MIM: Elucidating the Rules of Cooperation and Resiliency in Microbial Communities through Stochastic Graph Grammars

MIM:通过随机图语法阐明微生物群落的合作和弹性规则

基本信息

  • 批准号:
    2125965
  • 负责人:
  • 金额:
    $ 87.45万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Standard Grant
  • 财政年份:
    2021
  • 资助国家:
    美国
  • 起止时间:
    2021-10-01 至 2026-09-30
  • 项目状态:
    未结题

项目摘要

Microbial communities in aquatic ecosystems are central to maintaining the resiliency of these important environments. These dense microbial populations are rich in species diversity and their genomes are dynamic because of processes such as gene duplication and horizontal gene transfer. Despite extensive genomic flux due to these evolutionary processes, microbial communities cooperate and maintain stable interactions and are resilient to environmental perturbations. This project aims to develop a suite of computational tools for deciphering the rules that govern cooperation and resiliency in hot spring microbial mats, or biofilms, from Yellowstone Park. These well-studied environments are ideal for examining how critical environmental parameters such as temperature, light and nutrients influence the diversity, abundance, and evolution of microbial populations. Novel computational tools will be developed to identify rules that govern relevant biological processes. Understanding how microbiomes evolve and adapt, especially with respect to the environment and to perturbations is crucial to understand many aspects of life. Thus, the results obtained from this project will have a significant impact on biology, health, conservation efforts, and animal and plant management. Furthermore, this research will support the interdisciplinary development of a diverse cohort of PhD and undergraduate students at Rice University and Carnegie Institution for Science located on the Stanford University campus. This project will also support the development of a summer REU focused on bioinformatics, ecology, evolution, and microbiology, and will also include summer training opportunities for graduate students with collaborators at the Pasteur Institute in Paris, France. This collaborative, multidisciplinary project presents an innovative plan for combining education and outreach activities to achieve real and lasting impact. All software developed will be made available on open-source code repositories. The overall goal of the project is to understand how microbiomes evolve and adapt, especially with respect to the environment and to perturbations. To meet these goals, the team of researchers will introduce methodological advances at the intersection of graph theory, formal languages, and machine learning to identify rules governing gene duplication and horizontal gene transfer from metagenomic sequencing data. In Aim 1, the project will construct and correlate species abundance networks with genome exchange networks through genome assembly graphs. In Aim 2, the project will produce a stochastic graph grammar framework for modeling network evolution over time, as well as unveil new rules with deep graph generators. In Aim 3, genome-level simulations will be combined with the genomic events identified in Aims 1 and 2 to assess the evolutionary benefits of these biological processes and their associated rates. The final project aim will focus on characterizing cooperation and resiliency through the study of graph grammars and network analysis techniques. The open-source computational methods developed across all four project aims will be evaluated on four distinct metagenomic datasets, including both environmental and host-associated microbiomes. Finally, a wide variety of metagenomic datasets will be used to show generalizability of the computational approaches to host-associated microbiomes.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.
水生生态系统中的微生物群落对于维持这些重要环境的弹性至关重要。这些密集的微生物种群具有丰富的物种多样性,由于基因复制和水平基因转移等过程,它们的基因组是动态的。尽管这些进化过程导致了广泛的基因组通量,但微生物群落合作并保持稳定的相互作用,并对环境扰动具有弹性。该项目旨在开发一套计算工具,用于破译黄石公园温泉微生物垫或生物膜中控制合作和弹性的规则。这些经过充分研究的环境是研究温度、光线和营养等关键环境参数如何影响微生物种群的多样性、丰度和进化的理想环境。将开发新的计算工具来确定管理相关生物过程的规则。了解微生物群是如何进化和适应的,特别是在环境和扰动方面,对于理解生命的许多方面至关重要。因此,从该项目获得的成果将对生物学、卫生、保护工作和动植物管理产生重大影响。此外,这项研究将支持位于斯坦福大学校园内的莱斯大学和卡内基科学研究所的博士和本科生的跨学科发展。该项目还将支持一个以生物信息学、生态学、进化和微生物学为重点的夏季REU的发展,并将为研究生与法国巴黎巴斯德研究所的合作者提供夏季培训机会。这个合作的多学科项目提出了一个创新的计划,将教育和外展活动结合起来,以实现真正和持久的影响。所有开发的软件都将在开源代码存储库上提供。该项目的总体目标是了解微生物群是如何进化和适应的,特别是在环境和扰动方面。为了实现这些目标,研究团队将在图论、形式语言和机器学习的交叉点引入方法学上的进步,以确定控制基因复制和宏基因组测序数据水平基因转移的规则。在目标1中,该项目将通过基因组组装图构建物种丰度网络并将其与基因组交换网络相关联。在目标2中,该项目将生成一个随机图语法框架,用于建模网络随时间的演变,并揭示使用深度图生成器的新规则。在目标3中,基因组水平的模拟将与目标1和目标2中确定的基因组事件相结合,以评估这些生物过程及其相关速率的进化益处。最后的项目目标将集中于通过研究图语法和网络分析技术来描述合作和弹性。在所有四个项目目标中开发的开源计算方法将在四个不同的宏基因组数据集上进行评估,包括环境和宿主相关微生物组。最后,将使用各种宏基因组数据集来展示宿主相关微生物组计算方法的通用性。该奖项反映了美国国家科学基金会的法定使命,并通过使用基金会的知识价值和更广泛的影响审查标准进行评估,被认为值得支持。

项目成果

期刊论文数量(5)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Differential Phototactic Behavior of Closely Related Cyanobacterial Isolates from Yellowstone Hot Spring Biofilms
黄石温泉生物膜中密切相关的蓝藻分离株的差异趋光行为
  • DOI:
    10.1128/aem.00196-22
  • 发表时间:
    2022
  • 期刊:
  • 影响因子:
    4.4
  • 作者:
    Bunbury, Freddy;Rivas, Carlos;Calatrava, Victoria;Shelton, Amanda N.;Grossman, Arthur;Bhaya, Devaki
  • 通讯作者:
    Bhaya, Devaki
Expansion of the global RNA virome reveals diverse clades of bacteriophages
  • DOI:
    10.1016/j.cell.2022.08.023
  • 发表时间:
    2022-10-13
  • 期刊:
  • 影响因子:
    64.5
  • 作者:
    Neri, Uri;Wolf, Yuri I.;Gophna, Uri
  • 通讯作者:
    Gophna, Uri
{{ item.title }}
{{ item.translation_title }}
  • DOI:
    {{ item.doi }}
  • 发表时间:
    {{ item.publish_year }}
  • 期刊:
  • 影响因子:
    {{ item.factor }}
  • 作者:
    {{ item.authors }}
  • 通讯作者:
    {{ item.author }}

数据更新时间:{{ journalArticles.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ monograph.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ sciAawards.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ conferencePapers.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ patent.updateTime }}

Devaki Bhaya其他文献

A survey of computational approaches for characterizing microbial interactions in microbial mats
  • DOI:
    10.1186/s13059-025-03634-2
  • 发表时间:
    2025-06-16
  • 期刊:
  • 影响因子:
    9.400
  • 作者:
    Vanesa L. Perillo;Michael Nute;Nicolae Sapoval;Kristen D. Curry;Logan Golia;Yongze Yin;Huw A. Ogilvie;Luay Nakhleh;Santiago Segarra;Devaki Bhaya;Diana G. Cuadrado;Todd J. Treangen
  • 通讯作者:
    Todd J. Treangen
Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity
  • DOI:
    10.1007/s11120-014-0066-9
  • 发表时间:
    2014-12-17
  • 期刊:
  • 影响因子:
    3.700
  • 作者:
    Michelle Davison;Eric Hall;Richard Zare;Devaki Bhaya
  • 通讯作者:
    Devaki Bhaya
Amplification & Analysis of the Synechococcus Os-B' Crispr Region from Single Cells
  • DOI:
    10.1016/j.bpj.2009.12.2188
  • 发表时间:
    2010-01-01
  • 期刊:
  • 影响因子:
  • 作者:
    Eric Hall;Samuel Kim;Michelle Davis;Huibin Wei;Devaki Bhaya;Richard N. Zare
  • 通讯作者:
    Richard N. Zare
Evolutionary origins of photosynthetic organisms
  • DOI:
    10.1186/gb-2000-1-2-reports0055
  • 发表时间:
    2000-04-01
  • 期刊:
  • 影响因子:
    9.400
  • 作者:
    Devaki Bhaya
  • 通讯作者:
    Devaki Bhaya
Changes in the antenna size of Photosystem I and Photosystem II in Synechococcus sp. strain PCC 7942 grown in the presence of SANDOZ 9785 — a Photosystem II inhibitor
  • DOI:
    10.1007/bf00019408
  • 发表时间:
    1994-08-01
  • 期刊:
  • 影响因子:
    3.700
  • 作者:
    Madhulika Srivastava;Devaki Bhaya;Salil Bose
  • 通讯作者:
    Salil Bose

Devaki Bhaya的其他文献

{{ item.title }}
{{ item.translation_title }}
  • DOI:
    {{ item.doi }}
  • 发表时间:
    {{ item.publish_year }}
  • 期刊:
  • 影响因子:
    {{ item.factor }}
  • 作者:
    {{ item.authors }}
  • 通讯作者:
    {{ item.author }}

{{ truncateString('Devaki Bhaya', 18)}}的其他基金

Novel Aspects of Phosphorus Metabolism in Thermophilic Cyanobacteria
嗜热蓝藻中磷代谢的新方面
  • 批准号:
    1024755
  • 财政年份:
    2010
  • 资助金额:
    $ 87.45万
  • 项目类别:
    Continuing Grant
Regulation of Light Directed Movement in Cyanobacteria
蓝藻中光定向运动的调节
  • 批准号:
    0110544
  • 财政年份:
    2001
  • 资助金额:
    $ 87.45万
  • 项目类别:
    Continuing Grant

相似海外基金

CAREER: Elucidating Biogenic Control of Heterogenous Ice Nucleation
职业:阐明异质冰核的生物控制
  • 批准号:
    2336558
  • 财政年份:
    2024
  • 资助金额:
    $ 87.45万
  • 项目类别:
    Continuing Grant
CAREER: Elucidating the Correlative Interfacial Solvation, Nucleation, and Growth Processes in Battery Electrolytes
职业:阐明电池电解质中相关的界面溶剂化、成核和生长过程
  • 批准号:
    2339175
  • 财政年份:
    2024
  • 资助金额:
    $ 87.45万
  • 项目类别:
    Continuing Grant
Elucidating mechanisms of biological hydrogen conversion through model metalloenzymes
通过模型金属酶阐明生物氢转化机制
  • 批准号:
    2419343
  • 财政年份:
    2024
  • 资助金额:
    $ 87.45万
  • 项目类别:
    Standard Grant
CAREER: Elucidating spatial and epigenetic regulation of gene expression during human development using photopatterning and single-cell multiomics
职业:利用光模式和单细胞多组学阐明人类发育过程中基因表达的空间和表观遗传调控
  • 批准号:
    2339849
  • 财政年份:
    2024
  • 资助金额:
    $ 87.45万
  • 项目类别:
    Continuing Grant
Elucidating Hydrodynamics at Confined Interfaces for Artificial Active Fluidics and Beyond
阐明人工主动流体学及其他领域的受限界面处的流体动力学
  • 批准号:
    MR/X03660X/1
  • 财政年份:
    2024
  • 资助金额:
    $ 87.45万
  • 项目类别:
    Fellowship
Elucidating the function of a protective protein in a novel in vitro reconstitution system for disaggregation of ubiquitinated amyloid fibrils
阐明保护蛋白在新型体外重构系统中用于解聚泛素化淀粉样蛋白原纤维的功能
  • 批准号:
    24K10522
  • 财政年份:
    2024
  • 资助金额:
    $ 87.45万
  • 项目类别:
    Grant-in-Aid for Scientific Research (C)
Elucidating the Trigger and Feedback Mechanisms of the Most Concentrated Quasars at Cosmic Noon
阐明宇宙正午最集中的类星体的触发和反馈机制
  • 批准号:
    24K17084
  • 财政年份:
    2024
  • 资助金额:
    $ 87.45万
  • 项目类别:
    Grant-in-Aid for Early-Career Scientists
2022BBSRC-NSF/BIO Generating New Network Analysis Tools for Elucidating the Functional Logic of 3D Vision Circuits of the Drosophila Brain
2022BBSRC-NSF/BIO 生成新的网络分析工具来阐明果蝇大脑 3D 视觉电路的功能逻辑
  • 批准号:
    BB/Y000234/1
  • 财政年份:
    2024
  • 资助金额:
    $ 87.45万
  • 项目类别:
    Research Grant
Elucidating the involvement of transient receptor potential vanilloid-type 4 in mechanical stimuli-induced swallowing reflex
阐明瞬时受体电位香草酸4型在机械刺激诱导的吞咽反射中的参与
  • 批准号:
    24K19847
  • 财政年份:
    2024
  • 资助金额:
    $ 87.45万
  • 项目类别:
    Grant-in-Aid for Early-Career Scientists
CAREER: Elucidating the Impact of Side-Chain Topology on the Structure-Property Relationship in Bottlebrush Polymers
职业:阐明侧链拓扑对洗瓶刷聚合物结构-性能关系的影响
  • 批准号:
    2340664
  • 财政年份:
    2024
  • 资助金额:
    $ 87.45万
  • 项目类别:
    Continuing Grant
{{ showInfoDetail.title }}

作者:{{ showInfoDetail.author }}

知道了