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现代微生物学:通过跨尺度整合拥抱复杂性。

Modern microbiology: Embracing complexity through integration across scales.

机构信息

Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany; Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany; Marine Biological Laboratory, Woods Hole, MA, USA; Max Planck Institute for Marine Microbiology, Bremen, Germany.

Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; Department of Environmental Science Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.

出版信息

Cell. 2024 Sep 19;187(19):5151-5170. doi: 10.1016/j.cell.2024.08.028.

DOI:10.1016/j.cell.2024.08.028
PMID:39303684
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11450119/
Abstract

Microbes were the only form of life on Earth for most of its history, and they still account for the vast majority of life's diversity. They convert rocks to soil, produce much of the oxygen we breathe, remediate our sewage, and sustain agriculture. Microbes are vital to planetary health as they maintain biogeochemical cycles that produce and consume major greenhouse gases and support large food webs. Modern microbiologists analyze nucleic acids, proteins, and metabolites; leverage sophisticated genetic tools, software, and bioinformatic algorithms; and process and integrate complex and heterogeneous datasets so that microbial systems may be harnessed to address contemporary challenges in health, the environment, and basic science. Here, we consider an inevitably incomplete list of emergent themes in our discipline and highlight those that we recognize as the archetypes of its modern era that aim to address the most pressing problems of the 21st century.

摘要

微生物是地球历史上大部分时间里唯一的生命形式,它们仍然占据着生命多样性的绝大多数。它们将岩石转化为土壤,产生我们呼吸的大部分氧气,处理我们的污水,并维持农业。微生物对行星健康至关重要,因为它们维持着生物地球化学循环,产生和消耗主要的温室气体,并支持大型食物网。现代微生物学家分析核酸、蛋白质和代谢物;利用复杂的遗传工具、软件和生物信息学算法;并处理和整合复杂和异构的数据集,以便利用微生物系统来解决健康、环境和基础科学方面的当代挑战。在这里,我们考虑了我们学科中不可避免的不完整主题列表,并强调了那些我们认为是其现代时代原型的主题,旨在解决 21 世纪最紧迫的问题。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3565/11450119/f76e71367e43/nihms-2026252-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3565/11450119/f76e71367e43/nihms-2026252-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3565/11450119/f76e71367e43/nihms-2026252-f0001.jpg

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The simplicity of protein sequence-function relationships.蛋白质序列与功能关系的简单性。
Nat Commun. 2024 Sep 11;15(1):7953. doi: 10.1038/s41467-024-51895-5.
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AlphaFind: discover structure similarity across the proteome in AlphaFold DB.AlphaFind:在 AlphaFold DB 中发现蛋白质组中的结构相似性。
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Accurate structure prediction of biomolecular interactions with AlphaFold 3.利用 AlphaFold 3 进行生物分子相互作用的精确结构预测。
化学特征向量通过非靶向质谱数据描绘自然生物群落的化学空间。
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Cross-feeding creates tipping points in microbiome diversity.交叉喂养在微生物群落多样性中创造了临界点。
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Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities.核糖体蛋白系统地理学为微生物群落基因组解析调查的功效提供了定量见解。
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Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess.通过 PlasX 和 MobMess 揭示人类肠道宏基因组中的多种质粒系统及其生态。
Nat Microbiol. 2024 Mar;9(3):830-847. doi: 10.1038/s41564-024-01610-3. Epub 2024 Mar 4.
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A cryptic plasmid is among the most numerous genetic elements in the human gut.隐秘质粒是人类肠道中数量最多的遗传元件之一。
Cell. 2024 Feb 29;187(5):1206-1222.e16. doi: 10.1016/j.cell.2024.01.039.
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