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Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome

Author

Listed:
  • Congying Chen

    (Jiangxi Agricultural University)

  • Yunyan Zhou

    (Jiangxi Agricultural University)

  • Hao Fu

    (Jiangxi Agricultural University)

  • Xinwei Xiong

    (Jiangxi Agricultural University)

  • Shaoming Fang

    (Jiangxi Agricultural University)

  • Hui Jiang

    (Jiangxi Agricultural University)

  • Jinyuan Wu

    (Jiangxi Agricultural University)

  • Hui Yang

    (Jiangxi Agricultural University)

  • Jun Gao

    (Jiangxi Agricultural University)

  • Lusheng Huang

    (Jiangxi Agricultural University)

Abstract

Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog named pig integrated gene catalog (PIGC), containing 17,237,052 complete genes clustered at 90% protein identity from 787 gut metagenomes, of which 28% are unknown proteins. Using binning analysis, 6339 metagenome-assembled genomes (MAGs) were obtained, which were clustered to 2673 species-level genome bins (SGBs), among which 86% (2309) SGBs are unknown based on current databases. Using the present gene catalog and MAGs, we identified several strain-level differences between the gut microbiome of wild boars and commercial Duroc pigs. PIGC and MAGs provide expanded resources for swine gut microbiome-related research.

Suggested Citation

  • Congying Chen & Yunyan Zhou & Hao Fu & Xinwei Xiong & Shaoming Fang & Hui Jiang & Jinyuan Wu & Hui Yang & Jun Gao & Lusheng Huang, 2021. "Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21295-0
    DOI: 10.1038/s41467-021-21295-0
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    Cited by:

    1. Shanlin Ke & Scott T. Weiss & Yang-Yu Liu, 2022. "Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Bin Ma & Caiyu Lu & Yiling Wang & Jingwen Yu & Kankan Zhao & Ran Xue & Hao Ren & Xiaofei Lv & Ronghui Pan & Jiabao Zhang & Yongguan Zhu & Jianming Xu, 2023. "A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. Feng Tong & Teng Wang & Na L. Gao & Ziying Liu & Kuiqing Cui & Yiqian Duan & Sicheng Wu & Yuhong Luo & Zhipeng Li & Chengjian Yang & Yixue Xu & Bo Lin & Liguo Yang & Alfredo Pauciullo & Deshun Shi & G, 2022. "The microbiome of the buffalo digestive tract," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    4. Chiranjib Chakraborty & Ashish Ranjan Sharma & Garima Sharma & Manojit Bhattacharya & Sang-Soo Lee, 2023. "Exploring the status of global terrestrial and aquatic microbial diversity through ‘Biodiversity Informatics’," Environment, Development and Sustainability: A Multidisciplinary Approach to the Theory and Practice of Sustainable Development, Springer, vol. 25(10), pages 10567-10598, October.
    5. Yunyan Zhou & Jingquan Li & Fei Huang & Huashui Ai & Jun Gao & Congying Chen & Lusheng Huang, 2023. "Characterization of the pig lower respiratory tract antibiotic resistome," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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