Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates.

IF 7.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY npj Biofilms and Microbiomes Pub Date : 2024-11-06 DOI:10.1038/s41522-024-00597-3
Bo Xu, Pengfei Song, Feng Jiang, Zhenyuan Cai, Haifeng Gu, Hongmei Gao, Bin Li, Chengbo Liang, Wen Qin, Jingjie Zhang, Jingyan Yan, Daoxin Liu, Guo Sun, Tongzuo Zhang
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Abstract

Trillions of microbes colonize the ungulate gastrointestinal tract, playing a pivotal role in enhancing host nutrient utilization by breaking down cellulose and hemicellulose present in plants. Here, through large-scale metagenomic assembly, we established a catalog of 131,416 metagenome-assembled genomes (MAGs) and 11,175 high-quality species-level genome bins (SGBs) from 17 species of ungulates in China. Our study revealed the convergent evolution of high relative abundances of carbohydrate-active enzymes (CAZymes) in the gut microbiomes of plateau-dwelling ungulates. Notably, two significant factors contribute to this phenotype: structural variations in their gut microbiome genomes, which contain more CAZymes, and the presence of novel gut microbiota species, particularly those in the genus Cryptobacteroides, which are undergoing independent rapid evolution and speciation and have higher gene densities of CAZymes. Furthermore, these enrichment CAZymes in the gut microbiomes are highly enrichment in known metabolic pathways for short-chain fatty acid (SCFA) production. Our findings not only provide a valuable genomic resource for understanding the gut microbiomes of ungulates but also offer fresh insights into the interaction between gut microbiomes and their hosts, as well as the co-adaptation of hosts and their gut microbiomes to their environments.

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大规模元基因组组装为了解高原蹄类动物肠道微生物群的遗传进化提供了新的视角。
数以万亿计的微生物在蹄类动物的胃肠道中定植,通过分解植物中的纤维素和半纤维素,在提高宿主营养利用率方面发挥着关键作用。在这里,我们通过大规模元基因组组装,从中国的17种蹄类动物中建立了一个包含131,416个元基因组组装基因组(MAGs)和11,175个高质量物种级基因组(SGBs)的目录。我们的研究揭示了高原蹄类动物肠道微生物组中碳水化合物活性酶(CAZymes)高相对丰度的趋同进化。值得注意的是,有两个重要因素促成了这种表型:一是它们肠道微生物组基因组的结构变异,其中含有更多的CAZymes;二是新型肠道微生物群物种的存在,特别是隐杆线虫属的物种,它们正在经历独立的快速进化和物种分化,具有更高的CAZymes基因密度。此外,肠道微生物群中这些富集的 CAZymes 在已知的短链脂肪酸(SCFA)生产代谢途径中也高度富集。我们的发现不仅为了解蹄类动物肠道微生物组提供了宝贵的基因组资源,而且为了解肠道微生物组与宿主之间的相互作用以及宿主及其肠道微生物组对环境的共同适应提供了新的见解。
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来源期刊
npj Biofilms and Microbiomes
npj Biofilms and Microbiomes Immunology and Microbiology-Microbiology
CiteScore
12.10
自引率
3.30%
发文量
91
审稿时长
9 weeks
期刊介绍: npj Biofilms and Microbiomes is a comprehensive platform that promotes research on biofilms and microbiomes across various scientific disciplines. The journal facilitates cross-disciplinary discussions to enhance our understanding of the biology, ecology, and communal functions of biofilms, populations, and communities. It also focuses on applications in the medical, environmental, and engineering domains. The scope of the journal encompasses all aspects of the field, ranging from cell-cell communication and single cell interactions to the microbiomes of humans, animals, plants, and natural and built environments. The journal also welcomes research on the virome, phageome, mycome, and fungome. It publishes both applied science and theoretical work. As an open access and interdisciplinary journal, its primary goal is to publish significant scientific advancements in microbial biofilms and microbiomes. The journal enables discussions that span multiple disciplines and contributes to our understanding of the social behavior of microbial biofilm populations and communities, and their impact on life, human health, and the environment.
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