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

Scientific Reports
Medelin OcejoAna Hurtado

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 ...Continue Reading

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Citations

Sep 17, 2019·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Francesca Romana MassacciNúria Mach
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Dec 7, 2021·Frontiers in Microbiology·Harald NothaftChristine M Szymanski

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Methods Mentioned

BETA
PCR

Software Mentioned

Phyloseq
Cutadapt
Sickle
DADA2
FastQC
DESeq2
R
PerMANOVA
LEfSe
Vegan

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