小柯机器人

美国康奈尔大学Iwijn De Vlaminck和Hao Shi研究组合作绘制了微生物群落的高度复用的空间图谱。这一研究成果于2020年12月2日发表在《自然》杂志上。

他们介绍了通过荧光原位杂交（HiPR-FISH）进行的高系统发育分辨率微生物组图谱分析，该技术是一种通用技术，它使用基于机器学习的二进制编码、光谱成像和解码来创建数百个位置和身份的微米级图谱复杂群体中的微生物种类。他们显示10位HiPR-FISH可以区分大肠埃希氏菌1,023个分离株，每个分离株都用独特的二进制条形码进行荧光标记。HiPR-FISH结合用于自动探针设计和单细胞图像分析的定制算法，揭示了响应于抗生素治疗的小鼠肠道微生物组中空间网络的破坏，以及人类口腔中空间结构的纵向稳定性菌斑微生物组。

结合超分辨率成像，HiPR-FISH显示了人口腔微生物组中分类单元所展现的核糖体组织的多种策略。HiPR-FISH提供了一个用于以单细胞分辨率分析环境微生物群落的空间生态框架。

据悉，由于环境微生物群落中物种的高密度和丰富的多样性以及光学成像技术的局限性，以高分类和空间分辨率在原地绘制微生物群落的复杂生物地理构成了一项重大挑战。

附：英文原文

Title: Highly multiplexed spatial mapping of microbial communities

Author: Hao Shi, Qiaojuan Shi, Benjamin Grodner, Joan Sesing Lenz, Warren R. Zipfel, Ilana Lauren Brito, Iwijn De Vlaminck

Issue&Volume: 2020-12-02

Abstract: Mapping the complex biogeography of microbial communities in situ with high taxonomic and spatial resolution poses a major challenge because of the high density1 and rich diversity2 of species in environmental microbiomes and the limitations of optical imaging technology3,4,5,6. 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.

DOI: 10.1038/s41586-020-2983-4

Source: https://www.nature.com/articles/s41586-020-2983-4

Nature：《自然》，创刊于1869年。隶属于施普林格·自然出版集团，最新IF：69.504
官方网址：http://www.nature.com/
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