Fusobacterium nucleatum, long known as a constituent of the oral microflora, has recently garnered renewed attention for its association with several different human cancers. The growing interest in this emerging cancer-associated bacterium contrasts with a paucity of knowledge about its basic gene expression features and physiological responses. As fusobacteria lack all established small RNA-associated proteins, post-transcriptional networks in these bacteria are also unknown. In the present study, using differential RNA-sequencing, we generate high-resolution global RNA maps for five clinically relevant fusobacterial strains—F. nucleatum subspecies nucleatum, animalis, polymorphum and vincentii, as well as F. periodonticum—for early, mid-exponential growth and early stationary phase. These data are made available in an online browser, and we use these to uncover fundamental aspects of fusobacterial gene expression architecture and a suite of non-coding RNAs. Developing a vector for functional analysis of fusobacterial genes, we discover a conserved fusobacterial oxygen-induced small RNA, FoxI, which serves as a post-transcriptional repressor of the major outer membrane porin FomA. Our findings provide a crucial step towards delineating the regulatory networks enabling F. nucleatum adaptation to different environments, which may elucidate how these bacteria colonize different compartments of the human body.

具核梭杆菌，长期以来被认为是口腔微生物群落的一种成分，最近因其与几种不同的人类癌症的关联而获得了新的关注。对这种新兴癌症相关细菌的兴趣与日俱增，但对其基本基因表达特征和生理反应的了解却很少。由于梭杆菌缺乏所有已建立的小 RNA 相关蛋白，这些细菌中的转录后网络也是未知的。在本研究中，我们使用差异 RNA 测序，为五种临床相关的梭杆菌菌株——具核梭杆菌亚种具核、动物、多形体和文森特生成高分辨率全局 RNA 图，以及牙周病菌——用于早期、中期指数生长和早期稳定期。这些数据可在在线浏览器中获得，我们使用这些数据来揭示梭杆菌基因表达结构和一组非编码 RNA 的基本方面。开发用于梭杆菌基因功能分析的载体，我们发现了一种保守的梭杆菌氧诱导的小 RNA，FoxI，它作为主要外膜孔蛋白 FomA 的转录后阻遏物。我们的研究结果为描绘使具核梭菌适应不同环境的调节网络迈出了关键的一步，这可能阐明这些细菌如何在人体的不同部位定殖。