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16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan

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 produ...

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Autores principales: Ocejo, Medelin, Oporto, Beatriz, Hurtado, Ana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385345/
https://www.ncbi.nlm.nih.gov/pubmed/30792439
http://dx.doi.org/10.1038/s41598-019-39323-x
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author Ocejo, Medelin
Oporto, Beatriz
Hurtado, Ana
author_facet Ocejo, Medelin
Oporto, Beatriz
Hurtado, Ana
author_sort Ocejo, Medelin
collection PubMed
description 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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spelling pubmed-63853452019-02-27 16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan Ocejo, Medelin Oporto, Beatriz Hurtado, Ana Sci Rep Article 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. Nature Publishing Group UK 2019-02-21 /pmc/articles/PMC6385345/ /pubmed/30792439 http://dx.doi.org/10.1038/s41598-019-39323-x Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Ocejo, Medelin
Oporto, Beatriz
Hurtado, Ana
16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan
title 16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan
title_full 16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan
title_fullStr 16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan
title_full_unstemmed 16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan
title_short 16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan
title_sort 16s rrna amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385345/
https://www.ncbi.nlm.nih.gov/pubmed/30792439
http://dx.doi.org/10.1038/s41598-019-39323-x
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