EBI Metagenomics Portal - Towards a better understanding of community metabolism

EBI 宏基因组学门户 - 更好地了解群落代谢

• 批准号: BB/M011755/1
• 负责人: Robert Finn
• 金额: $ 82.32万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM011755%2F1
• 关键词: EBI; Metagenomics; Portal; Towards; better

Metagenomics is a rapidly expanding field, where modern sequencing technologies are applied to the DNA isolated from an environment, such as soil, seawater or animal gut. This allows us to analyse the DNA from the collection of microorganisms that inhabit the environment, many of which may not have previously been sequenced due to their fastidious nature, making it difficult to culture them in the laboratory. Substantial amounts of sequencing data are produced, which typically only reflect a small fraction of the total DNA. However, after analysis, this DNA provides clues to the taxonomic diversity and functional potential that is found in that environment. Metagenomics is an exemplar of what is referred to as data-driven biology. The cost of DNA sequencing has fallen rapidly, such that most research groups have access to affordable institutional sequencing facilities. We now run the risk of each research group producing its own metagenomics analysis platform and storage repository. To help prevent such a fragmented situation, and to help reduce overall costs (both computational and staff), we have developed and implemented a centralised pipeline to provide a metagenomics data analysis and archiving platform. The EBI Metagenomics Portal (EBI-MP) has been developed as a collaborative UK effort at the EMBL-European Bioinformatics Institute (EMBL-EBI). The portal was launched in 2011 and has increasingly become established as a world leader in metagenomic analysis. Users submit their high-throughput metagenomic nucleotide sequence data, accompanied by contextual data describing their samples and experiments in a controlled and consistent manner. Once analysed by the portal, results including taxonomic and functional annotations can be visualised alongside project and sample descriptions, and can be downloaded for further analysis. In order to keep up with community needs, and to help cement the UK's position as a leader in the field of metagenomics research, the proposed project aims to further develop the portal. This will include the addition of analysis provenance, to ensure that analyses can be re-run in the future as new and updated tools and algorithms become available, without overwriting existing analysed data, which may form the basis of an existing publication. Further enhancements include extending the taxonomic and functional analyses to achieve a better picture of the microbial communities sampled, their composition and biological functions. The portal will also be developed to allow more sophisticated searches of its data, so that users can discover samples or environments based on the kind of microbe or protein function found there. We will also add the ability to perform statistically rigorous cross-sample comparisons, that will allow analysis results from different samples to be compared in a scientifically meaningful way, and provide visualisation tools for such comparisons. With today's modern sequencing technologies producing ever more data, better data compression is essential to speed up data transfer both into EBI-MP and internally within the resource. To this end, we will implement industry-standard compression data structures that have developed at EMBL-EBI.

宏基因组学是一个快速发展的领域，现代测序技术应用于从土壤、海水或动物肠道等环境中分离的 DNA。这使我们能够分析栖息在环境中的微生物的 DNA，其中许多微生物由于其挑剔的性质而之前可能没有被测序，因此很难在实验室中培养它们。产生大量测序数据，通常仅反映总 DNA 的一小部分。然而，经过分析，这种 DNA 为该环境中发现的分类多样性和功能潜力提供了线索。宏基因组学是数据驱动生物学的一个范例。 DNA 测序的成本迅速下降，因此大多数研究小组都可以使用负担得起的机构测序设施。我们现在面临着每个研究小组生产自己的宏基因组分析平台和存储库的风险。为了帮助防止这种分散的情况，并帮助降低总体成本（计算成本和人员成本），我们开发并实施了一个集中式管道来提供宏基因组数据分析和归档平台。 EBI 宏基因组学门户 (EBI-MP) 是英国 EMBL-欧洲生物信息学研究所 (EMBL-EBI) 合作开发的。该门户网站于 2011 年推出，现已逐渐成为宏基因组分析领域的世界领导者。用户提交高通量宏基因组核苷酸序列数据，并附上以受控且一致的方式描述其样本和实验的上下文数据。通过门户进行分析后，包括分类和功能注释在内的结果可以与项目和样本描述一起可视化，并且可以下载以进行进一步分析。为了满足社区需求，并帮助巩固英国在宏基因组学研究领域的领导者地位，拟议项目旨在进一步开发该门户。这将包括添加分析来源，以确保将来随着新的和更新的工具和算法可用而可以重新运行分析，而不会覆盖现有的分析数据，这可能构成现有出版物的基础。进一步的增强包括扩展分类学和功能分析，以更好地了解采样的微生物群落、其组成和生物功能。该门户还将开发为允许对其数据进行更复杂的搜索，以便用户可以根据在那里发现的微生物或蛋白质功能的种类来发现样本或环境。我们还将添加执行统计上严格的跨样本比较的能力，这将允许以具有科学意义的方式比较不同样本的分析结果，并为此类比较提供可视化工具。随着当今的现代测序技术产生越来越多的数据，更好的数据压缩对于加快数据传输到 EBI-MP 和资源内部的速度至关重要。为此，我们将实施 EMBL-EBI 开发的行业标准压缩数据结构。

项目成果

The European Nucleotide Archive in 2018.

2018 年欧洲核苷酸档案。

• DOI: http://dx.10.1093/nar/gky1078
• 发表时间: 2019
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Harrison PW

Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC.

使用 EukCC 评估从宏基因组分析中恢复的真核基因组的质量。

• DOI: http://dx.10.1186/s13059-020-02155-4
• 发表时间: 2020
• 期刊: Genome biology
• 影响因子: 12.3
• 作者: Saary P

The European Nucleotide Archive in 2019.

2019 年欧洲核苷酸档案。

• DOI: http://dx.10.1093/nar/gkz1063
• 发表时间: 2020
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Amid C

Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics.

使用扩增子测序和鸟枪法宏基因组学确定康普茶的微生物组成。

• DOI: http://dx.10.1111/1750-3841.14992
• 发表时间: 2020
• 期刊: Journal of food science
• 影响因子: 3.9
• 作者: Arikan M

A human gut bacterial genome and culture collection for improved metagenomic analyses.

用于改进宏基因组分析的人类肠道细菌基因组和培养物保藏。

• DOI: http://dx.10.1038/s41587-018-0009-7
• 发表时间: 2019
• 期刊: Nature biotechnology
• 影响因子: 46.9
• 作者: Forster SC