Microbial communities such as those residing in the human gut are highly diverse and complex, and many with important implications in health and diseases. The effects and functions of these microbial communities are determined not only by their species compositions and diversities but also by the dynamic intra- and inter-cellular states at the transcriptional level. Powerful and scalable technologies capable of acquiring single-microbe-resolution RNA sequencing information in order to achieve comprehensive understanding of complex microbial communities together with their hosts is therefore utterly needed. Here we report the development and utilization of a droplet-based smRNA-seq (single-microbe RNA sequencing) method capable of identifying large species varieties in human samples, which we name smRandom-seq2. Together with a triple-module computational pipeline designed for the bacteria and bacteriophage sequencing data by smRandom-seq2 in four human gut samples, we established a single-cell level bacterial transcriptional landscape of human gut microbiome, which included 29,742 single microbes and 329 unique species. Distinct adaptive responses states among species in Prevotella and Roseburia genus and intrinsic adaptive strategy heterogeneity in Phascolarctobacterium succinatutens were uncovered. Additionally, we identified hundreds of novel host-phage transcriptional activity associations in the human gut microbiome. Our results indicated the smRandom-seq2 is a high-throughput and high-resolution smRNA-seq technique that is highly adaptable to complex microbial communities in real-word situations and promises new perspectives in the understanding of human microbiomes.

中文翻译：

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高通量单微生物 RNA 测序揭示了人类肠道微生物组的适应性状态异质性和宿主噬菌体活性关联。


微生物群落（例如人类肠道中的微生物群落）高度多样化且复杂，其中许多对健康和疾病具有重要影响。这些微生物群落的影响和功能不仅取决于其物种组成和多样性，还取决于转录水平上的动态细胞内和细胞间状态。因此，迫切需要能够获取单微生物分辨率 RNA 测序信息的强大且可扩展的技术，以便全面了解复杂的微生物群落及其宿主。在这里，我们报告了基于液滴的 smRNA-seq（单微生物 RNA 测序）方法的开发和利用，该方法能够识别人类样本中的大型物种多样性，我们将其命名为 smRandom-seq2。结合 smRandom-seq2 为四个人类肠道样本中的细菌和噬菌体测序数据设计的三模块计算管道，我们建立了人类肠道微生物组的单细胞水平细菌转录景观，其中包括 29,742 个单一微生物和 329 个独特物种。揭示了普雷沃菌属和罗斯布里亚属物种之间不同的适应性反应状态以及琥珀酸杆菌的内在适应性策略异质性。此外，我们在人类肠道微生物组中发现了数百个新的宿主噬菌体转录活性关联。我们的结果表明 smRandom-seq2 是一种高通量、高分辨率的 smRNA-seq 技术，它高度适应现实情况下的复杂微生物群落，并为理解人类微生物组提供了新的视角。