Fems Microbiology Letters最新文献

Groundwater, rainwater, and leachate associated with a single landfill were analysed to detect extended-spectrum beta-lactamase (ESBL)-producing and carbapenemase (CP)-producing bacteria. After cultivation on three commercial selective-differential media, 240 bacterial isolates were obtained and identified by matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). Isolates from clinically relevant species were further genotyped by enterobacterial repetitive intergenic consensus polymerase chain reaction, and tested for antibiotic susceptibility and presence of CPs and ESBL enzymes. Two ESBL-producing isolates and two isolates producing CPs were detected in rainwater, groundwater, and leachate: Klebsiella oxytoca complex with the gene for the ESBL enzyme CTX-M-1 and the gene for the CP OXA-48, Serratia fonticola with the gene for the ESBL enzyme FONA-2, and Pseudomonas aeruginosa with the gene coding Verona integron-encoded Metallo-beta-lactamases (VIM) metallo-beta-lactamase. Our study indicates that bacteria with ESBL and CP genes can be present in landfill-associated waters.

Mountain glaciers are frequently assessed for their hydrological connectivity from glaciers to proglacial lakes. Ecological process on glacier surfaces and downstream ecosystems have often been investigated separately, but few studies have focused on the connectivity between the different glacial habitats. Therefore, it remains a limited understanding of bacterial community assembly across different habitats along the glacier hydrological continuum. In this study, we sampled along a glacial catchment from supraglacial snow, cryoconite holes, supraglacial runoff, ice-marginal moraine and proglacial lake on the Tibetan Plateau. The bacterial communities in these habitats were analyzed using high-throughput DNA sequencing of the 16S rRNA gene to determine the bacterial composition and assembly. Our results showed that each habitat hosted unique bacterial communities, with higher bacterial α-diversity in transitional habitats (e.g. runoff and ice-marginal moraine). Null model analysis indicated that deterministic processes predominantly shaped bacterial assembly in snow, cryoconite holes and lake, while stochastic process dominantly governed bacterial community in transitional habitats. Collectively, our findings suggest that local environment play a critical role in filtering bacterial community composition within glacier habitats. This study enhances our understanding of microbial assembly process in glacier environments and provides valuable insights into the factors governing bacterial community compositions across different habitats along the glacial hydrological continuum.

One of the debilitating causes of high mortality in the case of tuberculosis and other bacterial infections is the resistance development against standard drugs. There are limited studies so far to describe how a bacterial second messenger molecule can directly participate in distinctive antibiotic tolerance characteristics of a cell in a mechanism-dependent manner. Here we show that intracellular cyclic di-AMP (c-di-AMP) concentration can modulate drug sensitivity of Mycobacterium smegmatis by interacting with an effector protein or interfering with the 5'-UTR regions in mRNA of the genes and thus causing transcriptional downregulation of important genes in the pathways. We studied four antibiotics with different mechanisms of action: rifampicin, ciprofloxacin, erythromycin, and tobramycin and subsequently found that the level of drug sensitivity of the bacteria is directly proportional to the c-di-AMP concentration inside the cell. Further, we unraveled the underlying molecular mechanisms to delineate the specific genes and pathways regulated by c-di-AMP and hence result in differential drug sensitivity in M. smegmatis.

This retrospective study aimed to compare the difference of the levels of white blood cells (WBC), C-reactive protein (CRP), procalcitonin, and D-Dimer in the bloodstream infection (BSI) patients, and their values in distinguishing bacterial categories. A total of 847 BSI patients were analysed and divided into Gram-positive BSI (GP-BSI) and Gram-negative BSI (GN-BSI) groups. Most frequently isolated pathogens in GP-BSI were Staphylococcus epidermidis (35.75%), followed by Staphylococcus hominis (18.33%), and Streptococcus haemolyticus (10.16%), while in GN-BSI, Escherichia coli (30.07%), Klebsiella pneumoniae (23.98%), and Acinetobacter baumannii (13.18%) were the most common. The predictive value was evaluated based on 3 years of patient data, which showed an area under the curve (AUC) of 0.828. It was further validated using 2 years of data, which yielded an AUC of 0.925. Significant differences existed in the procalcitonin, D-Dimer, and CRP levels between GN-BSI and GP-BSI. The current results provide a more effective strategy for early differential diagnosis in bacterial categorization of BSI when combining WBC, CRP, procalcitonin, and D-Dimer measurements.

Aspergillus flavus is a common saprophytic aerobic fungus in oil crops that poses a serious threat worldwide with the carcinogenic aflatoxin. Prevention of aflatoxin B1 contamination has great significance to ensure food safety and reduce the economic loss. The present work focuses on the antagonistic activity against A. flavus growth in peanuts by fumigation with dimethyl trisulfide. The results indicated that dimethyl trisulfide exhibits great antifungal activity against A. flavus. The conidial germination and mycelial growth of A. flavus were completely suppressed after exposure to 15 and 20 µl/l of dimethyl trisulfide, respectively. Numerous deformed conidia were found after exposure to dimethyl trisulfide at high concentration (≥20 µl/l). Scanning electron microscope observation demonstrated that dimethyl trisulfide induced severely shrinking mycelia of A. flavus. The results of OD-260 nm absorption and rhodamine-123 fluorescent staining indicated that cell membrane and mitochondria may be legitimate antifungal targets of dimethyl trisulfide. Dimethyl triethyl has a significant inhibitory effect on A. flavus infection in peanuts. In addition, dimethyl trisulfide could reduce the production of aflatoxin B1 via down-regulation of toxin synthesis and regulatory gene expression. Dimethyl trisulfide can be a tremendous potential agent for the biological control of A. flavus and deepened our understanding of the anti-fungal mechanisms of volatile organic compounds.

Bacteriophage (phage) KHP40 was previously isolated from the supernatant of a culture of Helicobacter pylori KMT83 cells. In this study, we analysed the infection characteristics of KHP40, phage release pattern from KMT83 cells, and state of KHP40 DNA in KMT83 cells. The findings revealed that KHP40 phage showed varied adsorption efficiencies for different strains, long latent periods, and small burst sizes. Additionally, KHP40 activity was maintained at pH 2.5-12. KHP40 phages were released during the vegetative growth phase of the KMT83 cells. PCR analysis demonstrated that KHP40 DNA was stably maintained in KMT83 clones. Next-generation sequencing analysis revealed the presence of two distinct types of circular double-stranded DNA in H. pylori KMT83 cells. One was an H. pylori-specific DNA consisting of 1 578 403 bp, and the other was a 26 412-bp sequence that represented the episomal form of phage KHP40 DNA. Furthermore, defective KHP40-lysogenic DNA was detected in the H. pylori-specific DNA, the deleted portion of which appeared to have been transferred to another location in the bacterial genome. These findings indicate that KHP40 DNA exists in both episomal and defectively lysogenized states in KMT83 cells, and active phages are produced from KHP40-episomal DNA.

Salmonella remains the leading cause of foodborne infections globally. Environmental reservoirs, particularly aquatic bodies, serve as conduits for the fecal-oral transmission of this pathogen. While the gastrointestinal tract is traditionally considered the primary habitat of Salmonella, mounting evidence suggests the bacterium's capacity for survival in external environments. The application of advanced technological platforms, such as next-generation sequencing, facilitates a comprehensive analysis of Salmonella's genomic features. This study aims to characterize the genomic composition of Salmonella isolates from river water, contributing to a potential paradigm shift and advancing public health protection. A total of 25 river water samples were collected and processed, followed by microbiological isolation of Salmonella strains, which were then sequenced. Genomic characterization revealed adaptive mechanisms, including gene duplication. Furthermore, an open pangenome, predisposed to incorporating foreign genetic material, was identified. Notably, antibiotic resistance genes were found to be part of the core genome, challenging previous reports that placed them in the accessory genome.

Colistin is a cationic cyclic antimicrobial peptide used as a last resort against multidrug-resistant gram-negative bacteria. To understand the factors involved in colistin susceptibility, we screened colistin-sensitive mutants from an E. coli gene-knockout library (Keio collection). The knockout of purA, whose product catalyzes the synthesis of adenylosuccinate from IMP in the de novo purine synthesis pathway, resulted in increased sensitivity to colistin. Adenylosuccinate is subsequently converted to AMP, which is phosphorylated to produce ADP, a substrate for ATP synthesis. The amount of ATP was lower in the purA-knockout mutant than that in the wild-type strain. ATP synthesis is coupled with proton transfer, and it contributes to the membrane potential. Using the membrane potential probe, 3,3'-diethyloxacarbocyanine iodide [DiOC2(3)], we found that the membrane was hyperpolarized in the purA-knockout mutant compared to that in the wild-type strain. Treatment with the proton uncoupler, carbonyl cyanide m-chlorophenyl hydrazone (CCCP), abolished the hyperpolarization and colistin sensitivity in the mutant. The purA-knockout mutant exhibited increased sensitivity to aminoglycosides, kanamycin, and gentamicin; their uptake requires a membrane potential. Therefore, the knockout of purA, an adenylosuccinate synthase, decreases ATP synthesis concurrently with membrane hyperpolarization, resulting in increased sensitivity to colistin.

A comprehensive profiling of microbial diversity is essential to understand the ecosystem functions. Universal primer sets such as the 515Y/926R could amplify a part of 16S and 18S rRNA and infer the diversity of prokaryotes and eukaryotes. However, the analyses of mixed sequencing data pose a bioinformatics challenge; the 16S and 18S rRNA sequences need to be separated first and analysed individually/independently due to variations in the amplicon length. This study describes an alternative strategy, a merging and concatenation workflow, to analyse the mixed amplicon data without separating the 16S and 18S rRNA sequences. The workflow was tested with 24 mock community (MC) samples, and the analyses resolved the composition of prokaryotes and eukaryotes adequately. In addition, there was a strong correlation (cor = 0.950; P-value = 4.754e-10) between the observed and expected abundances in the MC samples, which suggests that the computational approach could infer the microbial proportions accurately. Further, 18 samples collected from the Sundarbans mangrove region were analysed as a case study. The analyses identified Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria, and Crenarchaeota as dominant bacterial phyla and eukaryotic divisions such as Metazoa, Gyrista, Cryptophyta, Chlorophyta, and Dinoflagellata were found to be dominant in the samples. Thus, the results support the applicability of the method in environmental microbiome research. The merging and concatenation workflow presented here requires considerably less computational resources and uses widely/commonly used bioinformatics packages, saving researchers analyses time (for equivalent sample numbers, compared to the conventional approach) required to infer the diversity of major microbial domains from mixed amplicon data at comparable accuracy.

Background: With an exponential growth in biological data and computing power, familiarity with bioinformatics has become a demanding and popular skill set both in academia and industry. There is a need to increase students' competencies to be able to take on bioinformatic careers, to get them familiarized with scientific professions in data science and the academic training required to pursue them, in a field where demand outweighs the supply.

Methods: Here we implemented a set of bioinformatic activities into a protein structure and function course of a graduate program. Concisely, students were given hands-on opportunities to explore the bioinformatics-based analyses of biomolecular data and structural biology via a semester-long case study structured as inquiry-based bioinformatics exercises. Towards the end of the term, the students also designed and presented an assignment project that allowed them to document the unknown protein that they identified using bioinformatic knowledge during the term.

Results: The post-module survey responses and students' performances in the lab module imply that it furthered an in-depth knowledge of bioinformatics. Despite having not much prior knowledge of bioinformatics prior to taking this module students indicated positive feedback.

Conclusion: The students got familiar with cross-indexed databases that interlink important data about proteins, enzymes as well as genes. The essential skillsets honed by this research-based bioinformatic pedagogical approach will empower students to be able to leverage this knowledge for their future endeavours in the bioinformatics field.