Collaborative Research: ABI Development: "The Microbial Genome Atlas (MiGA) project and its expansion to catalogue the uncultivated microbial majority"

合作研究：ABI 开发：“微生物基因组图谱 (MiGA) 项目及其扩展以对大多数未培养的微生物进行编目”

• 批准号: 1759831
• 负责人: Konstantinos Konstantinidis
• 金额: $ 59.89万
• 依托单位: Georgia Tech Research Corporation
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-01 至 2022-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1759831&HistoricalAwards=false
• 关键词: Collaborative; Research; ABI; Development; Microbial

The diversity of prokaryotic microbes on the planet is very large, estimated at over a billion species of bacteria, and most of it remains undiscovered. As genome sequencing can help characterizing this diversity and has recently become routine, most microbial scientists have been overwhelmed by the amount of available data. For many researchers, a complete and thorough analysis of the available genome data is not necessary. Instead, these users would be better served with straightforward methods that can identify their unknown DNA/RNA sequence(s), and be able to discriminate between well-understood taxa and those that are potentially novel. Tools that can help direct researchers to the most "interesting" genomes and genes among thousands of candidates will be important. Furthermore, metagenomics, which is the sequencing of environmental DNA, allows the genetic characterization of the majority of these prokaryotes that have resisted cultivation in the laboratory. However, current tools to analyze metagenomic data are clearly lagging behind the development of sequencing technologies (and data processing tools), and are typically limited to genome assembly and gene annotation. This is a major limitation for better understanding, studying and communicating about the biodiversity of uncultivated microorganisms that run the life-sustaining biogeochemical cycles on the planet, form critical associations with their plant and animal hosts, or produce products of biotechnological value. Therefore, new approaches to make the emerging genomic and metagenomic sequence information readily available to the non-expert user are timely and essential in order to advance our understanding of the diversity and function of microbial communities across the fields of ecology, systematics, evolution, engineering, agriculture and medicine. The overarching goal of this project is to develop a computational framework to organize and catalogue the genomic and metagenomic information of the "uncultivated majority" of bacteria and archaea that will scale-up with the available and forthcoming metagenomic data sets. To achieve this goal, the Microbial Genomes Atlas project (MiGA), which was originally designed to catalogue the diversity among isolate genomes, will be used and expanded with new tools and computational solutions that will allow it to encompass the "uncultivated majority". The new tools include -but are not limited to- a kmer-based approach to replace the alignment-based genome-average nucleotide identity (ANI) metric for estimating genetic relatedness among genomes and high-throughput tools for assessing genome completeness and quality, the pangenome of a group of genomes, and the level of genetic variation within natural sequence-discrete populations. This research effort will address critical limitations of the current 16S rRNA gene-based approaches in cataloging microbial diversity (e.g., lack of resolution at the species level and below), and will provide highly needed tools for the online analysis of high throughput genomic and metagenomic data from uncultivated microorganisms. The project will also provide multifaceted learning experiences to both undergraduate and graduate students at the interface of microbiology, evolution, genomics, bioinformatics, and computational biology, a pivotal area of contemporary research and education. See MiGA's website for further details at: www.microbial-genomes.org .This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

地球上的原核微生物的多样性非常大，估计有超过十亿种细菌，而且大多数仍未发现。由于基因组测序可以帮助表征这种多样性并最近成为常规，因此大多数微生物科学家都被可用数据量所淹没。对于许多研究人员来说，对可用基因组数据进行完整而彻底的分析是不需要的。取而代之的是，这些用户将通过直接的方法更好地提供，这些方法可以识别其未知的DNA/RNA序列，并能够区分熟悉的分类单元和潜在新颖的分类单元。可以帮助研究人员在成千上万候选人中引导研究人员和基因最“有趣的”基因组和基因的工具非常重要。此外，宏基因组是环境DNA的测序，允许对抗实验室培养的大多数这些原核生物的遗传表征。但是，当前分析元基因组数据的工具显然落后于测序技术（以及数据处理工具）的开发，并且通常仅限于基因组组装和基因注释。这是更好地理解，研究和沟通的主要局限性，即未经文化的微生物的生物多样性，这些微生物在地球上运行了维持生命的生物地球化学循环，与其动植物宿主建立关键关联，或产生生物技术价值的产物。因此，使非专家用户易于获得新兴的基因组和元基因组序列信息的新方法是及时且至关重要的，以促进我们对整个生态，系统，进化，工程，工程，农业和医学领域的微生物社区多样性和功能的理解。 该项目的总体目标是开发一个计算框架，以组织和分类细菌和古细菌“未经文化的多数”的基因组和元基因组信息，该信息将随着可用且即将出现的宏基因组数据集的扩展。为了实现这一目标，最初旨在对孤立基因组之间的多样性进行分类的微生物基因组计划（MIGA）将使用新工具和计算解决方案使用和扩展，这些工具和计算解决方案将允许其涵盖“未经文化的多数”。新工具包括 - 但不限于基于kmer的方法来替代基于基于基因组的基因组平均核苷酸认同（ANI）度量，用于估算基因组之间的遗传相关性和高通量工具，以评估基因组完整性和质量，一组基因组的PangeNome，以及在自然序列中的遗传变异水平。这项研究工作将解决当前基于16S rRNA基因的方法在分类微生物多样性（例如，物种水平及以下缺乏分辨率）中的关键局限性，并将为在线分析未经培养的微生物的高吞吐量和元数据组提供在线分析。该项目还将在微生物学，进化，基因组学，生物信息学和计算生物学的界面上为本科和研究生提供多方面的学习经验，这是当代研究和教育的关键领域。有关更多详细信息，请参见MIGA的网站：www.microbial-genomes.org。该奖项反映了NSF的法定任务，并被认为是值得通过基金会的知识分子优点和更广泛的影响评估标准通过评估来获得支持的。

项目成果

Phosphate addition increases tropical forest soil respiration primarily by deconstraining microbial population growth

• DOI: 10.1016/j.soilbio.2018.11.026
• 发表时间: 2019-03
• 期刊: Soil Biology and Biochemistry
• 影响因子: 9.7
• 作者: E. Johnston;Minjae Kim;J. Hatt;J. Phillips;Q. Yao;Yang Song;T. Hazen;M. Mayes;K. Konstantinidis

Comparison of vaginal microbiota in gynecologic cancer patients pre‐ and post‐radiation therapy and healthy women

• DOI: 10.1002/cam4.3027
• 发表时间: 2019-09
• 期刊: Cancer Medicine
• 影响因子: 4
• 作者: D. Tsementzi;A. Peña-Gonzalez;J. Bai;Yi-Juan Hu;P. Patel;J. Shelton;M. Dolan;J. Arluck;N. Khanna

Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations

• DOI: 10.1038/s41396-021-01149-9
• 发表时间: 2021-12-09
• 期刊: ISME JOURNAL
• 影响因子: 11
• 作者: Conrad, Roth E.;Viver, Tomeu;Konstantinidis, Konstantinos T.
• 通讯作者: Konstantinidis, Konstantinos T.

Sequence‐discrete species for prokaryotes and other microbes: A historical perspective and pending issues

• DOI: 10.1002/mlf2.12088
• 发表时间: 2023-12
• 期刊: Mlife
• 作者: K. Konstantinidis

Prevalence of viral photosynthesis genes along a freshwater to saltwater transect in Southeast USA

• DOI: 10.1111/1758-2229.12780
• 发表时间: 2019-07-16
• 期刊: ENVIRONMENTAL MICROBIOLOGY REPORTS
• 影响因子: 3.3
• 作者: Ruiz-Perez, Carlos A.;Tsementzi, Despina;Konstantinidis, Konstantinos T.
• 通讯作者: Konstantinidis, Konstantinos T.