High-throughput sequencing technology to reveal the composition and function of cecal microbiota in Dagu chicken.
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. 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.



Cecal 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.



The 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.
Department of Animal Husbandry & Veterinary Medicine, Liaoning Medical University, Jinzhou, Liaoning, 121000, China.
Yunhe
Y
Xu
Department of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
Huixin
H
Yang
Department of Food Science, Liaoning Medical University, Jinzhou, Liaoning, China.
Lili
L
Zhang
Department of Animal Husbandry & Veterinary Medicine, Liaoning Medical University, Jinzhou, Liaoning, 121000, China.
Yuhong
Y
Su
Department of Animal Husbandry & Veterinary Medicine, Liaoning Medical University, Jinzhou, Liaoning, 121000, China.
Donghui
D
Shi
Department of Animal Husbandry & Veterinary Medicine, Liaoning Medical University, Jinzhou, Liaoning, 121000, China.
Haidi
H
Xiao
Department of Animal Husbandry & Veterinary Medicine, Liaoning Medical University, Jinzhou, Liaoning, 121000, China. 13841607296@126.com.
Yumin
Y
Tian
D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D041963:Bacteroidetes / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D001483:Base Sequence; D002432:Cecum / Q000382:microbiology*; D002645:Chickens / Q000382:microbiology*; D002681:China; D002965:Classification; D003426:Crop, Avian / Q000382:microbiology; D005243:Feces; D005247:Feeding Behavior; D000069196:Gastrointestinal Microbiome; D057166:High-Throughput Screening Assays / Q000662:veterinary; D059013:Microbial Consortia / Q000235:genetics; D064307:Microbiota / Q000235:genetics; D010802:Phylogeny; D020560:Proteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000662:veterinary
D012336:RNA, Ribosomal, 16S
Cecal microbiota; Composition and function; Feeding modes; High-throughput sequencing technology