3 Biotech

, 9:316 | Cite as

Comparative metagenomic sequencing analysis of cecum microbiotal diversity and function in broilers and layers

  • Zhao Qi
  • Shuiqin Shi
  • Jian Tu
  • Shaowen LiEmail author
Original Article


The composition of the gastrointestinal microorganisms in poultry is closely associated with the host and its environment. In this study, using 16S rRNA and metagenomic techniques, we comprehensively analyzed the structure and diversity of the cecal microbiota of broiler chickens (BC) and laying hens (LH). The 16S rRNA sequencing analysis showed Firmicutes, Bacteroidetes, and Proteobacteria were the main cecal bacterial phyla in BC and LH. However, at the genus level, LH had a greater abundance of Bacteroides (P < 0.05), Rikenellaceae_RC9_gut_group (P < 0.01), Phascolarctobacterium (P < 0.05), Desulfovibrio (P < 0.05), Prevotellaceae_UCG-001 (P < 0.05), and unclassified_o_Bacteroidales (P < 0.05), whereas BC had a greater abundance of Alistipes (P < 0.05), Rikenella (P < 0.05), Ruminococcaceae_UCG-005 (P < 0.05), Lachnoclostridium (P < 0.05), and unclassified_f_Ruminococcaceae (P < 0.05). It is particularly noteworthy that the genus Desulfovibrio was significantly more abundant in the LH cecum than in the BC cecum (P < 0.05). A metagenomic analysis showed that the annotations in the LH dataset were significantly more abundant than in the BC dataset, and included replication, recombination and repair, energy production and transformation, cell wall/membrane/envelope biogenesis, and amino acid transport and metabolism-related functions (P < 0.05). This study indicates that microbial genotypic differences in chickens of the same species can cause changes in the abundances of the gut microbiota, but do not alter the structural composition or major functional characteristics of the gut microbiota.


16S rRNA sequencing Metagenomic sequencing Cecal microbiota Broiler chicken Laying hen Microbe composition Function 



We thank the National Science Foundation of China (grant no. 31772707) for supporting the high-throughput sequencing. The collection of the experimental samples was supported by the Integration and Demonstration of Quality and Safety Control Technology for Green Ecological Livestock and Poultry Products Industry Chain (grant no. 1604a0702033) and the Animal Food Quality and Safety Control, Anhui Province 115 Industry Innovation Team. We thank International Science Editing ( for editing this manuscript.

Author contributions

SL conceived and designed the experiments; ZQ and SS performed the experiments, and these authors contributed equally to this work; ZQ analyzed the data; SS and JT contributed reagents/materials/analysis tools, SS and ZQ wrote the paper. All authors critically read and contributed to the manuscript and approved the final version.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethics approval and consent to participate

This study was performed in accordance with the Chinese Laboratory Animal Administration Act of 1988. Before the experiments, the research protocol was reviewed and approved by the Research Ethics Committee of Anhui Agricultural University. Permission was obtained from all managers of the chicken farms studied before the samples were collected.

Supplementary material

13205_2019_1834_MOESM1_ESM.doc (123 kb)
Supplementary material 1 (DOC 123 kb)


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Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  1. 1.School of Information and ComputerAnhui Agricultural UniversityHefeiPeople’s Republic of China
  2. 2.Anhui Province Key Laboratory of Veterinary Pathobiology and Disease ControlAnhui Agricultural UniversityHefeiPeople’s Republic of China

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