Abstract
BackgroundThe chicken gut microbiota is an important and complicated ecosystem for the host. They play an important role in converting food into nutrient and energy. The coding capacity of microbiome vastly surpasses that of the host’s genome, encoding biochemical pathways that the host has not developed. An optimal gut microbiota can increase agricultural productivity. This study aims to explore the composition and function of cecal microbiota in Dagu chicken under two feeding modes, free-range (outdoor, OD) and cage (indoor, ID) raising.ResultsCecal samples were collected from 24 chickens across 4 groups (12-w OD, 12-w ID, 18-w OD, and 18-w ID). We performed high-throughput sequencing of the 16S rRNA genes V4 hypervariable regions to characterize the cecal microbiota of Dagu chicken and compare the difference of cecal microbiota between free-range and cage raising chickens. It was found that 34 special operational taxonomic units (OTUs) in OD groups and 4 special OTUs in ID groups. 24 phyla were shared by the 24 samples. Bacteroidetes was the most abundant phylum with the largest proportion, followed by Firmicutes and Proteobacteria. The OD groups showed a higher proportion of Bacteroidetes (>50 %) in cecum, but a lower Firmicutes/Bacteroidetes ratio in both 12-w old (0.42, 0.62) and 18-w old groups (0.37, 0.49) compared with the ID groups. Cecal microbiota in the OD groups have higher abundance of functions involved in amino acids and glycan metabolic pathway.ConclusionThe composition and function of cecal microbiota in Dagu chicken under two feeding modes, free-range and cage raising are different. The cage raising mode showed a lower proportion of Bacteroidetes in cecum, but a higher Firmicutes/Bacteroidetes ratio compared with free-range mode. Cecal microbiota in free-range mode have higher abundance of functions involved in amino acids and glycan metabolic pathway.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0877-2) contains supplementary material, which is available to authorized users.
Highlights
The chicken gut microbiota is an important and complicated ecosystem for the host
operational taxonomic units (OTUs) clustering and annotation The trimmed and assembled sequences were clustered at 97 % similarity by calling uclust from Qiime. 1217 OTUs were obtained through database alignment by blast in Qiime
The number of OTUs in each group slightly changed in the OD groups, whereas that increased in the ID groups within days
Summary
The chicken gut microbiota is an important and complicated ecosystem for the host. They play an important role in converting food into nutrient and energy. Chickens have proportionally smaller intestines and shorter transit digestion times than mammals, but do not appear to any less efficient at digestion than their mammalian counterparts [1, 2] Their digestive system is adapted to extract energy from difficult to digest food sources. This may be explained, in part, by the fact that the chicken gastrointestinal tract is home to a complex microbial community, the chicken gut microbiota, which underpins the links between diet and health [3, 4]. Studies on the composition and functions of gut microbiota in animals raised in different feeding modes is significant for the improvement of feedstuff efficiency and animal productivity. The composition and function of cecal microbiota under different feeding mode are unknown
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