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Endophytic microorganisms can metabolize organic contaminants and assist in plant growth, thus facilitating the phytoremediation of polluted environments. An endophytic bacterium capable of decoloring malachite green (MG) was isolated from the leaves of the wetland plant Suaeda salsa and was identified as Klebsiella aerogenes S27. Complete decolorization of MG (100 mg/l) was achieved in 8 h at 30 °C and pH 7.0. Ultraviolet-visible spectroscopy and Fourier-transform infrared spectroscopy analyses indicated the degradation of MG by the isolate. The enzymic assays of the strain showed the triphenylmethane reductase (TMR) activity. A gene encoding putative TMR-like protein (named as KaTMR) was cloned and heterologously expressed in Escherichia coli . KaTMR showed only 42.6–43.3% identities in amino acids compared with well-studied TMRs, and it phylogenetically formed a new branch in the family of TMRs. The degraded metabolites by recombinant KaTMR were detected by liquid chromatography-mass spectrometry, showing differences from the products of reported TMRs. The biotransformation pathway of MG was proposed. Phytotoxicity studies revealed the less-toxic nature of the degraded metabolites compared to the dye. This study presented the first report of an endophyte on the degradation and detoxification of triphenylmethane dye via a novel oxidoreductase, thus facilitating the study of the plant-endophyte symbiosis in the bioremediation processes.

Enterobacter cloacae and E. aerogenes have been increasingly reported as important opportunistic pathogens. In this study, a high prevalence of multi-drug resistant isolates from Brazil, harboring several β-lactamase encoding genes was found. Several virulence genes were observed in E. aerogenes, contrasting with the E. cloacae isolates which presented none.

As a transdermal drug delivery method, microneedles offer minimal invasiveness, painlessness, and precise in-situ treatment. However, current microneedles rely on passive diffusion, leading to uncontrollable drug penetration. To overcome this, we developed a pneumatic microneedle patch that uses live Enterobacter aerogenes as microengines to actively control drug delivery. These microbes generate gas, driving drugs into deeper tissues, with adjustable glucose concentration allowing precise control over the process. Our results showed that this microorganism-powered system increases drug delivery depth by over 200%, reaching up to 1000 μm below the skin. In a psoriasis animal model, the technology effectively delivered calcitriol into subcutaneous tissues, offering rapid symptom relief. This innovation addresses the limitations of conventional microneedles, enhancing drug efficiency, transdermal permeability, and introducing a creative paradigm for on-demand controlled drug delivery. Microneedles offer a minimally invasive transdermal drug delivery method with advantages like painless administration. Here, the authors developed a pneumatic microneedle patch powered by live Enterobacter aerogenes to enhance and control drug delivery, significantly improving treatment outcomes in a psoriasis model.

2,3-Butanediol (2,3-BDO) is an important gateway molecule for many chemical derivatives. Currently, microbial production is gradually being recognized as a green and sustainable alternative to petrochemical synthesis, but the titer, yield, and productivity of microbial 2,3-BDO remain suboptimal. Here, we used systemic metabolic engineering strategies to debottleneck the 2,3-BDO production in Enterobacter aerogenes . Firstly, the pyruvate metabolic network was reconstructed by deleting genes for by-product synthesis to improve the flux toward 2,3-BDO synthesis, which resulted in a 90% increase of the product titer. Secondly, the 2,3-BDO productivity of the IAM1183-LPCT/D was increased by 55% due to the heterologous expression of DR1558 which boosted cell resistance to abiotic stress. Thirdly, carbon sources were optimized to further improve the yield of target products. The IAM1183-LPCT/D showed the highest titer of 2,3-BDO from sucrose, 20% higher than that from glucose, and the yield of 2,3-BDO reached 0.49 g/g. Finally, the titer of 2,3-BDO of IAM1183-LPCT/D in a 5-L fermenter reached 22.93 g/L, 85% higher than the wild-type strain, and the titer of by-products except ethanol was very low. Key points Deletion of five key genes in E. aerogenes improved 2,3-BDO production The titer of 2,3-BDO was increased by 90% by regulating metabolic flux Response regulator DR1558 was expressed to increase 2,3-BDO productivity Graphical abstract

This work investigates the efficacy of plasma-activated water (PAW) and plasma-activated acidified buffer (PAAB) on Enterobacter aerogenes in aqueous system and fruit systems. Reactive oxygen and nitrogen species in PAW have been suggested to provide antimicrobial and acidifying effects, causing the pH of treated water to drop. To isolate the effect of pH in microbial inactivation and to study the interactive effects of pH and reactive species on microbial inactivation, a citrate-phosphate buffer (pH 3.1) and PAAB (citrate-phosphate) were studied. A 1.92 ± 0.70 log CFU/mL reduction in E. aerogenes was observed in PAW, while no reduction was achieved in the buffer, suggesting that the inactivation was due to the reactive species in PAW and not the acidic pH. PAAB achieved a 5.11 ± 0.63 log CFU/mL reduction, suggesting an interactive effect of reactive species and low pH. Electrical conductivity and oxidation-reduction potential measurements suggest potential mechanisms for the greater antimicrobial efficacy of PAAB over PAW. Four surfaces of increasing roughness (glass slides, grape tomatoes, limes, and spiny gourds) were spot inoculated and washed with distilled water, PAW, buffer, and PAAB for 3 min. The smoothest surface (glass) showed the highest reduction (6.32 ± 0.43 log CFU per surface), while the roughest surface (spiny gourd) showed a significantly lower reduction (2.52 ± 0.46 log CFU per surface) when treated with PAAB. For treatment with PAW, no significant differences were observed between glass slides, limes, and spiny gourds. With PAW treatment, significantly lower reduction was observed on spiny gourds (1.70 ± 0.21 log CFU per surface) than on grape tomatoes (4.65 ± 1.34 log CFU per surface). PAW and PAAB both showed potential for their use in fresh produce sanitation.

Here, we sequenced the 5,419,609 bp circular genome of an Enterobacter aerogenes clinical isolate that killed a patient and was resistant to almost all current antibiotics (except gentamicin) commonly used to treat Enterobacterial infections, including colistin. Genomic and phylogenetic analyses explain the discrepancies of this bacterium and show that its core genome originates from another genus, Klebsiella. Atypical characteristics of this bacterium (i.e., motility, presence of ornithine decarboxylase, and lack of urease activity) are attributed to genomic mosaicism, by acquisition of additional genes, such as the complete 60,582 bp flagellar assembly operon acquired “en bloc” from the genus Serratia. The genealogic tree of the 162,202 bp multidrug-resistant conjugative plasmid shows that it is a chimera of transposons and integrative conjugative elements from various bacterial origins, resembling a rhizome. Moreover, we demonstrate biologically that a G53S mutation in the pmrA gene results in colistin resistance. E. aerogenes has a large RNA population comprising 8 rRNA operons and 87 cognate tRNAs that have the ability to translate transferred genes that use different codons, as exemplified by the significantly different codon usage between genes from the core genome and the “mobilome.” On the basis of our findings, the evolution of this bacterium to become a “killer bug” with new genomic repertoires was from three criteria that are “opportunity, power, and usage” to indicate a sympatric lifestyle: “opportunity” to meet other bacteria and exchange foreign sequences since this bacteria was similar to sympatric bacteria; “power” to integrate these foreign sequences such as the acquisition of several mobile genetic elements (plasmids, integrative conjugative element, prophages, transposons, flagellar assembly system, etc.) found in his genome; and “usage” to have the ability to translate these sequences including those from rare codons to serve as a translator of foreign languages.

2,3-Butanediol is an important bio-based chemical product, because it can be converted into several C4 industrial chemicals. In this study, a lactate dehydrogenase-deleted mutant was constructed to improve 2,3-butanediol productivity in Enterobacter aerogenes. To delete the gene encoding lactate dehydrogenase, λ Red recombination method was successfully adapted for E. aerogenes. The resulting strain produced a very small amount of lactate and 16.7% more 2,3-butanediol than that of the wild-type strain in batch fermentation. The mutant and its parental strain were then cultured with six different carbon sources, and the mutant showed higher carbon source consumption and microbial growth rates in all media. The 2,3-butanediol titer reached 69.5 g/l in 54 h during fed-batch fermentation with the mutant, which was 27.4% higher than that with the parental strain. With further optimization of the medium and aeration conditions, 118.05 g/l 2,3-butanediol was produced in 54 h during fed-batch fermentation with the mutant. This is by far the highest titer of 2,3-butanediol with E. aerogenes achieved by metabolic pathway engineering.[PUBLICATION ABSTRACT]

Circadian rhythms are fundamental properties of most eukaryotes, but evidence of biological clocks that drive these rhythms in prokaryotes has been restricted to Cyanobacteria. In vertebrates, the gastrointestinal system expresses circadian patterns of gene expression, motility and secretion in vivo and in vitro, and recent studies suggest that the enteric microbiome is regulated by the host's circadian clock. However, it is not clear how the host's clock regulates the microbiome. Here, we demonstrate at least one species of commensal bacterium from the human gastrointestinal system, Enterobacter aerogenes, is sensitive to the neurohormone melatonin, which is secreted into the gastrointestinal lumen, and expresses circadian patterns of swarming and motility. Melatonin specifically increases the magnitude of swarming in cultures of E. aerogenes, but not in Escherichia coli or Klebsiella pneumoniae. The swarming appears to occur daily, and transformation of E. aerogenes with a flagellar motor-protein driven lux plasmid confirms a temperature-compensated circadian rhythm of luciferase activity, which is synchronized in the presence of melatonin. Altogether, these data demonstrate a circadian clock in a non-cyanobacterial prokaryote and suggest the human circadian system may regulate its microbiome through the entrainment of bacterial clocks.

As the effectiveness of current treatments against the development of antimicrobial resistance is declining, new strategies are required. A great source of novel secondary metabolites with therapeutics effects are the endophytic bacteria present in medicinal plants. In this study, Klebsiella aerogenes (an endophytic bacteria belonging to the Enterobacteriaceae family) was isolated from Kalanchoe blossfeldiana (a medicinal plant”. The bacterial secondary metabolites were identified using GC-MS techniques. Furthermore, the antibacterial potentials were investigated against multi-drug resistance (MDR) Salmonella typhi and Staphylococcus aureus . The GC-MS chromatogram of K . aerogenes secondary metabolites extract displayed total of 36 compounds. Ethyl acetate extracts of K . aerogenes , showed mean zone of growth inhibition of 15.00 ± 1.00 against S . typhi and 7.00 ± 1.00mm against S . aureus , respectively. The extract demonstrated significant antibacterial effectiveness against S . typhi and moderate antibacterial efficacy against S . aureus , with minimum inhibitory concentration (MIC) values ranging from 0.089 to 0.39 mg/mL. The time-kill kinetics profile of the ethyl acetate extract against S . typhi revealed a decrease in the number of viable cells during the initial 5, 6, and 24 hours. Conversely, there was a sudden increase in viable cells up to 6 hours for S . aureus . The identified secondary metabolite with high percentage than others, benzeneethanamine exhibited favorable interactions (−7.2 kcal/mol) with the penicillin-binding protein (PBP2a) of S . aureus and (−7.5 kcal/mol) osmoporin (OmpC) of S . typhi , indicating its potential as a candidate for drug development against these MDR bacteria. This study reported for the first time, bacterial endophytes associated with K . blossfeldiana with antibacterial activities.

Background Klebsiella aerogenes is an opportunistic pathogen that causes a wide variety of infections. Due to the rising problem of antibiotic resistance, novel antibiotics and strategies to combat bacterial infections are needed. Host-specific bacteriophages are natural enemies of bacteria and can be used in phage therapy as an alternative form of treatment against bacterial infections. Jumbo phages are defined as phages with genomes larger than 200 kb. Relatively few studies have been done on jumbo phages compared to smaller phages. Results A novel phage, fENko-Kae01, was isolated from a commercial phage cocktail. Genomic analysis revealed that fENko-Kae01 is a lytic jumbo phage with a 360 kb genome encoding 578 predicted genes. No highly similar phage genomes were identified and fENko-Kae01 may be a completely new genus representative. No known genes associated with lysogenic life cycle, bacterial virulence, or antibiotic resistance were identified. The phage had myovirus morphology and a narrow host range. Phage resistant bacterial mutants emerged under phage selection. Whole genome sequencing revealed that the biogenesis of the flagellum was affected in four mutants and the lack of functional flagellum was confirmed in motility assays. Furthermore, phage fENKo-Kae01 failed to adsorb on the non-motile mutants indicating that the bacterial flagellum is the phage-binding receptor. Conclusions fENko-Kae01 is a novel jumbo bacteriophage that is considered safe for phage therapy. fENko-Kae01 uses the flagellum as the phage-binding receptor and may represent a completely novel genus.