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Highly multiplexed spatial mapping of microbial communities

机译：微生物社区的高度复用空间映射

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摘要

Mapping the complex biogeography of microbial communities in situ with high taxonomic and spatial resolution poses a major challenge because of the high density~(1)and rich diversity~(2)of species in environmental microbiomes and the limitations of optical imaging technology~(3-6). Here we introduce high-phylogenetic-resolution microbiome mapping by fluorescence in situ hybridization (HiPR-FISH), a versatile technology that uses binary encoding, spectral imaging and decoding based on machine learning to create micrometre-scale maps of the locations and identities of hundreds of microbial species in complex communities. We show that 10-bit HiPR-FISH can distinguish between 1,023 isolates of Escherichia coli, each fluorescently labelled with a unique binary barcode. HiPR-FISH, in conjunction with custom algorithms for automated probe design and analysis of single-cell images, reveals the disruption of spatial networks in the mouse gut microbiome in response to treatment with antibiotics, and the longitudinal stability of spatial architectures in the human oral plaque microbiome. Combined with super-resolution imaging, HiPR-FISH shows the diverse strategies of ribosome organization that are exhibited by taxa in the human oral microbiome. HiPR-FISH provides a framework for analysing the spatial ecology of environmental microbial communities at single-cell resolution.
机译：原位用高分分类和空间分辨率映射微生物社区的复杂生物地理，因为在环境微生物瘤中的高密度〜（1）和丰富的多样性〜（2）〜（2）的光学成像技术的限制〜（3 -6）。在这里，我们引入了荧光原位杂交（HIPR-FISH）的高音发育分辨率微生物组映射，这是一种使用二进制编码，基于机器学习的频谱成像和解码来创建数百个地点的微米级绘制地图的多功能技术复杂社区中的微生物物种。我们表明，10位HIPR鱼可以区分大肠杆菌的1,023个分离物，每个荧光标记用独特的二元条码标记​​。 HIPR-FISH与自动探头设计和单细胞图像分析的定制算法一起揭示了响应于抗生素治疗的小鼠肠道微生物组中的空间网络的破坏，以及人口中的空间架构的纵向稳定性斑块微生物组。结合超分辨率的成像，Hipr-Fish显示了人口腔微生物组中的核糖体组织的各种策略。 HIPR-Fish提供了一种分析单细胞分辨率环境微生物群落的空间生态学的框架。

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  • 来源
    《Nature》 |2020年第7839期|676-681|共6页
  • 作者

    Hao Shi; Qiaojuan Shi; Benjamin Grodner; Joan Sesing Lenz; Warren R Zipfel; Ilana Lauren Brito; Iwijn De Vlaminck;

  • 作者单位

    Nancy E. and Peter C. Meinig School of Biomedical Engineering Cornell University;

    Nancy E. and Peter C. Meinig School of Biomedical Engineering Cornell University;

    Nancy E. and Peter C. Meinig School of Biomedical Engineering Cornell University;

    Nancy E. and Peter C. Meinig School of Biomedical Engineering Cornell University;

    Nancy E. and Peter C. Meinig School of Biomedical Engineering Cornell University;

    Nancy E. and Peter C. Meinig School of Biomedical Engineering Cornell University;

    Nancy E. and Peter C. Meinig School of Biomedical Engineering Cornell University;

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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  • 正文语种 eng
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