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环境中分离的DNA，如土壤，海水或动物肠道。这使我们能够分析栖息在环境中的微生物集合的DNA，其中许多微生物由于其挑剔的性质而以前可能没有被测序，因此很难在实验室中培养它们。产生大量的测序数据，其通常仅反映总DNA的一小部分。然而，经过分析，这种DNA提供了在该环境中发现的分类多样性和功能潜力的线索。宏基因组学是所谓的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。我们现在面临的风险是，每个研究小组都有自己的宏基因组学分析平台和存储库。为了帮助防止这种分散的情况，并帮助降低整体成本（包括计算和员工），我们开发并实施了一个集中的管道，以提供宏基因组学数据分析和存档平台。EBI宏基因组学门户网站（EBI-MP）是由EMBL-European Bioinformatics Institute（EMBL-EBI）联合英国共同开发的。该门户网站于2011年推出，并日益成为宏基因组分析的世界领导者。用户提交他们的高通量宏基因组核苷酸序列数据，以及以受控和一致的方式描述他们的样品和实验的上下文数据。一旦通过门户进行分析，包括分类和功能注释在内的结果可以与项目和样品描述一起可视化，并可以下载以进行进一步分析。为了跟上社区的需求，并帮助巩固英国作为宏基因组学研究领域的领导者的地位，拟议的项目旨在进一步开发该门户网站。这将包括增加分析来源，以确保今后在有新的和更新的工具和算法可用时可以重新进行分析，而不需要重复现有的分析数据，这些数据可能构成现有出版物的基础。进一步的改进包括扩大分类和功能分析，以更好地了解取样的微生物群落、其组成和生物功能。该门户网站还将进行开发，以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。我们还将增加进行统计上严格的跨样本比较的能力，这将允许以科学上有意义的方式比较不同样本的分析结果，并为这种比较提供可视化工具。随着当今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和资源内部至关重要。为此，我们将实现EMBL-EBI开发的行业标准压缩数据结构。

项目成果

An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities.

• DOI: 10.1038/s41598-021-89881-2
• 发表时间: 2021-05-19
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: O'Sullivan DM;Doyle RM;Temisak S;Redshaw N;Whale AS;Logan G;Huang J;Fischer N;Amos GCA;Preston MD;Marchesi JR;Wagner J;Parkhill J;Motro Y;Denise H;Finn RD;Harris KA;Kay GL;O'Grady J;Ransom-Jones E;Wu H;Laing E;Studholme DJ;Benavente ED;Phelan J;Clark TG;Moran-Gilad J;Huggett JF
• 通讯作者: Huggett JF

The European Nucleotide Archive in 2018.

• DOI: 10.1093/nar/gky1078
• 发表时间: 2019-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Harrison PW;Alako B;Amid C;Cerdeño-Tárraga A;Cleland I;Holt S;Hussein A;Jayathilaka S;Kay S;Keane T;Leinonen R;Liu X;Martínez-Villacorta J;Milano A;Pakseresht N;Rajan J;Reddy K;Richards E;Rosello M;Silvester N;Smirnov D;Toribio AL;Vijayaraja S;Cochrane G
• 通讯作者: Cochrane G

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.

• DOI: 10.1093/nar/gkx967
• 发表时间: 2018-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Mitchell AL;Scheremetjew M;Denise H;Potter S;Tarkowska A;Qureshi M;Salazar GA;Pesseat S;Boland MA;Hunter FMI;Ten Hoopen P;Alako B;Amid C;Wilkinson DJ;Curtis TP;Cochrane G;Finn RD
• 通讯作者: Finn RD

Biocuration of functional annotation at the European nucleotide archive.

• DOI: 10.1093/nar/gkv1311
• 发表时间: 2016-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Gibson R;Alako B;Amid C;Cerdeño-Tárraga A;Cleland I;Goodgame N;Ten Hoopen P;Jayathilaka S;Kay S;Leinonen R;Liu X;Pallreddy S;Pakseresht N;Rajan J;Rosselló M;Silvester N;Smirnov D;Toribio AL;Vaughan D;Zalunin V;Cochrane G
• 通讯作者: Cochrane G

Microbiota Characterization of Agricultural Green Waste-Based Suppressive Composts Using Omics and Classic Approaches

• DOI: 10.3390/agriculture10030061
• 发表时间: 2020-03
• 期刊: Agriculture
• 作者: R. Scotti;A. Mitchell;C. Pane;R. Finn;M. Zaccardelli