathogen drug resistance. Their potential as feed additives to improve growth, promote beneficial gastrointestinal microbiota, and reduce human-associated pathogens, has been well documented. However, their mechanisms remain relatively unknown. Prebiotics increasing short chain fatty acid (SCFA) production in the cecum have long since been considered a potential source for pathogen reduction. It has been previously concluded that prebiotics can improve the safety of poultry products by promoting the overall health and well-being of the bird as well as provide for an intestinal environment that is unfavorable for foodborne pathogens such as Salmonella. To better understand the precise benefit conferred by several prebiotics, "omic" technologies have been suggested and utilized. The data acquired from emerging technologies of microbiomics and metabolomics may be able to generate a more comprehensive detailed understanding of the microbiota and metabolome in the poultry gastrointestinal tract. This understanding, in turn, may allow for improved administration and optimization of prebiotics to prevent foodborne illness as well as elucidate unknown mechanisms of prebiotic actions. This review explores the use of prebiotics in poultry, their impact on gut Salmonella populations, and how utilization of next-generation technologies can elucidate the underlying mechanisms of prebiotics as feed additives.
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Affiliation(s)
- Andrew C. Micciche
- Department of Food Science, Center for Food Safety, University of ArkansasFayetteville, AR, United States
| | - Steven L. Foley
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug AdministrationJefferson, AR, United States
| | | | | | - Steven C. Ricke
- Department of Food Science, Center for Food Safety, University of ArkansasFayetteville, AR, United States
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245
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Liu L, Lin L, Zheng L, Tang H, Fan X, Xue N, Li M, Liu M, Li X. Cecal microbiome profile altered by Salmonella enterica, serovar Enteritidis inoculation in chicken. Gut Pathog 2018; 10:34. [PMID: 30087697 PMCID: PMC6074038 DOI: 10.1186/s13099-018-0261-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 07/27/2018] [Indexed: 12/21/2022] Open
Abstract
Background Salmonella enterica, serovar Enteritidis (S. Enteritidis), an important zoonotic foodborne pathogen, can affect the microbiota of the chicken intestine and cause many enteric diseases, such as acute gastroenteritis. The gut microbiota contributes to the development and function of the host immune system and competes with pathogenic microbes. The interaction between S. Enteritidis and the host cecal microbiota is still not fully understood. We investigated the microbiome composition in both treated and control groups through 16S ribosomal RNA (rRNA) gene sequencing at 1, 3, 7, 14, 21, 28, and 35 days post-S. Enteritidis inoculation (dpi) in the current study. Results Chao1 richness and Shannon diversity significantly increased with chicken development in both the treated and control groups (P < 0.05). The Chao1 index was significantly lower in the treated group than that in the control group at 14 dpi (P < 0.05). Phyla Proteobacteria and Firmicutes were most dominant at 1 and 3 dpi. S. Enteritidis inoculation influenced cecal microbiota mainly at 7 and 14 dpi. S. Enteritidis inoculation significantly altered the relative abundance of 18 genera at different time points (P < 0.05) with relative abundance significantly changed after 14 dpi. The abundance of those genera changed dramatically between 28 and 35 dpi in the treated group compared to control group. Positive correlations existed between Bacillus and Blautia and between Coprococcus and Flavonifractor following S. Enteritidis inoculation. Conclusions Our results indicated that both development and S. Enteritidis have effect on chicken cecal microbiota profiles. S. Enteritidis inoculation in young chicks influences the cecal microbiota mainly at 7 and 14 dpi. The cecal microbiota exhibited immunity to S. Enteritidis inoculation at 28 dpi. These findings will provide basic knowledge of the role that chicken cecal microbiota play in response to S. Enteritidis inoculation.
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Affiliation(s)
- Liying Liu
- 2College of Life Science, Shandong Agricultural University, Tai'an, 271000 Shandong China
| | - Lili Lin
- 1College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271000 Shandong China
| | - Linna Zheng
- 1College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271000 Shandong China
| | - Hui Tang
- 1College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271000 Shandong China
| | - Xinzhong Fan
- 1College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271000 Shandong China
| | - Nianguo Xue
- 1College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271000 Shandong China
| | - Min Li
- 1College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271000 Shandong China
| | - Min Liu
- 1College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271000 Shandong China
| | - Xianyao Li
- 1College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271000 Shandong China.,3Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an, 271018 Shandong China
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Physiological alterations of poultry to the high environmental temperature. J Therm Biol 2018; 76:101-106. [PMID: 30143284 DOI: 10.1016/j.jtherbio.2018.07.012] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 06/05/2018] [Accepted: 07/21/2018] [Indexed: 01/12/2023]
Abstract
Heat stress has become a serious problem in poultry industry along with rising of the global temperatures. High environmental temperature causes deleterious impacts on physiology and immunology of poultry and impairs their productivity. Heat stress is linked to compromised productivity through a decline in growth rate, feed utilization, blood biochemistry and immunity. In addition, heat stress induced adverse effects on mineral balance of birds and the extent of such effects depended on the type of mineral and the severity of heat stress. Exposure of broilers to high temperature adversely affects mineral metabolism and their excretion route and reduced the retention of some minerals like P, Na, K, S, Mg, Mn, Zn and Cu. On the other hand, the effect of climate on intestinal microbiota has been described in a number of studies. Where, exposure to heat stress can also increase the colonization of Salmonella in the intestine and increase the susceptibility of birds to E. coli and change ileal contents. It is also characterized by decreased antioxidant enzymes in poultry species, resulting in increased oxidative stress that means presence of reactive oxygen species (ROS) in excess of the available antioxidant capacity of animal cells. However, further studies are still required to increase the information and knowledge of basic mechanisms associated with the consequences of heat stress on poultry. This article focuses on the scientific evidence available on the negative role of heat stress on physiological responses, biochemical blood parameters, immunity, antioxidant, mineral balance, acid-base balance, osmoregulation, body and rectal temperature, intestinal and ileal microbiota as well as the parameters related to thyroid, liver and kidney functions in some poultry species.
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Yacoubi N, Saulnier L, Bonnin E, Devillard E, Eeckhaut V, Rhayat L, Ducatelle R, Van Immerseel F. Short-chain arabinoxylans prepared from enzymatically treated wheat grain exert prebiotic effects during the broiler starter period. Poult Sci 2018; 97:412-424. [PMID: 29140465 DOI: 10.3382/ps/pex297] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Indexed: 11/20/2022] Open
Abstract
Carbohydrate-degrading multi-enzyme preparations (MEP) are used to improve broiler performances. Their mode of action is complex and not fully understood. In this study, we compared the effect of water-soluble fractions isolated at the pilot scale from wheat grain incubated with (WE) and without (WC) MEP. The fractions were incorporated in a wheat-based diet (0.1% w/w) to feed Ross PM3 broilers and compared with a non-supplemented control group (NC). The body weight gain (BWG), feed intake (FI), and feed conversion ratio (FCR) until d 14 were determined. At d 14, ileal and cecal contents and tissue samples were collected from euthanized animals. The intestinal contents were used to measure the short-chain fatty acids (SCFA) concentration using gas chromatography and to determine the abundance and composition of microbiota using 16S sequencing. Villi length of ileal samples was measured, while L-cell and T-cell densities were determined using immuno-histochemistry. The MEP treatment increased the amount of water-soluble arabinoxylans (AX) and reduced their molecular weight while retaining their polymer behavior. The WE fraction significantly (P < 0.05) increased FI by 13.8% and BWG by 14.7% during the first wk post hatch when compared to NC. No significant effect on FCR was recorded during the trial. The WE increased the abundance of Enterococcus durans and Candidatus arthromitus in the ileum and of bacteria within the Lachnospiraceae and Ruminococcaceae families, containing abundant butyrate-producing bacteria, in the ceca. It also increased the concentration of SCFA in the ceca, decreased the T-lymphocyte infiltration in the intestinal mucosa, and increased the glucagon-like-peptide-2 (GLP-2)-producing L-cell density in the ileal epithelium compared with WC and NC. No significant effects were observed on villi length. These results showed that AX present in the WE fraction altered the microbiota composition towards butyrate producers in the ceca. Butyrate may be responsible for the reduction of inflammation, as suggested by the decrease in T-lymphocyte infiltration, which may explain the higher feed intake leading to improved animal growth.
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Affiliation(s)
- N Yacoubi
- INRA, UR1268 Biopolymers Interactions Assemblies, BP 71627, F-44316 Nantes, France.,Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium.,Adisseo France SAS, Center of Expertise and Research in Nutrition, F-03600 Commentry, France
| | - L Saulnier
- INRA, UR1268 Biopolymers Interactions Assemblies, BP 71627, F-44316 Nantes, France
| | - E Bonnin
- INRA, UR1268 Biopolymers Interactions Assemblies, BP 71627, F-44316 Nantes, France
| | - E Devillard
- Adisseo France SAS, Center of Expertise and Research in Nutrition, F-03600 Commentry, France
| | - V Eeckhaut
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - L Rhayat
- Adisseo France SAS, Center of Expertise and Research in Nutrition, F-03600 Commentry, France
| | - R Ducatelle
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - F Van Immerseel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
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248
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Long C, Wang J, Zhang HJ, Wu SG, Qi GH. Effects of dietary rapeseed meal supplementation on cecal microbiota in laying hens with different flavin-containing monooxygenase 3 genotypes. Poult Sci 2018; 96:1748-1758. [PMID: 28339985 DOI: 10.3382/ps/pew449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 11/16/2016] [Indexed: 12/13/2022] Open
Abstract
To evaluate the effect of dietary rapeseed meal (RM) supplementation on cecal trimethylamine and bacteria in laying hens with different flavin-containing monooxygenase 3 (FMO3) genotypes, a 3 × 2 2-factorial arrangement was employed using FMO3 genotypes (AA, AT, and TT) and dietary RM (0 and 14% of diet) as the main effects. At 50 wk of age, 36 hens of AT genotype and 36 hens of TT genotype were randomly allotted to one of the 2 dietary treatments, and each dietary treatment consisted of 3 replicates with 6 birds each. A total of 12 hens with AA genotype were allotted to one of the 2 dietary treatments that consisted of 3 replicates with 2 hens. Hens were fed 0% RM in a corn-soybean (SM) diet for one wk before the 6-week feeding trial period. Dietary RM supplementation increased trimethylamine (TMA) concentrations in both egg yolks (P < 0.0001) and cecal chyme (P < 0.0001). Dietary RM supplementation increased bacterial abundance and diversity (P < 0.0001). Weighted UniFrac, Nonmetric Multidimensional Scaling, and analysis of similarity (R-ANOSIM = 0.1516; P-value = 0.014) indicated distinct clustering was dependent on diets rather than FMO3 genotypes. Twenty-four phyla (most dominant, Bacteroides, Firmicutes, and Proteobacteria) and 229 genera were identified in the cecal samples. Compared with the SM diets, RM diets increased the proportion of Firmicutes (P = 0.004), Proteobacteria (P = 0.006), and Firmicutes:Bacteroides (P = 0.001), and some low-abundance phyla (P < 0.01), whereas the abundance of Bacteroides was lower (P = 0.0002). The abundance of 42 genera varied with dietary types. Six phyla and 35 genera were positively correlated with TMA concentration in the cecal chyme. In conclusion, the major TMA-producing bacteria in cecal were from Firmicutes and Proteobacteria phyla. The major TMA-producing bacterial genera could be from the genera that positively correlated with TMA concentration.
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249
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Xiao Y, Xiang Y, Zhou W, Chen J, Li K, Yang H. Microbial community mapping in intestinal tract of broiler chicken. Poult Sci 2018; 96:1387-1393. [PMID: 28339527 DOI: 10.3382/ps/pew372] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/02/2016] [Indexed: 01/05/2023] Open
Abstract
Domestic chickens are valuable sources of protein associated with producing meat and eggs for humans. The gastrointestinal tract (GIT) houses a large microbial community, and these microbiota play an important role in growth and health of chickens, contributing to the enhancement of nutrient absorption and improvement of the birds' immune systems. To improve our understanding of the chicken intestinal microbial composition, microbiota inhabiting 5 different intestinal locations (duodenum, jejunum, ileum, cecum, and colon) of 42-day-old broiler chickens were detected based on 16S rRNA gene sequence analysis. As a result, 1,502,554 sequences were clustered into 796 operational taxonomic units (OTUs) at the 97% sequence similarity value and identified into 15 phyla and 288 genera. Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Cyanobacteria were the major microbial groups and Firmicutes was the dominant phylum in duodenum, jejunum, ileum and colon accounting for > 60% of sequences, while Bacteroidetes was the dominant phylum in cecum (>50% of sequences), but little in the other four gut sections. At the genus level, the major microbial genera across all gut sections were Lactobacillus, Enterococcus, Bacteroides, and Corynebacterium. Lactobacillus was the predominant genus in duodenum, jejunum, and ileum (>35%), but was rarely present in cecum, and Bacteroides was the most dominant group in cecum (about 40%), but rarely present in the other 4 intestinal sections. Differences of microbial composition between the 5 intestinal locations might be a cause and consequence of gut functional differences and may also reflect host selection mediated by innate or adaptive immune responses. All these results could offer some information for the future study on the relationship between intestinal microbiota and broiler chicken growth performance as well as health.
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Affiliation(s)
- Yingping Xiao
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.,State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yun Xiang
- Animal Husbandry and Veterinary Institute, Jinhua Academy of Agricultural Sciences, Jinhua, 321017, China
| | - Weidong Zhou
- Animal Husbandry and Veterinary Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jinggang Chen
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.,State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kaifeng Li
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.,State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hua Yang
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.,State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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250
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Reed S, Knez M, Uzan A, Stangoulis JCR, Glahn RP, Koren O, Tako E. Alterations in the Gut ( Gallus gallus) Microbiota Following the Consumption of Zinc Biofortified Wheat ( Triticum aestivum)-Based Diet. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:6291-6299. [PMID: 29871482 DOI: 10.1021/acs.jafc.8b01481] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The structure and function of cecal microbiota following the consumption of a zinc (Zn) biofortified wheat diet was evaluated in a well-studied animal model of human nutrition ( Gallus gallus) during a six-week efficacy trial. Using 16S rRNA gene sequencing, a significant increase in β- but not α-microbial diversity was observed in the animals receiving the Zn biofortified wheat diet, relative to the control. No significant taxonomic differences were found between the two groups. Linear discriminant analysis revealed a group of metagenomic biomarkers that delineated the Zn replete versus Zn deficient phenotypes, such that enrichment of lactic acid bacteria and concomitant increases in Zn-dependent bacterial metabolic pathways were observed in the Zn biofortified group, and expansion of mucin-degraders and specific bacterial groups able to participate in maintaining host Zn homeostasis were observed in the control group. Additionally, the Ruminococcus genus appeared to be a key player in delineating the Zn replete microbiota from the control group, as it strongly predicts host Zn adequacy. Our data demonstrate that the gut microbiome associated with Zn biofortified wheat ingestion is unique and may influence host Zn status. Microbiota analysis in biofortification trials represents a crucial area for study as Zn biofortified diets are increasingly delivered on a population-wide scale.
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Affiliation(s)
- Spenser Reed
- College of Medicine , University of Arizona , Tucson , Arizona 85724 , United States
- USDA/ARS, Robert W. Holley Center for Agriculture and Health , Cornell University , Ithaca , New York 14853 , United States
| | - Marija Knez
- College of Science and Engineering , Flinders University , Adelaide South Australia 5001 , Australia
| | - Atara Uzan
- Azrieli Faculty of Medicine , Bar-Ilan University , Safed 1311502 , Israel
| | - James C R Stangoulis
- College of Science and Engineering , Flinders University , Adelaide South Australia 5001 , Australia
| | - Raymond P Glahn
- USDA/ARS, Robert W. Holley Center for Agriculture and Health , Cornell University , Ithaca , New York 14853 , United States
| | - Omry Koren
- Azrieli Faculty of Medicine , Bar-Ilan University , Safed 1311502 , Israel
| | - Elad Tako
- USDA/ARS, Robert W. Holley Center for Agriculture and Health , Cornell University , Ithaca , New York 14853 , United States
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