Current Microbiology最新文献

We investigated the in vitro antibacterial activity of the combination rifampicin (RIF) + polymyxin B (PB) against extensively drug-resistant (XDR) Klebsiella pneumoniae isolates. We evaluated clinical isolates co-resistant to PB (non-mcr carriers; eptB, mgrB, pmr operon, and ramA mutations) and to carbapenems (KPC, CTX-M, and SHV producers; including KPC + NDM co-producer), belonging to sequence types (ST) ST16, ST11, ST258, ST340, and ST437. We used the standard broth microdilution method to determine RIF and PB minimum inhibitory concentration (MIC) and the checkerboard assay to evaluate the fractional inhibitory concentration index (FICI) of RIF + PB as well as to investigate the lowest concentrations of RIF and PB that combined (RIF + PB) had antibacterial activity. Time-kill assays were performed to evaluate the synergistic effect of the combination against selected isolates. PB MIC (32-256 µg/mL) and RIF MIC (32-1024 µg/mL) were determined. FICI (<0.5) indicated a synergistic effect for all isolates evaluated for the combination RIF + PB. Our results showed that low concentrations of PB (PB minimal effective antibiotic concentration [MEAC], ≤0.25-1 µg/mL) favor RIF (≤0.03-0.125 µg/mL) to reach the bacterial target and exert antibacterial activity against PB-resistant isolates, and the synergistic effect was also observed in time-kill results. The combination of RIF + PB showed in vitro antibacterial activity against XDR, carbapenem-, and PB-resistant K. pneumoniae and could be further studied as a potential combination therapy, with cost-effectiveness and promising efficacy.

The bacteriophage F8 belongs to the Myoviridae group of phages and is a pathogen of Pseudomonas aeruginosa. Since Pseudomonas aeruginosa is a multidrug-resistant opportunistic bacterium and can cause serious challenges for health services, studying the potential use of phages against them is a promising approach. Pseudomonas aeruginosa can be found on medical devices because bacteria can attach to surfaces and develop biofilms, which are difficult to eradicate because of their high resistance to environmental conditions and antimicrobial therapeutics. Phage therapy is becoming promising as an alternative for the treatment of antibiotic-resistant infections, but there is still a lack of standardized protocols approved by health organizations for possible use in the clinic. In our research, we focused on the potential use of 1-octanol, which was previously used by our team to develop a method for phage purification from bacterial lysate. 1-octanol is a fatty alcohol that is mostly used in the cosmetics industry, and its advantage is that it is approved by the FDA as a food additive. In this paper, we studied the protective properties of the addition of 1-octanol for storing phage liquid preparations. We demonstrated the stabilization effect of 1-octanol addition on F8 bacteriophage preparation during storage under various conditions. Interestingly, more effective biofilm reduction was observed after treatment with the purified bacteriophage and with 1-octanol addition compared to crude lysate.

In the present study, using genome mining, Streptomyces sp. JL1001, which possesses a leinamycin-type gene cluster, was identified from 14 strains of Streptomyces originating from the rhizosphere soil of Polygonatum cyrtonema Hua. The complete genome of Streptomyces sp. JL1001 was sequenced and analyzed. The genome of Streptomyces sp. JL1001 consists of a 7,943,495 bp chromosome with a 71.71% G+C content and 7315 protein-coding genes. We also identified 36 biosynthetic gene clusters (BGCs) for secondary metabolites in Streptomyces sp. JL1001. Twenty-seven BGCs had low (< 50%) or moderate (50-80%) similarity to other known secondary metabolite BGCs. In addition, a comparative analysis was conducted between the leinamycin-type gene cluster in Streptomyces sp. JL1001 and the biosynthetic gene clusters of leinamycin and largimycin. This study aims to provide a comprehensive analysis of the genomic features of rhizosphere Streptomyces sp. JL1001. It establishes the foundation for further investigation into experimental trials involving novel bioactive metabolites such as AT-less type I polyketides that have important potential applications in medicine and agriculture.

Multidrug resistance in clinical pathogens is a significant challenge in healthcare, requiring the development of novel approaches to combat infections. In this study, we report the identification of novel antimicrobial biosynthetic gene clusters from Brevibacillus parabrevis WGTm-23, the bacterial strain isolated from a termitarium. This strain showed an antagonistic effect against drug-resistant clinical pathogens, such as Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella paratyphi, Streptococcus gordonii, and enteropathogenic Escherichia coli. The whole genome of this strain was sequenced using the Illumina platform. The genome mining revealed a total of 17 biosynthetic gene clusters (BGCs) responsible for the synthesis of secondary metabolites. The metabolites produced by this strain were predicted by constructing an identity network of the BGCs and performing a comparative analysis with genetically related strains. The genome contains multiple BGCs coding for ribosomally synthesized and post-translationally modified peptides (RiPPs). In the genome of Br. parabrevis WGTm-23, we identified BGCs that code for ulbactin F, ulbactin G, gramicidin, and bacillopaline with the highest identity. We also identified a few BGCs with less than 50% sequence identity to MC-LR/MC-LHty/MC-HphHty/MC-LHph/MC-HphHph, xenocoumacin 1/xenocoumacin II, and tyrocidine. In addition, we found fourteen BGCs that do not resemble or show identity to any entries within the antiSMASH database. Therefore, Br. parabrevis WGTm-23 has the potential to synthesize new classes of antimicrobial compounds.

In post-COVID-19 syndrome, clinical presentation of the nerve fiber dysfunction plays an important role. The possibility of autoantigen cross-mimicry of human coronaviruses and the peripheral nervous system needs to be investigated. The bioinformatic analysis was applied to search for possible common protein sequences located in the immunoreactive epitopes. Among the autoantigens of the human nervous system, fibroblast growth factor receptor protein 3, myelin protein P0, myelin protein P2, sodium channel protein type 9, alpha protein subunit, plexin-D1 protein and ubiquitin-carboxyl-terminal hydrolase protein of the L1 isoenzyme were selected. The original “Alignmentaj” analytical program was created. The UniProt database, Protein Data Bank, and AlphaFold databases were used. The analysis of protein sequence similarities of spike glycoproteins in human coronaviruses revealed common pentapeptides of the MERS-CoV-2 virus with the fibroblast growth factor receptor 3 and myelin protein P2. Among seasonal coronaviruses, common peptide sequences were identified in HCoV-HKU-1 virus with sodium channel protein type 9 subunit alpha and Plexin-D1, HCoV-OC43 with Plexin-D1, as well as HCoV-NL63 with Plexin-D1 and Ubiquitin carboxyl-terminal hydrolase isozyme L1. Some shared peptides belong to immunoreactive epitopes. The most important targets for the molecular similarities are the sodium channel subunits and fibroblast growth factor receptor 3, both for seasonal and highly pathogenic coronaviruses. The data obtained make it possible to identify new potential targets for the development of autoimmune reactions that may occur against the background of the infections with highly pathogenic as well as seasonal coronaviruses.

Alternaria species (Deuteromycetes, Ascomycota) as ubiquitous fungi and prolific producers of a variety of toxic compounds are a part of microbiomes of plants, humans, and animals, mainly causing disease, allergic reactions, and toxicosis. However, some species have also been reported as endophytic microorganisms with highly bioactive metabolites. Our previous results indicate that potentially endophytic Alternaria species from Cupressaceae produce bioactive metabolites that possibly contribute to plant holobiont's health. Here, a possible mechanism behind this bioactivity is elucidated. As some endophytic fungi are reported to produce cytotoxic taxane diterpenoids, eight potentially endophytic Alternaria isolates from our collection were analyzed for the presence of the key genes of the paclitaxel (Taxol) biosynthetic pathway, i.e., taxadin synthase (ts), 10-deacetylbaccatin III-10-O-acetyltransferase (dbat), and C-13-phenylpropanoid side-chain CoA acyltransferase (bapt). The presence of all genes, i.e., ts, dbat, and bapt, was detected by PCR in six isolates and dbat and bapt in two isolates. Chemical analyses of the fermentation broths by TLC and HPLC chromatography and IR spectroscopy indicated the synthesis of the final product, i.e., paclitaxel. So, we introduce the synthesis of taxane diterpenoids as a possible mechanism by which Alternaria occupies the plant niches and protects the plant holobiont in the presence of competing microorganisms.

Benthic habitats are the largest habitats on Earth, being essential for marine ecosystem functioning. Benthic habitats are particularly vulnerable towards pollution and anthropogenetic influence due to general oligotrophic nature. We, therefore, simulated pollution events involving nitrate and sulphate, in combination with organic carbon. We then observed the microbiota composition the following month. Surprisingly, upon nitrate addition, an abrupt response was observed between two and three weeks after the pollution event. We observed a threefold reduction in species richness, with a dominance of the genus Pseudarchobacter within the Campylobacteriota phylum, concurring with a decrease in nitrification potential and an increase in Dissimilatory Nitrate Reduction to Ammonium (DNRA) and a regain in denitrification. Likewise, addition of sulphate contributed to a delayed response with reduction in species richness albeit weaker than for nitrate, leading to a shift towards potential spore-forming Firmicutes. There was also an increase in DNRA, but only for the oxic conditions, concurring with a regain in sulphate reductio and denitrification. For the nitrate addition experiments, the delay in response could potentially be attributed to the genus Pseudarchobacter which rely on sulphides for denitrification, while for the sulphate addition experiments, the delayed response might be explained by the germination of spores. The late increase of DNRA may indicate a shift towards a different metabolic regime for nitrogen. In conclusion, our microcosm experiments revealed delayed abrupt microbiota shifts resembling tipping points that can potentially be overlooked in natural ecosystems.

This study employs genome-based methodologies to explore the taxonomic relationship between Caldicoprobacter faecalis DSM 20678^T and Caldicoprobacter oshimai DSM 21659^T. The genome-based similarity indices calculations consisting of digital DNA–DNA Hybridization (dDDH), Average Amino Aid Identity (AAI), and Average Nucleotide Identity (ANI) between the genomes of these two type strains yielded percentages of 91.2%, 98.9%, and 99.1%, respectively. These values were above the recommended thresholds of 70% (dDDH) and 95–96% (ANI and AAI) for bacterial species delineation, indicating a shared taxonomic position for C. faecalis and C. oshimai. Furthermore, analysis utilizing the 'Bacterial Pan Genome Analysis' (BPGA) pipeline and constructing a Maximum Likelihood core-genes tree using FastTree2 consistently demonstrated the close relationship between C. faecalis DSM 20678^T and C. oshimai DSM 21659^T, evident from their clustering in the core-genes phylogenomic tree. Based on these comprehensive findings, we propose the reclassification of C. faecalis as a later heterotypic synonym of C. oshimai.

Limosilactobacillus reuteri is a probiotic microorganism used in the treatment of gastrointestinal disorders. The effect of oxygen transfer on cultures of L. reuteri ATCC 53608 at shake flask and stirred tank bioreactor scales was studied, using MRS and molasses-based media. At shake flask scale, in MRS medium, a maximum bacterial concentration of 2.01 ± 0.02 g L⁻¹ was obtained; the oxygen transfer coefficient was 2.01 ± 0.04 h⁻¹. Similarly, in a 7.5 L bioreactor, in MRS, a maximum bacterial concentration of 2.46 ± 0.16 g L⁻¹ was achieved (k_La = 2.64 ± 0.06 h⁻¹). In contrast, using a molasses-based medium, bacterial concentration reached 3.13 ± 0.17 g L⁻¹ in the 7.5 L bioreactor. A progressive reduction in lactic acid concentration and yield was observed as the oxygen transfer coefficient increased, at shake flask scale. Also, the oxygen transfer coefficient strongly affected the growth of L. reuteri in shake flask and bioreactor and allowed us to successfully scale up L. reuteri culture, producing similar maximum bacterial concentrations in both scales (2.01 g L⁻¹ and 2.46 g L⁻¹ in MRS). This is the first study on oxygen transfer coefficients in L. reuteri, and it is a valuable contribution to the field as it provides important insights about how this organism tolerates oxygen and adapts its metabolism for larger biomass production.

Graphical Abstract

Powdered infant formula (PIF) is rich in nutrients that support the survival and growth of bacteria that trigger food safety disorders in deprived infants through life-threatening illnesses. The study aims to examine and identify the incidence of pathogenic bacteria of concern in PIF upon reconstitution in lukewarm water. A total of 172 samples consisting of 38 brands of PIF available in the Lagos metropolis were sampled, suspended in water (10 g in 100 mL), and bacteria strains were isolated using combinational enrichment and selective culture techniques. Pure bacterial strains were characterized and identified based on their physiology and 16S rRNA gene sequence homology. While 85 bacterial strains were isolated from the enriched culture system, 20 strains were selectively isolated based on tolerance to sodium deoxycholate. Approximately 13% of the selected bacteria were identified as Cronobacter spp., exhibiting virulence traits including extracellular protease production, coagulation and proteolysis of casein, haem-agglutination, and β-haemolysis of human blood. Approximately 82% of the Cronobacter strains tolerated NaCl (10%) and bile salt; and exhibited resistance to cefotaxime, ceftriaxone, gentamicin, and Amoxicillin-clavulanic acid antibiotics. The presence of Cronobacter spp. in 13% of the PIF brands available to infants calls for concern about the safety of deprived infants that might be fed with such PIF. Consequently, PIF safety alerts need to be activate while further studies on critical points at which the pathogens get introduced to the PIFs need to be identified.