Tigecycline is considered to be the last resort of defense against diseases caused by broad-spectrum resistant Gram-negative bacteria. In this study, we systematically analyzed the prevalence and genetic environments of the resistance gene tet (X4) in a pig slaughterhouse and farms and the evolutionary relationship of 533 tet (X4)-positive Escherichia coli strains, including 509 tet (X4)-positive E. coli strains selected from the 27,802 assembled genomes of E. coli from the NCBI between 2002 and 2022.

Motivation: Spatial transcriptome (ST) technology is a revolutionary method that enables the analysis of gene expression while preserving spatial location information, providing a powerful tool for revealing tissue structure and function. However, with the continuous development and diversification of spatial transcriptome technologies, the effective selection and use of appropriate analysis tools has become a challenge. Results: To address this issue, we have developed the Spatial Transcriptome Analysis Hub (STASH, http://cailab.labshare.cn:7004), a comprehensive, systematic, and user-friendly database of spatial transcriptome analysis tools. STASH collects and categorizes the 260 tools currently available and provides a wealth of information and features to help researchers quickly find the right tool for their needs. Furthermore, we have conducted a trend analysis of the tools in the database to highlight the current state and direction of spatial transcriptome research, which could help researchers develop better tools. STASH is a resource worthy of attention and use that will facilitate the spatial analysis of transcriptome data. Availability and Implementation: Freely available on the web at http://cailab.labshare.cn:7004.

Functional circular RNAs have been extensively studied in eukaryotes and progressively discovered in archaea, but not been identified in bacteria except some byproducts of self-spliced introns, devoid of biological function. In this study, using an experimental and computational pipeline, we confirm that a regulatory noncoding RNA DucS exists in both linear and circular conformations in Bacillus altitudinis. The 3’ end sequences of linear RNA are critical to RNA circularization. DucS promotes the tolerance of host to H2O2 stress through its linear forms, partly due to upregulating the translation of a stress-responsive gene htrA, whereas its circular forms can promote the degradation of linear cognates. Through re-evaluating published RNA-seq data from 30 bacteria and experimental identification, we demonstrate that circular RNAs also exist in other bacteria, occurred unexpectedly in some well-known noncoding RNAs. Our results reveal firstly a functional circular RNA in bacteria, highlighting the universal existence of functional circular RNAs in all three domains of life.