PDF(Pubmed)
Abstract：
The frequent exchange of mobile genetic elements (MGEs) between bacteria accelerates the spread of functional traits, including antimicrobial resistance, within the human microbiome. Yet, progress in understanding these intricate processes has been hindered by the lack of tools to map the spatial spread of MGEs in complex microbial communities, and to associate MGEs to their bacterial hosts. To overcome this challenge, we present an imaging approach that pairs single molecule DNA Fluorescence In Situ Hybridization (FISH) with multiplexed ribosomal RNA FISH, thereby enabling the simultaneous visualization of both MGEs and host bacterial taxa. We used this methodology to spatially map bacteriophage and antimicrobial resistance (AMR) plasmids in human oral biofilms, and we studied the heterogeneity in their spatial distributions and demonstrated the ability to identify their host taxa. Our data revealed distinct clusters of both AMR plasmids and prophage, coinciding with densely packed regions of host bacteria in the biofilm. These results suggest the existence of specialized niches that maintain MGEs within the community, possibly acting as local hotspots for horizontal gene transfer. The methods introduced here can help advance the study of MGE ecology and address pressing questions regarding antimicrobial resistance and phage therapy.
摘要：
细菌之间移动遗传元件（MGEs）的频繁交换加速了功能性状的传播，包括抗菌素耐药性，在人类微生物组中。然而，由于缺乏工具来绘制复杂微生物群落中MGE的空间传播图，因此阻碍了理解这些复杂过程的进展。并将MGE与它们的细菌宿主联系起来。为了克服这一挑战，我们提出了一种成像方法，将单分子DNA荧光原位杂交（FISH）与多重核糖体RNAFISH配对，从而能够同时可视化MGE和宿主细菌分类群。我们使用这种方法对人类口腔生物膜中的噬菌体和抗菌素耐药性（AMR）质粒进行了空间定位，我们研究了其空间分布的异质性，并证明了识别其宿主分类单元的能力。我们的数据揭示了AMR质粒和原蛋白的不同簇，与生物膜中宿主细菌的密集堆积区域一致。这些结果表明，在社区中存在维持MGE的专门生态位，可能是水平基因转移的局部热点。本文介绍的方法可以帮助推进MGE生态学的研究，并解决有关抗生素耐药性和噬菌体治疗的紧迫问题。
