美国加州理工学院Dianne K. Newman、Long Cai等研究人员合作揭示单细胞分辨率下细菌群体的空间转录组。2021年8月13日出版的《科学》杂志发表了这项成果。

研究人员提出了par-seqFISH（平行序列荧光原位杂交），这是一种转录组成像方法，以单细胞和分子的分辨率记录微尺度集合内的基因表达和空间背景。研究人员将这种方法应用于机会型病原体铜绿假单胞菌，分析了浮游培养和生物膜培养物中几十种情况下的约60万个个体。研究人员确定了在浮游生长过程中动态出现的许多代谢和毒力相关的转录状态，以及固着群体中高度空间分辨率的代谢异质性。

这些数据显示，不同的生理状态可以在同一生物膜中共存，且只有几微米的距离，从而强调了微环境的重要性。这些结果说明了微生物种群的复杂动态，并提出了一种高分辨率研究它们的新方法。

据介绍，在相关的时空尺度上捕捉微生物种群的异质性表型是非常具有挑战性的。

附：英文原文

Title: Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution

Author: Daniel Dar, Nina Dar, Long Cai, Dianne K. Newman

Issue&Volume: 2021/08/13

Abstract: Capturing the heterogeneous phenotypes of microbial populations at relevant spatiotemporal scales is highly challenging. Here, we present par-seqFISH (parallel sequential fluorescence in situ hybridization), a transcriptome-imaging approach that records gene expression and spatial context within microscale assemblies at a single-cell and molecule resolution. We applied this approach to the opportunistic pathogen Pseudomonas aeruginosa, analyzing about 600,000 individuals across dozens of conditions in planktonic and biofilm cultures. We identified numerous metabolic- and virulence-related transcriptional states that emerged dynamically during planktonic growth, as well as highly spatially resolved metabolic heterogeneity in sessile populations. Our data reveal that distinct physiological states can coexist within the same biofilm just several micrometers away, underscoring the importance of the microenvironment. Our results illustrate the complex dynamics of microbial populations and present a new way of studying them at high resolution.

DOI: 10.1126/science.abi4882

Source: https://science.sciencemag.org/content/373/6556/eabi4882