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Gut Microbial Composition Differs Extensively among Indian Native Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-Specific, as Well as Across-Breed Core Microbiomes, Are Found

Gut microbiota plays an important role in the health and performance of the host. Characterizations of gut microbiota, core microbiomes, and microbial networks in different chicken breeds are expected to provide clues for pathogen exclusion, improving performance or feed efficiency. Here, we charact...

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Autores principales: Paul, Shyam Sundar, Chatterjee, Rudra Nath, Raju, Mantena Venkata Lakshmi Narasimha, Prakash, Bhukya, Rama Rao, Savaram Venkata, Yadav, Satya Pal, Kannan, Alagarsamy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7918296/
https://www.ncbi.nlm.nih.gov/pubmed/33672925
http://dx.doi.org/10.3390/microorganisms9020391
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author Paul, Shyam Sundar
Chatterjee, Rudra Nath
Raju, Mantena Venkata Lakshmi Narasimha
Prakash, Bhukya
Rama Rao, Savaram Venkata
Yadav, Satya Pal
Kannan, Alagarsamy
author_facet Paul, Shyam Sundar
Chatterjee, Rudra Nath
Raju, Mantena Venkata Lakshmi Narasimha
Prakash, Bhukya
Rama Rao, Savaram Venkata
Yadav, Satya Pal
Kannan, Alagarsamy
author_sort Paul, Shyam Sundar
collection PubMed
description Gut microbiota plays an important role in the health and performance of the host. Characterizations of gut microbiota, core microbiomes, and microbial networks in different chicken breeds are expected to provide clues for pathogen exclusion, improving performance or feed efficiency. Here, we characterized the gut microbiota of “finishing” chickens (at the end of production life) of indigenous Indian Nicobari, Ghagus, and Aseel breeds, originating from the Nicobari island, coastal India, and the Indian mainland, respectively, as well as a global commercial broiler line, VenCobb 400, using 16S rDNA amplicon sequencing. We found that diversity, as well as richness of microbiota, was higher in indigenous breeds than in the broiler line. Beta diversity analysis indicated the highest overlap between Ghagus and Nicobari breeds and a very low overlap between the broiler line and all indigenous breeds. Linear discriminant analysis effect size (LEfSe) revealed 82 breed- or line-specific phylotype operational taxonomic unit (OTU) level biomarkers. We confirm the presence of breed specific and across-breed core microbiomes. Additionally, we show the existence of breed specific complex microbial networks in all groups. This study provides the first (and comprehensive) insight into the gut microbiota of three indigenous breeds and one commercial broiler line of chickens reared without antimicrobials, and underscores the need to study microbial diversity in other indigenous breeds.
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spelling pubmed-79182962021-03-02 Gut Microbial Composition Differs Extensively among Indian Native Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-Specific, as Well as Across-Breed Core Microbiomes, Are Found Paul, Shyam Sundar Chatterjee, Rudra Nath Raju, Mantena Venkata Lakshmi Narasimha Prakash, Bhukya Rama Rao, Savaram Venkata Yadav, Satya Pal Kannan, Alagarsamy Microorganisms Article Gut microbiota plays an important role in the health and performance of the host. Characterizations of gut microbiota, core microbiomes, and microbial networks in different chicken breeds are expected to provide clues for pathogen exclusion, improving performance or feed efficiency. Here, we characterized the gut microbiota of “finishing” chickens (at the end of production life) of indigenous Indian Nicobari, Ghagus, and Aseel breeds, originating from the Nicobari island, coastal India, and the Indian mainland, respectively, as well as a global commercial broiler line, VenCobb 400, using 16S rDNA amplicon sequencing. We found that diversity, as well as richness of microbiota, was higher in indigenous breeds than in the broiler line. Beta diversity analysis indicated the highest overlap between Ghagus and Nicobari breeds and a very low overlap between the broiler line and all indigenous breeds. Linear discriminant analysis effect size (LEfSe) revealed 82 breed- or line-specific phylotype operational taxonomic unit (OTU) level biomarkers. We confirm the presence of breed specific and across-breed core microbiomes. Additionally, we show the existence of breed specific complex microbial networks in all groups. This study provides the first (and comprehensive) insight into the gut microbiota of three indigenous breeds and one commercial broiler line of chickens reared without antimicrobials, and underscores the need to study microbial diversity in other indigenous breeds. MDPI 2021-02-14 /pmc/articles/PMC7918296/ /pubmed/33672925 http://dx.doi.org/10.3390/microorganisms9020391 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Paul, Shyam Sundar
Chatterjee, Rudra Nath
Raju, Mantena Venkata Lakshmi Narasimha
Prakash, Bhukya
Rama Rao, Savaram Venkata
Yadav, Satya Pal
Kannan, Alagarsamy
Gut Microbial Composition Differs Extensively among Indian Native Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-Specific, as Well as Across-Breed Core Microbiomes, Are Found
title Gut Microbial Composition Differs Extensively among Indian Native Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-Specific, as Well as Across-Breed Core Microbiomes, Are Found
title_full Gut Microbial Composition Differs Extensively among Indian Native Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-Specific, as Well as Across-Breed Core Microbiomes, Are Found
title_fullStr Gut Microbial Composition Differs Extensively among Indian Native Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-Specific, as Well as Across-Breed Core Microbiomes, Are Found
title_full_unstemmed Gut Microbial Composition Differs Extensively among Indian Native Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-Specific, as Well as Across-Breed Core Microbiomes, Are Found
title_short Gut Microbial Composition Differs Extensively among Indian Native Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-Specific, as Well as Across-Breed Core Microbiomes, Are Found
title_sort gut microbial composition differs extensively among indian native chicken breeds originated in different geographical locations and a commercial broiler line, but breed-specific, as well as across-breed core microbiomes, are found
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7918296/
https://www.ncbi.nlm.nih.gov/pubmed/33672925
http://dx.doi.org/10.3390/microorganisms9020391
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