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

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PubMed ID: 30792439

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Ocejo M, Oporto B, Hurtado A

Sci Rep. Feb 2019. doi: 10.1038/s41598-019-39323-x

COMMENT: Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the complex microbial community that inhabits the chicken gut, including the ceca. By 16S rRNA high throughput sequencing, the authors provide a complete description of the chicken cecal microbiome throughout their whole productive period. Two different breeds of chickens under different productions systems have been studied. 


The aim of this study was to thoroughly characterize the caecal microbiota in two breeds of chickens fed with different diets and bred under different production systems throughout their complete lifespan; Ross-308 broilers reared for 42 days, as the fast-growing breed used in intensive chicken meat production, and a slow-growing breed (Sasso-T451A) reared in a free-range system for 84 days. The effect of breed, diet and production system was assessed to obtain a comprehensive knowledge of how microbiota develops as chickens grow in the different phases of their productive life. 


When comparing broilers and FRC*, the latter showed higher values in all alpha diversity indices.

In both breeds, the overall microbial community structure exhibited clear and significant shifts by age (total variance explained R2 = 0.45, p < 0.001 in broilers and R2 = 0.44, p < 0.001 in FRC).

Tthe diversity and composition of caecal microbiome in both breeds were strongly influenced by age, increasing in complexity and biodiversity as the chickens grew.

(...) three developmental stages of microbiota composition were identified in broilers during their lifespan and four in FRC, with an intermediate stage. The first stage, represented by 3-day-old broilers and 4 day-old FRC, showed a clearly immature microbiota dominated by Proteobacteria and Firmicutes. However, in broilers, Proteobacteria predominated (Citrobacter as main contributor) over Firmicutes (Enterococcus), and in FRC Firmicutes (Ruminococcus, fam. Lachnospiraceae) was more abundant than Proteobacteria (E. coli). In the second stage, represented by 14 day-old broilers and 18 day-old FRC, a drop in Proteobacteria proportion to less than 5% (E. coli) was observed resulting in an absolute dominance of the phylum Firmicutes (around 90%) represented by the families Lachnospiraceae and Ruminococcaceae, at similar levels in broilers but enriched in Ruminococcaceae over Lachnospiraceae in FRC. The third stage would be represented by 42 day-old broilers and 58 day-old FRC, where a replacement of members of Firmicutes with Bacteroidetes occurred, in a more gradual manner in FRC than in broilers. Firmicutes was still represented by Lachnospiraceae and Ruminococcaceae in broilers, whereas in FRC Veillonellaceae accounted for almost half of the Firmicutes, with Megamonas as the most abundant genus. The very rich and diverse caecal microbiome of 81 day-old FRC would constitute stage 4, represented by 14 phyla. The most prevalent phyla were Bacteroidetes, Firmicutes and Euryarchaeota, with Bacteroidaceae, Methanocorpusculaceae and Veillonellaceae as the most representative families, respectively.

*FRC: Free-Range Chickens


In conclusion, age was the strongest influencing factor in caecal microbiota composition of chicken (...). However, there were substantial differences in the phylogenetic composition of caecal microbiota between broilers and FRC, microbiota being richer and more complex in FRC, which had access to grass and soil outside, than in broilers reared intensively on a more limited diet. Broilers are under higher presure than FRC to grow rapidly and need a microbial community that provides optimal recovery of energy from food, whereas FRC grow slowly and have contact with complex microbial ecosystems in the environment. The higher diversity in microbial community and the presence exclusively or at higher levels in FRC of some taxa that have been associated with healthy gut, suggested that FRC harboured a more healthy microbiota.


Raquel Ruiz-Arroyo