Microbiology-Sgm最新文献

Exposure to microbes is essential to promote the development of the host's immune system. Commensal microbes (i.e. the microbiota) which are acquired early in life play a vital role in immune priming. Whilst many organisms within the microbiota are harmless, some can be considered opportunistic pathogens. Examples include Staphylococcus aureus, Streptococcus pneumoniae and Pseudomonas aeruginosa, and these organisms can also contribute to the development of a healthy host immune system. At the extreme end of the spectrum, pathogens which typically do not form part of the microbiota (e.g. Mycobacterium tuberculosis, Bordetella pertussis and Salmonella Typhimurium) have been shown to provide cross-protection against infectious and non-infectious diseases in mice. Attenuated strains of these pathogens, such as BPZE1, could have clinical applications, whilst Bacillus Calmette-Guérin, a live-attenuated Mycobacterium bovis strain, has been shown to have non-specific effects against cancers and other diseases. A wide range of organisms, from harmless microbiota to potentially life-threatening infections, interact with the host immune system and can prime or modulate the immune response in different ways. In this review, we discuss the important role that pathogens, including opportunistic components of the microbiota, play in the development and maintenance of host immunity to a wide range of infectious and non-infectious diseases.

The intramembrane 'rhomboid' protease family is almost ubiquitous across evolution, with its well-conserved transmembrane domains typified in crystal structures of bacterial representatives, such as the Escherichia coli GlpG. In contrast with accumulating data on rhomboid function in higher organisms, where roles in human disease are an incentive for study, findings remain sparse about the functions and substrates of the prokaryotic enzymes, even though these provided the earliest protein structures. In particular, nothing at all is known about the rhomboid proteases of photosynthetic prokaryotes despite the importance of cyanobacteria as relatives of the progenitor of chloroplasts. Findings relating to the cyanobacterial enzymes would complement data on plant plastid rhomboids from work in Arabidopsis thaliana. Synechocystis sp. PCC 6803 was used, therefore, to investigate conserved photosynthetic functions across evolution for this protein family. Reverse-genetics studies using Slr1461, the single rhomboid protease of Synechocystis 6803, did not reveal a non-photochemical quenching phenotype as observed for the Arabidopsis RBL10 null mutant, which lacked a chloroplast outer membrane rhomboid. The Slr1461 mutant exhibited a marginal change in pigment composition, and its growth rate was only slightly different from that of WT under optimal light intensity. The most dramatic effect of the inactivation of Slr1461 was the mutant's distinct inability to reduce photosynthetic activity under mixotrophic conditions. Concurrent phototrophy and heterotrophy in mixotrophic growth aids survival and competitiveness in phytoplankton, allowing conservation of energy by reducing the need for uptake and fixing of CO₂ when an organic carbon source is available. It was notable, therefore, that, in the absence of the Slr1461 rhomboid, the steady-state mRNA levels were reduced for a subset of genes encoding facilitators of high-affinity CO₂ import and of transcriptional regulators of the carbon-concentrating mechanism (CCM). Slr1461 activity was also linked with that of another membrane protease, the AAA protease FtsH2, which was likewise observed to act within regulatory networks for the cyanobacterial carbon uptake mechanism. Aberrant transcript levels were most evident specifically under high CO₂ conditions, when the impact of Slr1461 enzymatic activity appeared to be upstream of NdhR, a central, controlling transcription factor of the CCM.

Cationic peptides, particularly those rich in arginine and/or lysine residues, are usually promising antimicrobial agents effective at low concentrations in laboratory settings. However, their applicability in pharmaceutics and biotechnology is currently limited due to their susceptibility to biological enzymatic processes and (in some cases) toxicity to host cells. To address this, we screened eight linear arginine-rich peptides for their haemolytic properties and antimicrobial activity using a set of computational and experimental assays. Inspired by our previous results on R4F4, we then designed three modified peptides based on an R4F4 backbone, R4F4-C16, D-R4F4 and cyclic R4F4, and one based on R4 (R4-C16). Amongst the tested linear peptides containing only natural amino acids, R4F4 exhibited the strongest antibacterial activity; however, this effect was reduced in the presence of human serum and trypsin. Conversely, our study demonstrated that cyclization and substitution to its d-amino acid enantiomer significantly enhanced stability and activity of R4F4, whilst in the presence of proteases. As revealed by fluorescence imaging, microscopy RNA sequencing analysis, the mode of action involves complex and dynamic events. This multifaceted antimicrobial mechanism integrates alterations in membrane permeability, modulation of intracellular reactive oxygen species levels and changes in transcriptomic signature profiles. At the molecular level, notable changes were observed in the bacterial expression of genes associated with metabolic pathways and biological processes. Furthermore, R4F4-derived peptides showed substantial antibiofilm activity in preventing the formation and disruption of mature biofilms, together with good cytocompatibility, highlighting the potential for clinical applicability. In conclusion, this study emphasizes the importance of optimizing the stability of peptide-based antimicrobials, particularly those rich in arginine, and highlights the advantages of incorporating d-amino acids and cyclization for enhanced performance. This information will prove useful in the future design of antimicrobial peptides. In addition, the molecular perspective on peptide-induced gene expression changes, as identified by RNA-seq, broadens our understanding of antimicrobial peptides' activities and provides a clearer picture of their versatile mechanisms.

The Clostridia are a phylogenetically diverse group of anaerobic, spore-forming bacteria that include species of medical, veterinary and industrial importance. The last two decades have seen major advances in our understanding of Clostridial biology despite the difficulties of anaerobic microbiology and the challenges associated with limited genetic tools. Effort has largely focused on the human pathogen Clostridioides difficile, but many of the methods developed have also proven useful in other species. Here, we present a collection of new genetic tools, including an array of promoters of varying strength, that we have characterized in C. difficile, the food spoilage bacterium Clostridium sporogenes and industrially important Clostridium saccharoperbutylacetonicum. We also present a set of modular plasmids that allow expression of proteins with a variety of tags, including for protein purification and fluorescence microscopy and a method for genetic barcoding of C. difficile to facilitate competitive index experiments. We make these tools available in the hope that they will prove useful to the community in support of our growing understanding of these important bacteria.

Paracoccus denitrificans is a metabolically versatile alphaproteobacterium first isolated in 1910 by Martinus Beijerinck. Similarities between the aerobic respiratory chain and membrane composition of P. denitrificans and those of eukaryotic mitochondria have stimulated the use of P. denitrificans as a model for oxidative phosphorylation. The organism has also been used extensively as a model for studies of denitrification, cytochrome c biogenesis, lithotrophy using thiosulphate as a source of energy, methylotrophy, and carbon metabolism more broadly. Through the application of structural biology and modern genome-based approaches, work on P. denitrificans continues to make significant contributions across multiple areas of microbiology.

This study describes an alternative role of the general stress response (GSR) regulated by Sigma B, via the two-component system RsbKY, which is methylated via RsbM, in motility regulation for the peritrichously flagellated, motile, foodborne pathogen Bacillus cereus. Using a set of Sigma B-related mutants, we found reduced surface spreading on low-agar plates for all mutants compared to the WT of B. cereus ATCC 14579. The GSR mutants still contained flagella similar to WT in the samples taken from the edge of colonies with reduced surface spreading. Using cell trajectory analysis of selected mutants and WT, we found that the Sigma B-controlled Hpr-like phosphocarrier bc1009 mutant had a reduced duration of the run phase, resulting in an overall lower persistence and coverage of the surface area over a given time. Indeed, prolonged incubation of low-agar 'swimming' plates resulted in full coverage by all GSR mutants, indicating functional motility, but reduced efficiency. Proteome analysis of samples from low-agar plates showed overall lower expression levels of motility-related proteins and, in particular, significantly lower values for proteins related to the C-ring, involved in the regulation of the run-and-tumble motion of bacteria. The bc1009 mutant showed an additional downregulation of a subset of methyl-accepting chemotaxis proteins, involved in the activation of the key chemotaxis regulators CheA and CheY. We propose a new chemotaxis model, in which CheA and CheY are still key regulators, but an additional regulatory role on the run-and-tumble motion is proposed for the Sigma B-regulated Hpr-like protein Bc1009 via the unique two-component system RsbKY.

The VIM-1 metallo-β-lactamase enzyme, encoded within class 1 integrons, is found in Gram-negative clinical isolates worldwide and has been linked to outbreaks of bacterial pathogens in nosocomial settings. Six vim-1+ clinical isolates, from the genera Escherichia, Klebsiella and Enterobacter, were obtained from Kingston, Ontario, Canada. Whole-genome sequencing revealed that vim-1 was plasmid-borne in all strains and situated as the first gene in In916 or In110 integrons. Analysis of related plasmids suggested that these vim-1-containing plasmids are globally disseminated and have spread via horizontal gene transfer and autochthonous vertical spread within Ontario. Interestingly, the MICs of ertapenem and meropenem, two clinically relevant carbapenem antibiotics, against these six isolates varied more than tenfold, suggesting that the effects of VIM-1 are dependent on the genomic content of the host microbe. Introducing vim-1 into three common Enterobacterales laboratory strains was not sufficient to confer resistance to ertapenem and meropenem. Instead, adaptive laboratory evolution of the vim-1 ⁺ laboratory strains revealed that vim-1-mediated carbapenem resistance in these strains was dependent on epistatic interactions with ompC mutations, likely due to decreased outer membrane permeability to these antibiotics. Together, these results provide additional support for the role of gene epistasis in modulating the antimicrobial resistance phenotypes of acquired resistance genes, as well as previous results suggesting that the presence of a β-lactamase gene is insufficient to confer strong resistance to carbapenems without being paired with reduced outer membrane permeability.

Bacteriophages are key drivers of bacterial evolution, particularly through their integration as prophages within host genomes. However, the diversity and host specificity of prophages in relevant pathogens such as Enterobacter species remain poorly characterized. In this study, we revealed the diversity of prophages, mapped their distribution and explored their relationships with their bacterial hosts. We analysed 3,661 prophage sequences identified from the genomes of 20 different Enterobacter species. This analysis uncovered an extensive hidden diversity, comprising 1,617 phage genera and 2,423 phage species - nearly 80% of which were singletons - highlighting an exceptionally rich prophage landscape. We found substantial variation in prophage species richness across host species and isolation sources, with Enterobacter kobei and environmental isolates exhibiting the highest richness. Prophage populations showed strong host specificity and limited cross-species transmission. Moreover, prophages exhibited geographic structuring and significant congruence between host and prophage phylogenies, as well as with the ecological lifestyles of their bacterial hosts. Although we found phages of the same species infecting different host species, these events were infrequent. Finally, bacterial genomes encoded diverse defence systems, mainly PDC-S07, RM type I-II and gabija, whereas only 8.9% of prophages encoded anti-defence systems, mostly anti-CBASS and anti-RM. Overall, this study provides new insights into the diversity of Enterobacter prophages and underscores their ecological and clinical relevance in shaping host adaptation and phage-host dynamics.

The modern antibiotic era began in the early twentieth century, but humans have long used materials from the natural world to attempt to treat the symptoms of infection. In this primer, we will discuss the rationale for attempting to reconstruct historical infection remedies in order to assess their antimicrobial activity and how this approach could aid the discovery of molecular cocktails with potential for development into novel treatments for infection.