近日，美国莱斯大学教授James Chappell及其研究组报道了使用通用RNA条形码的微生物群落信息存储。这一研究成果发表在2025年3月18日出版的国际学术期刊《自然—生物技术》上。

通过将信息写入核糖酶主题的rRNA，并读取天然和修饰的rRNA主题扩增子测序，该课题组发现来自20个分类目的微生物群落成员参与了与大肠杆菌供菌株的质粒偶联，并观察了不同扩增子序列变体之间16S rRNA条形码信号的差异。多路rRNA条形码主题质粒与pBBR1或ColE1复制起源揭示宿主范围的差异。这种自主RNA可寻址的修饰提供了不需要翻译的基因转移信息，并将使微生物组工程能够跨越不同的生态环境，研究基因转移和细胞摄取细胞外物质的环境控制。

据了解，基因转移可以通过基因编码报告体或宏基因组测序进行研究，但这些方法在监测微生物群落中移动DNA宿主范围时受到敏感性的限制。为了记录废水微生物组中基因转移的信息，合成了一种催化RNA，对高度保守的核糖体RNA （rRNA）片段进行了编码。

附：英文原文

Title: Information storage across a microbial community using universal RNA barcoding

Author: Kalvapalle, Prashant B., Staubus, August, Dysart, Matthew J., Gambill, Lauren, Reyes Gamas, Kiara, Lu, Li Chieh, Silberg, Jonathan J., Stadler, Lauren B., Chappell, James

Issue&Volume: 2025-03-18

Abstract: Gene transfer can be studied using genetically encoded reporters or metagenomic sequencing but these methods are limited by sensitivity when used to monitor the mobile DNA host range in microbial communities. To record information about gene transfer across a wastewater microbiome, a synthetic catalytic RNA was used to barcode a highly conserved segment of ribosomal RNA (rRNA). By writing information into rRNA using a ribozyme and reading out native and modified rRNA using amplicon sequencing, we find that microbial community members from 20 taxonomic orders participate in plasmid conjugation with an Escherichia coli donor strain and observe differences in 16S rRNA barcode signal across amplicon sequence variants. Multiplexed rRNA barcoding using plasmids with pBBR1 or ColE1 origins of replication reveals differences in host range. This autonomous RNA-addressable modification provides information about gene transfer without requiring translation and will enable microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials.

DOI: 10.1038/s41587-025-02593-0

Source: https://www.nature.com/articles/s41587-025-02593-0