Menaquinone (MK) is an important electron transporter in Escherichia coli. This isoprenoid quinone can transfer electrons to many terminal acceptors, such as fumarate and nitrate, which helps this organism survive under diverse and challenging conditions. As the isoprenoid quinones with various length of isoprenyl tail are widely distributed in nature, the heterologous expression of polyprenyl diphosphate synthases (PDSs) has been investigated using its counterpart, ubiquinone (UQ). In this study, we investigated the MK production by the expression of various heterologous PDS genes from prokaryotic and eukaryotic species, including Saccharomyces cerevisiae COQ1 (hexa-PDS), Haemophilus influenzae hi0881 (hepta-PDS), Synechocystis sp. strain PCC6803 slr0611 (nona-PDS) and Glunocobacter suboxydans ddsA (deca-PDS) in E. coli. We detected specific isoforms of MK, including MK7, MK9, and MK10, via the expression of HI0881, Slr0611 and DdsA respectively, but rarely detect MK6 via the expression of Coq1. As UQ6 was detected in E. coli harboring COQ1, the acceptance of the side chain lengths by MenA (prenyl transferase for MK) was narrower than UbiA (prenyl transferase for UQ). We also identified a mutation in menA in the E. coli AN386 strain and a transposon insertion of IS186 in menC in E. coli KO229 (∆ispB) and its parental strain FS1576. Taken together, these results elucidate the different nature of MenA from UbiA.

Streptomyces rochei is a species of Streptomyces with a diverse range of biological activities. S. rochei strain A144 was isolated from desert soils and exhibits antagonistic activity against several plant pathogenic fungi. The genome of S. rochei A144 was sequenced and revealed the presence of one linear chromosome and one plasmid. The chromosome length was found to be 8,085,429 bp, with a GC content of 72.62%, while the Plas1 length was 177,399 bp, with a GC content of 69.08%. Comparative genomics was employed to analyse the S. rochei group. There is a high degree of collinearity between the genomes of S. rochei strains. Based on pan-genome analysis, S. rochei has 10,315 gene families, including 4051 core and 2322 unique genes. AntiSMASH was used to identify the gene clusters for secondary metabolites, identifying 33 secondary metabolite genes on the A144 genome. Among them, 18 clusters were found to be >70% identical to known biosynthetic gene clusters (BGCs), indicating that A144 has the potential to synthesize secondary metabolites. The majority of the BGCs were found to be conserved within the S. rochei group, including those encoding polyketide synthases (PKS), terpenes, non-ribosomal peptide synthetases (NRPS), other ribosomally synthesised and post-translationally modified peptides (RiPP), nicotianamine-iron transporters, lanthipeptides, and a few other types. The S. rochei group can be a potential genetic source of useful secondary metabolites with applications in medicine and biotechnology.

Divulsuperbac (DSB) is an outreach project involving a Service-Learning component aimed at the educational community. Launched in 2019, it has involved Biology degree students in a Microbiology-focused initiative within the Valencian Community (Spain) for four academic years. The DSB project includes various outreach activities designed to raise awareness of the threat posed by superbugs among pre-university students. Under the supervision of their professors, university students created an exhibition featuring 14 infographics on antimicrobial resistance. These infographics were presented at 23 high schools (HS), where university students explained the issue to HS students (aged 15-16) and assessed their understanding of the topic. The activity was supported by HS teachers. Surveys indicated scores of around 4 out of 5 in terms of overall scientific interest and knowledge gained about antibiotic resistance. These positive results have inspired us to expand the project to other regions of the world.

Adaptation to environmental change during both colonization and infection is essential to the pathogenesis of Staphylococcus aureus. Like other bacterial pathogens that require potassium to fulfill nutritional and chemiosmotic requirements, S. aureus has been shown to utilize potassium transport to modulate virulence gene expression, antimicrobial resistance, and osmotic tolerance. Recent studies examining the role for potassium uptake in mediating S. aureus physiology have also described its contribution in mediating carbon flux within central metabolism and generation of a proton motive force. Here, we utilize a pH-sensitive green fluorescent protein to examine the temporal regulation of S. aureus intracellular pH by potassium and sodium under various environmental conditions, including extracellular pH and antibiotic stress. Our results distinguish unique conditions and transport mechanisms that utilize these ions to modulate cytoplasmic pH homeostasis, and they identify these processes as a novel mechanism of intrinsic ampicillin resistance in S. aureus.

To conduct an origin tracking and genomic study of the Brucella strain B. melitensis bv.3 ARQ-070, with the aim of addressing the challenges posed by the highly conserved genome of Brucella to conventional typing methods and to gain an understanding of the geographic distribution and interspecies transmission of this pathogen in China.

Nano-picoplankton are the dominant primary producers during the post-upwelling period in St Helena Bay, South Africa. Their dynamics on short time scales are not well understood and neither are the community composition, structure, and potential functionality of the surrounding microbiome. Samples were collected over five consecutive days in March 2018 from three depths (1 m, 25 m, 50 m) at a single sampling station in St Helena Bay. There was clear depth-differentiation between the surface and depth in both diversity and function throughout the sampling period for the archaea, bacteria and eukaryotes. Daily difference in eukaryote diversity, was more pronounced at 1 m and 25 m with increased abundances of Syndiniales and Bacillariophyta. Surface waters were dominated by photosynthetic and photoheterotrophic microorganisms, while samples at depth were linked to nitrogen cycling processes, with high abundances of nitrifiers and denitrifiers. Strong depth gradients found in the nutrient transporters for ammonia were good indicators of measured uptake rates. This study showed that nano-picoplankton dynamics were driven by light availability, nutrient concentrations, carbon biomass and oxygenation. The nano-picoplankton help sustain ecosystem functioning in St Helena Bay through their ecological roles, which emphasizes the need to monitor this size fraction of the plankton.

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). SEM 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 production of aflatoxin B1 via downregulation 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 anti-fungal mechanisms of volatile organic compounds.

In this study, we developed a mycelial dispersion strain by disrupting the pkac2 gene in the white-rot fungus Pleurotus ostreatus. pkac2 is a catalytic subunit gene of protein kinase A, which regulates several transcription factors related to cell wall synthesis. Liquid cultures of the Δpkac2 strains showed very high mycelial dispersibility and were visibly different from the wild-type strain (WT). Although growth on agar medium was slower than that of WT, Δpkac2 strains grew faster in liquid culture and had approximately twice the mycelial dry weight of WT after 5 d of culture. Microscopic observations showed that the cell walls of the Δpkac2 strains were thinner compared to WT. The β-glucan content in the cell walls decreased in the pkac2 disruptants, although the transcription levels of β-glucan synthase genes increased. Furthermore, the Δpkac2 strains showed decreased hydrophobicity and stress tolerance compared to WT. These results indicate that disruption of the pkac2 gene in P. ostreatus alters the structure of the cell wall surface layer, resulting in high-density cultures due to mycelial dispersion.

The aim of this study was to investigate the relationship among pollutant removal performance, microbial community structure and potential gene function of immobilized microorganisms in coking wastewater (CWW) treatment process. The results showed that the immobilized biomass containing strain Comamonas sp. ZF-3 displayed greater resistance to CWW and higher COD, NH4+-N removal efficiency (92%, 60%) than free cells (48%, 7%), meanwhile, the results from GC-MS proved main organic pollutants in CWW including phenolic compounds, heterocyclic compounds and polycyclic aromatic hydrocarbons were basically removed by immobilized microorganisms. During 123 days of degradation experiment, high-throughput 16S rRNA gene sequencing analysis of immobilized carriers showed more stable and diverse microbial community, which was consistent with simultaneous removal of COD and NH4+-N observed in carrier experiment. Among them, Comamonas sp. ZF-3 continuously remained at the highest proportion (23.25%) in immobilized carrier, while Nitrosomonas (1.47%) and Nitrospira (1.90%) were simultaneously detected. Moreover, microbial community of immobilized carriers showed higher relative abundance of potential function in membrane transport and xenobiotics biodegradation and metabolism, which may indirectly displayed biodegradation activity of immobilized functional microorganisms. This work illustrated the survival status and potential gene function of immobilized microorganisms, and provided basis for practical application of immobilized carriers in CWW treatment.

The increasing trend of carbapenem resistance amongst Escherichia coli poses a major public health crisis and requires active surveillance of resistance mechanisms to control the threat. Quorum Sensing system plays a role in bacterial resistance to antibiotics. Quorum Sensing is a cell-cell communication system where bacteria alter their gene expression in response to specific stimuli. Here, in this study we investigated the transcriptional response of quorum sensing receptor, sdiA in E.coli under sub-inhibitory concentration of carbapenem in presence of quorum sensing signal molecules. Two E.coli isolates harbouring blaNDM were subjected to treatment with 10% SDS for 20 consecutive days of which blaNDM encoding plasmid was successfully eliminated from one isolate. Both the wild type and the cured mutant were then allowed to grow under eight different inducing conditions and the transcriptional response of sdiA gene was studied by quantitative real time PCR method. We found different response levels of sdiA in wild type and cured mutant under exogenous AHL and imipenem and when co-cultured with P.aeruginosa under imipenem stress. This study highlighted that sub-inhibitory concentration of imipenem in combination with AHL is acting as signal to SdiA, a quorum sensing receptor in E.coli.

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 bloodstream infection patients were analyzed 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 three years of patient data, which showed an area under the curve (AUC) of 0.828. It was further validated using two 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.

Food contamination by mycotoxigenic fungi is one of the principal factors that cause food loss and economic losses in the food industry. The objective of this work was to incorporate the essential oil from Corymbia citriodora Hook and its constituents citronellal and β-citronellol into poly(lactic acid) nanofibers; to characterize the nanofibers by scanning electron microscopy (SEM), Fourier transform infrared spectroscopy and differential scanning calorimetry; to evaluate the antifungal activity by the fumigation method; to evaluate the antimycotoxigenic activity against Aspergillus carbonarius, Aspergillus ochraceus, Aspergillus westerdijkiae, Aspergillus flavus, and Aspergillus parasiticus; and to evaluate the morphology of these microorganisms. All the nanofibers had a regular, smooth, and continuous morphology. FTIR analyses confirmed that the active ingredients were incorporated into the polymer matrix. All samples exhibited antifungal and ochratoxigenic inhibitory activities of up to 100% and 99%, respectively, with the best results observed for (PLA + 30 wt% β-citronellol) nanofibers and (PLA + 30 wt% citronellal) nanofibers. However, 100% inhibition of the production of aflatoxin B1 and B2 was not observed. The images obtained by SEM indicated that the nanofibers caused damage to the hyphae, caused a decrease in the production of spores, and caused deformation, rupture, and non-formation of the conid head, might be an alternative for the control of mycotoxigenic fungi.

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.

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.

Glyphosate is the most used herbicide on Earth. After a half-century of use we know only two biodegradative pathways, each of which appears to degrade glyphosate incidentally. One pathway begins with oxidation of glyphosate catalysed by glycine oxidase (GO). To date, no naturally occurring GO enzymes preferentially oxidize glyphosate but nonetheless are sufficiently active to initiate its degradation. However, GO enzymes that preferentially oxidize glyphosate over glycine-i.e. glyphosate oxidases (GOXs)-may have evolved in environments facing prolonged glyphosate exposure. To test this hypothesis, we screened a metagenomic library from glyphosate-exposed agricultural soil and identified a GOX from clone 11AW19 (GO19) that prefers glyphosate over glycine by four orders of magnitude. This is the first GO isolated from a natural source exhibiting a glyphosate preference. Not only have we discovered the first GOX in nature, but we have also demonstrated the utility of functional metagenomics to find a GOX with greater catalytic efficiency and specificity than those engineered using directed evolution.

This study explores the relationship between microbial diversity and disease status in human lung cancer tissue microbiomes, using a sample size of 1212. Analysis divided the data into primary tumour (PT) and normal tissue (NT) categories. Differences in microbial diversity between PT and NT were significant in 57% of comparisons, although dataset dependence was a factor in the diversity levels. Shared species analysis (SSA) indicated no significant differences between PT and NT in over 90% of comparisons. Network diversity assessments revealed significant differences between NT and PT regarding species relative abundances and network link abundances for q = 0-3. Additionally, significant variations were found between NT and lung squamous cell carcinoma (LUSC) at q = 0. in network link probabilities, illustrating the diversity in species interactions. Our findings suggest a stable overall microbiome diversity and composition in lung cancer patients' lung tissues despite patients with diagnosed lung tumours, indicating modified microbial interactions within the tumour. These results highlight an association between altered microbiome interaction patterns and lung tumours, offering new insights into the ecological dynamics of lung cancer microbiomes.

Biological soil crusts (BSCs), a vital component of ecosystems, are pivotal in carbon sequestration, nutrient enrichment, and microbial diversity conservation. However, their impact on soil microbiomes in alpine regions remains largely unexplored. Therefore, this study aimed to determine the influence of BSCs on alpine grassland soil microbiomes, by collecting 24 pairs of soils covered by biological and physical crusts along a transect on the Qinghai-Tibetan Plateau. We found that BSCs significantly increased the contents of soil moisture, organic carbon, total nitrogen, and many available nutrients. They also substantially altered the soil microbiomes. Specifically, BSCs significantly increased the relative abundance of Cyanobacteria, Verrucomicrobiota, and Ascomycota, while decreasing the proportions of Gemmatimonadota, Firmicutes, Nitrospirae, Mortierellomycota, and Glomeromycota. By contrast, microbial abundance and α-diversity demonstrated low sensitivity to BSCs across most study sites. Under the BSCs, the assembly of prokaryotic communities was more affected by homogeneous selection and drift, but less affected by dispersal limitation. Conversely, soil fungal community assembly mechanisms showed an inverse trend. Overall, this study provides a comprehensive understanding of the effects of BSCs on soil properties and microbial communities, offering vital insights into the ecological roles of BSCs.

The genus Flavobacterium comprises a diversity of species, including fish pathogens. Multiple techniques have been used to identify isolates of this genus, such as phenotyping, polymerase chain reaction genotyping, and in silico whole-genome taxonomy. In this study, we demonstrate that whole-genome-based taxonomy, using average nucleotide identity and molecular phylogeny, is the most accurate approach for Flavobacterium species. We obtained various isolated strains from official collections; these strains had been previously characterized by a third party using various identification methodologies. We analyzed isolates by PCR genotyping using previously published primers targeting gyrB and gyrA genes, which are supposedly specific to the genus Flavobacterium and Flavobacterium psychrophilum, respectively. After genomic analysis, nearly half of the isolates had their identities re-evaluated: around a quarter of them were re-assigned to other genera and two isolates are new species of flavobacteria. In retrospect, the phenotyping method was the least accurate. While gyrB genotyping was accurate with the isolates included in this study, bioinformatics analysis suggests that only 70% of the Flavobacterium species could be appropriately identified using this approach. We propose that whole-genome taxonomy should be used for accurate Flavobacterium identification, and we encourage bacterial collections to review the identification of isolates identified by phenotyping.

Gut microbiome plays crucial roles in animal adaptation and evolution. However, research on adaptation and evolution of small wild high-altitude mammals from the perspective of gut microbiome is still limited. In this study, we compared differences in intestinal microbiota composition and function in Plateau pikas (Ochotona curzoniae) and Daurian pikas (O. daurica) using metagenomic sequencing. Our results showed that microbial community structure had distinct differences in different pika species. Prevotella, Methanosarcina, Rhizophagus, and Podoviridae were abundant bacteria, archaea, eukaryotes, and viruses in Plateau pikas, respectively. However, Prevotella, Methanosarcina, Ustilago, and Retroviridae were dominated in Daurian pikas. Functional pathways related to carbohydrate metabolism that refer to the utilization of pectin, hemicellulose, and debranching enzymes were abundant in Plateau pikas, while the function for degradation of chitin, lignin, and cellulose was more concentrated in Daurian pikas. Pika gut had abundant multidrug resistance genes, followed by glycopeptide and beta-lactamase resistance genes, as well as high-risk antibiotic resistance genes, such as mepA, tetM, and bacA. Escherichia coli and Klebsiella pneumoniae may be potential hosts of mepA. This research provided new insights for adaptation and evolution of wild animals from perspective of gut microbiome and broadened our understanding of high-risk antibiotic resistance genes and potential pathogens of wild animals.

Historically, Xanthomonas species are primarily known for their pathogenicity against plants, but recently, there have been more findings of non-pathogenic xanthomonads. In the present study, we report isolates from healthy rice seeds that belong to a new species, Xanthomonas protegens, a protector of the rice plants against a serious pathogenic counterpart, i.e. X. oryzae pv. oryzae upon leaf clip co-inoculation. The new member species is non-pathogenic to rice and lacks a type III secretion system. The pangenome investigation revealed a large number of unique genes, including a novel lipopolysaccharide biosynthetic gene cluster, that might be important in its adaptation. The phylo-taxonogenomic analysis revealed that X. protegens is a taxonomic outlier species of X. sontii, a core, vertically transmitted rice seed endophyte with numerous probiotic properties. Interestingly, X. sontii is also reported as a keystone species of healthy rice seed microbiome. The findings and resources will help in the development of unique gene markers and evolutionary studies of X. sontii as a successful symbiont and X. oryzae as a serious pathogen. Here, we propose X. protegens sp. nov. as a novel species of the genus Xanthomonas with PPL118 = MTCC 13396 = CFBP 9164 = ICMP 25181 as the type strain. PPL117, PPL124, PPL125, and PPL126 are other strains of the species.

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.