Streptomyces coelicolor is a model for studying bacteria renowned as the foremost source of natural products used clinically. Post-genomic studies have revealed complex patterns of gene expression and links to growth, morphological development and individual genes. However, the underlying regulation remains largely obscure, but undoubtedly involves steps after transcription initiation. Here we identify sites involved in RNA processing and degradation as well as transcription within a nucleotide-resolution map of the transcriptional landscape. This was achieved by combining RNA-sequencing approaches suited to the analysis of GC-rich organisms. Escherichia coli was analysed in parallel to validate the methodology and allow comparison. Previously, sites of RNA processing and degradation had not been mapped on a transcriptome-wide scale for E. coli. Through examples, we show the value of our approach and data sets. This includes the identification of new layers of transcriptional complexity associated with several key regulators of secondary metabolism and morphological development in S. coelicolor and the identification of host-encoded leaderless mRNA and rRNA processing associated with the generation of specialized ribosomes in E. coli. New regulatory small RNAs were identified for both organisms. Overall the results illustrate the diversity in mechanisms used by different bacterial groups to facilitate and regulate gene expression.

SsgA-like proteins are a family of actinomycete-specific regulatory proteins that control cell division and spore maturation in streptomycetes. SsgA and SsgB together activate sporulation-specific cell division by controlling the localization of FtsZ. Here we report the identification of novel regulators that control the transcription of the ssgA-like genes. Transcriptional regulators controlling ssg gene expression were identified using a DNA-affinity capture assay. Supporting transcriptional and DNA binding studies showed that the ssgA activator gene ssgR is controlled by the TetR-family regulator AtrA, while the γ-butyrolactone-responsive AdpA (SCO2792) and SlbR (SCO0608) and the metabolic regulator Rok7B7 (SCO6008) were identified as candidate regulators for the cell division genes ssgA, ssgB and ssgG. Transcription of the cell division gene ssgB depended on the sporulation genes whiA and whiH, while ssgR, ssgA and ssgD were transcribed independently of the whi genes. Our work sheds new light on the mechanisms by which sporulation-specific cell division is controlled in Streptomyces.Electronic supplementary materialThe online version of this article (doi:10.1007/s10482-015-0479-2) contains supplementary material, which is available to authorized users.

A total of 60 samples were isolated from surgical wound infections, nares, and UTI's. Eight samples were positive for Staphylococcus aureus biochemical tests. These samples were collected from the Dr. Khalid General hospital in Koya city. Analysis of plasmids that digested by EcoRI and Hind III showed that plasmids conferring different resistance phenotypes showed different restriction profiles, while plasmids conferring similar resistance phenotypes may have shared one or more bands in common. Generally, Staphylococcus aureus isolates were highly diverse, as shown by their differing chromosome and plasmid patterns, and antibiotic resistance profiles. Plasmids isolated from surgical wound infections showed similarity with plasmids isolated from urinary tract infections depending on the antibiotic resistance and deportation gel electrophoresis. There was no similarity between the plasmids isolated from isolates of non pathogenic and pathogenic state.

The invasion of intestinal cells by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may have an impact on the gut bacteria. This study investigated the alteration of gut bacteria during SARS-CoV-2 viral infection and after recovery. Faecal samples were collected from ten RT-PCR-confirmed COVID-19 patients and five healthy participants (served as a control group) from November 21st, 2021 to April 1st, 2022. The faeces samples were collected three times, at the time of infection, after seven days of the infection and on day fifty after clearance of SARS-CoV-2. Serum samples were used to perform serological tests for the control group and COVID-19 survived patients. Pure culture techniques and classical and molecular approaches were used to isolate and identify the bacterial population in the collected faeces. The faecal bacterial communities of patients with COVID-19, those who recovered, and the five healthy people were compared. Significant alteration in culturable gut bacteria was observed in COVID-19 patients compared to the control group. This alteration was expressed by the existence of four bacterial species, which were Escherichia fergusonii, Citrobacter portucalensis, Comamonas kerstersii, and Shigella flexneri. In addition, two respiratory tract-associated bacterial pathogens, Klebsiella pneumoniae and Klebsiella aerogenes were recovered from the faecal samples of 40% of COVID-19 patients. The results even revealed that Staphylococcus aureus was more prevalent in faeces samples from those with SARS-CoV-2 infections than the healthy individuals. Faecal analysis of COVID-19 patients showed the existence and elevation of pathogenic bacteria in the large intestine in comparison to the healthy group. Further studies are required to highlight how an alteration of gut microbiomes affects the course of COVID-19 infection.