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The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens

The ISME Journal (2019) | Download Citation


The gut microbiota has an important role in animal health and performance, but its contribution is difficult to determine, in particular given the effects of host genetic factors. Here, whole-genome sequencing of the hosts and 16S rRNA gene sequencing of the microbiota were performed to separate the effects between host genetics and the microbiota in the duodenum, jejunum, ileum, caecum and faeces on fat deposition in 206 yellow broilers reared under identical conditions. Despite the notable spatial variation in the diversity, composition and potential function of the gut microbiota, host genetics exerted limited effects on the gut microbial community. The duodenal and caecal microbiota made greater contributions to fat deposition and could separately account for 24% and 21% of the variance in the abdominal fat mass after correcting for host genetic effects. We further identified two caecal microbial taxa, Methanobrevibacter and Mucispirillum schaedleri, which were significantly correlated with fat deposition. Chickens with a lower Methanobrevibacter abundance had significantly lower abdominal fat content than those with a higher abundance of Methanobrevibacter (35.51 vs. 55.59 g), and the body weights of these chickens did not notably differ. Chickens with a higher M. schaedleri abundance exhibited lower abdominal fat accumulation (39.88 vs. 55.06 g) and body weight (2.23 vs. 2.41 kg) than those with a lower abundance of this species. These findings may aid the development of strategies for altering the gut microbiota to control fat deposition during broiler production.

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This work was supported by Programs for Changjiang Scholars and Innovative Research in Universities (IRT_15R62) and Chinese Universities Scientific Fund (2018TC026 and 2018QC030). We thank Dr Bingkun Zhang from the Department Animal Nutrition and Feed Sciences of China Agricultural University for helpful discussion on chicken nutrition and gastrointestinal physiology.

Author contributions:

NY and JZ conceived and designed this study. CW, WY, JZ, CS, CJ, QZ and DZ performed the phenotype and sample collection. CW analyzed the data and wrote the manuscript. WY assisted in the 16S rRNA gene sequencing data analysis. CS assisted in the whole-genome sequencing data analysis. NY, CS and JZ contributed to the revisions. All authors reviewed and approved the final manuscript.

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  1. These authors contributed equally: Chaoliang Wen, Wei Yan, Congjiao Sun


  1. National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China

    • Chaoliang Wen
    • , Wei Yan
    • , Congjiao Sun
    • , Qianqian Zhou
    • , Jiangxia Zheng
    •  & Ning Yang
  2. Guangdong Wen’s Nanfang Poultry Breeding Co. Ltd, Xinxing, 527400, Guangdong Province, China

    • Congliang Ji
    •  & Dexiang Zhang


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