Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces
American cranberry (<i>Vaccinium macrocarpon</i>) and lowbush/wild blueberry (<i>V. angustifolium</i>) pomace are polyphenol-rich products having potentially beneficial effects in broiler chickens. This study investigated the cecal microbiome of broiler-vaccinated or non-vacc...
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| Format: | Article |
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MDPI AG
2023-04-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/5/1184 |
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| author | Chongwu Yang Quail Das Muhammad A. Rehman Xianhua Yin Julie Shay Martin Gauthier Calvin Ho-Fung Lau Kelly Ross Moussa S. Diarra |
| author_facet | Chongwu Yang Quail Das Muhammad A. Rehman Xianhua Yin Julie Shay Martin Gauthier Calvin Ho-Fung Lau Kelly Ross Moussa S. Diarra |
| author_sort | Chongwu Yang |
| collection | DOAJ |
| description | American cranberry (<i>Vaccinium macrocarpon</i>) and lowbush/wild blueberry (<i>V. angustifolium</i>) pomace are polyphenol-rich products having potentially beneficial effects in broiler chickens. This study investigated the cecal microbiome of broiler-vaccinated or non-vaccinated birds against coccidiosis. Birds in each of the two groups (vaccinated or non-vaccinated) were fed a basal non-supplemented diet (NC), a basal diet supplemented with bacitracin (BAC), American cranberry (CP), and lowbush blueberry (BP) pomace alone or in combination (CP + BP). At 21 days of age, cecal DNA samples were extracted and analyzed using both whole-metagenome shotgun sequencing and targeted-resistome sequencing approaches. Ceca from vaccinated birds showed a lower abundance of <i>Lactobacillus</i> and a higher abundance of <i>Escherichia coli</i> than non-vaccinated birds (<i>p</i> < 0.05). The highest and lowest abundance of <i>L. crispatus</i> and <i>E. coli</i>, respectively, were observed in birds fed CP, BP, and CP + BP compared to those from NC or BAC treatments (<i>p</i> < 0.05). Coccidiosis vaccination affected the abundance of virulence genes (VGs) related to adherence, flagella, iron utilization, and secretion system. Toxin-related genes were observed in vaccinated birds (<i>p</i> < 0.05) in general, with less prevalence in birds fed CP, BP, and CP + BP than NC and BAC (<i>p</i> < 0.05). More than 75 antimicrobial resistance genes (ARGs) detected by the shotgun metagenomics sequencing were impacted by vaccination. Ceca from birds fed CP, BP, and CP + BP showed the lowest (<i>p</i> < 0.05) abundances of ARGs related to multi-drug efflux pumps, modifying/hydrolyzing enzyme and target-mediated mutation, when compared to ceca from birds fed BAC. Targeted metagenomics showed that resistome from BP treatment was distant to other groups for antimicrobials, such as aminoglycosides (<i>p</i> < 0.05). Significant differences in the richness were observed between the vaccinated and non-vaccinated groups for aminoglycosides, β-lactams, lincosamides, and trimethoprim resistance genes (<i>p</i> < 0.05). Overall, this study demonstrated that dietary berry pomaces and coccidiosis vaccination significantly impacted cecal microbiota, virulome, resistome, and metabolic pathways in broiler chickens. |
| first_indexed | 2024-03-11T03:28:38Z |
| format | Article |
| id | doaj.art-9f4f00ca08394921ae0f254edf207175 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-11T03:28:38Z |
| publishDate | 2023-04-01 |
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| series | Microorganisms |
| spelling | doaj.art-9f4f00ca08394921ae0f254edf2071752023-11-18T02:33:01ZengMDPI AGMicroorganisms2076-26072023-04-01115118410.3390/microorganisms11051184Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry PomacesChongwu Yang0Quail Das1Muhammad A. Rehman2Xianhua Yin3Julie Shay4Martin Gauthier5Calvin Ho-Fung Lau6Kelly Ross7Moussa S. Diarra8Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, CanadaGuelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, CanadaGuelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, CanadaGuelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, CanadaOttawa Laboratory (Carling) Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1Y 4K7, CanadaBiological Informatics Centre of Excellence, AAFC, Saint-Hyacinthe, QC J2S 8E3, CanadaOttawa Laboratory (Carling) Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1Y 4K7, CanadaSummerland Research and Development Center, AAFC, Summerland, BC V0H 1Z0, CanadaGuelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, CanadaAmerican cranberry (<i>Vaccinium macrocarpon</i>) and lowbush/wild blueberry (<i>V. angustifolium</i>) pomace are polyphenol-rich products having potentially beneficial effects in broiler chickens. This study investigated the cecal microbiome of broiler-vaccinated or non-vaccinated birds against coccidiosis. Birds in each of the two groups (vaccinated or non-vaccinated) were fed a basal non-supplemented diet (NC), a basal diet supplemented with bacitracin (BAC), American cranberry (CP), and lowbush blueberry (BP) pomace alone or in combination (CP + BP). At 21 days of age, cecal DNA samples were extracted and analyzed using both whole-metagenome shotgun sequencing and targeted-resistome sequencing approaches. Ceca from vaccinated birds showed a lower abundance of <i>Lactobacillus</i> and a higher abundance of <i>Escherichia coli</i> than non-vaccinated birds (<i>p</i> < 0.05). The highest and lowest abundance of <i>L. crispatus</i> and <i>E. coli</i>, respectively, were observed in birds fed CP, BP, and CP + BP compared to those from NC or BAC treatments (<i>p</i> < 0.05). Coccidiosis vaccination affected the abundance of virulence genes (VGs) related to adherence, flagella, iron utilization, and secretion system. Toxin-related genes were observed in vaccinated birds (<i>p</i> < 0.05) in general, with less prevalence in birds fed CP, BP, and CP + BP than NC and BAC (<i>p</i> < 0.05). More than 75 antimicrobial resistance genes (ARGs) detected by the shotgun metagenomics sequencing were impacted by vaccination. Ceca from birds fed CP, BP, and CP + BP showed the lowest (<i>p</i> < 0.05) abundances of ARGs related to multi-drug efflux pumps, modifying/hydrolyzing enzyme and target-mediated mutation, when compared to ceca from birds fed BAC. Targeted metagenomics showed that resistome from BP treatment was distant to other groups for antimicrobials, such as aminoglycosides (<i>p</i> < 0.05). Significant differences in the richness were observed between the vaccinated and non-vaccinated groups for aminoglycosides, β-lactams, lincosamides, and trimethoprim resistance genes (<i>p</i> < 0.05). Overall, this study demonstrated that dietary berry pomaces and coccidiosis vaccination significantly impacted cecal microbiota, virulome, resistome, and metabolic pathways in broiler chickens.https://www.mdpi.com/2076-2607/11/5/1184berry pomacesbroiler chickenscoccidiosis vaccinemicrobiotavirulomeresistome |
| spellingShingle | Chongwu Yang Quail Das Muhammad A. Rehman Xianhua Yin Julie Shay Martin Gauthier Calvin Ho-Fung Lau Kelly Ross Moussa S. Diarra Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces Microorganisms berry pomaces broiler chickens coccidiosis vaccine microbiota virulome resistome |
| title | Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces |
| title_full | Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces |
| title_fullStr | Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces |
| title_full_unstemmed | Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces |
| title_short | Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces |
| title_sort | microbiome of ceca from broiler chicken vaccinated or not against coccidiosis and fed berry pomaces |
| topic | berry pomaces broiler chickens coccidiosis vaccine microbiota virulome resistome |
| url | https://www.mdpi.com/2076-2607/11/5/1184 |
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