GutMetaNet:探索人类肠道微生物组中水平基因转移和功能冗余的综合数据库

IF 16.6 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Nucleic Acids Research Pub Date : 2024-11-11 DOI:10.1093/nar/gkae1007
Yiqi Jiang, Yanfei Wang, Lijia Che, Shuo Yang, Xianglilan Zhang, Yu Lin, Yucheng Shi, Nanhe Zou, Shuai Wang, Yuanzheng Zhang, Zicheng Zhao, Shuai Cheng Li
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引用次数: 0

摘要

元基因组研究揭示了复杂的微生物相互作用(包括水平基因转移(HGT)和功能冗余(FR))在塑造肠道微生物组的功能能力和恢复力方面的关键作用。然而,由于缺乏全面的数据整合和系统的分析方法,限制了对大规模肠道微生物组数据集的 HGT 和 FR 动态的深入探索。为了填补这一空白,我们推出了 GutMetaNet (https://gutmetanet.deepomics.org/),它是首个将大量人类肠道微生物组数据与全面的 HGT 和 FR 分析整合在一起的数据库。GutMetaNet 包含 21 567 个人类肠道元基因组样本,以及与各种健康状况相关的全基因组霰弹枪测序数据。通过系统分析,我们确定了分类特征和FR特征,并使用共享的参考基因组数据库在收集的样本中发现了14 636个HGT事件。这些 HGT 事件被归纳为 8049 个群组,其中注释了分类的移动遗传元件,包括转座子、噬菌体、整合可移动元件、基因组岛、整合共轭元件和 II 组内含子。此外,GutMetaNet 还包括对 HGT 事件和 FR 的自动分析和可视化,是深入探讨肠道微生物群分类群之间的相互作用及其对人类健康影响的高效平台。
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GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome
Metagenomic studies have revealed the critical roles of complex microbial interactions, including horizontal gene transfer (HGT) and functional redundancy (FR), in shaping the gut microbiome’s functional capacity and resilience. However, the lack of comprehensive data integration and systematic analysis approaches has limited the in-depth exploration of HGT and FR dynamics across large-scale gut microbiome datasets. To address this gap, we present GutMetaNet (https://gutmetanet.deepomics.org/), a first-of-its-kind database integrating extensive human gut microbiome data with comprehensive HGT and FR analyses. GutMetaNet contains 21 567 human gut metagenome samples with whole-genome shotgun sequencing data related to various health conditions. Through systematic analysis, we have characterized the taxonomic profiles and FR profiles, and identified 14 636 HGT events using a shared reference genome database across the collected samples. These HGT events have been curated into 8049 clusters, which are annotated with categorized mobile genetic elements, including transposons, prophages, integrative mobilizable elements, genomic islands, integrative conjugative elements and group II introns. Additionally, GutMetaNet incorporates automated analyses and visualizations for the HGT events and FR, serving as an efficient platform for in-depth exploration of the interactions among gut microbiome taxa and their implications for human health.
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来源期刊
Nucleic Acids Research
Nucleic Acids Research 生物-生化与分子生物学
CiteScore
27.10
自引率
4.70%
发文量
1057
审稿时长
2 months
期刊介绍: Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.
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