In the presented work identification of microorganisms isolated from various types of honeys was performed. Martix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) ...and 16S rDNA sequencing were applied to study environmental bacteria strains.With both approches, problematic spore-forming Bacillus spp, but also Staphylococcus spp., Lysinibacillus spp., Micrococcus spp. and Brevibacillus spp were identified. However, application of spectrometric technique allows for an unambiguous distinction between species/species groups e.g.B. subtilis or B. cereus groups. MALDI TOF MS and 16S rDNA sequencing allow for construction of phyloproteomic and phylogenetic trees of identified bacterial species. Furthermore, the correlation beetween physicochemical properties, geographical and botanical origin and the presence bacterial species in honey samples were investigated.
Lipidomic profiling has emerged as a powerful tool for the comprehensive characterization of bacterial species, particularly in the context of clinical diagnostics. Utilizing matrix-assisted laser ...desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), this study aims to elucidate the lipidomic landscapes of bacterial strains isolated from diabetic foot infections (DFI). Our analysis successfully identified a diverse array of lipids in the cellular membranes of both Gram-positive and Gram-negative bacteria, revealing a total of 108 unique fatty acid combinations. Specifically, we identified 26 LPG, 33 LPE, 43 PE, 114 PG, 89 TAG, and 120 CLP in Gram-positive bacteria and 10 LPG, 14 LPE, 124 PE, 37 PG, 13 TAG, and 22 CLP in Gram-negative strains. Key fatty acids, such as palmitic acid, palmitoleic acid, stearic acid, and oleic acid, were prominently featured. Univariate analysis further highlighted distinct lipidomic signatures among the bacterial strains, revealing elevated levels of phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) in Gram-negative bacteria associated with DFI. In contrast, Gram-positive strains demonstrated increased or uniquely fluctuating levels of triglyceride (TAG) and cardiolipin (CLP). These findings not only underscore the utility of MALDI-TOF MS in bacterial lipidomics but also provide valuable insights into the lipidomic adaptations of bacteria in diabetic foot infections, thereby laying the groundwork for future studies aimed at constructing microbial lipid libraries for enhanced bacterial identification.
remains a major health problem responsible for many epidemic outbreaks. Therefore, the development of efficient and rapid methods for studying molecular profiles of
strains for its further typing is ...in high demand. Among many techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS) represents a timely, cost-effective, and reliable strain typing approach, which is still rarely used due to insufficient knowledge about the impact of sample preparation and analysis conditions on the molecular profiles and strain classification efficiency of
. The aim of this study was to evaluate the effect of the culture conditions and matrix type on the differentiation of molecular profiles of various
strains via the MALDI TOF MS analysis and different computational methods. The analysis revealed that by changing the culture conditions, matrix type, as well as a statistical method, the differentiation of
strains can be significantly improved. Therefore, to accelerate the incorporation of the MALDI-based strain typing in routine laboratories, further studies on the standardization and searching of optimal conditions on a larger number of isolates and bacterial species are of great need.
Rhizosphere and endophytic bacteria are well known producers of siderophores, organic compounds that chelate ferric iron (Fe3+), and therefore play an important role in plant growth promotion in ...metalliferous areas, thereby improving bioremediation processes. However, in addition to their primary function in iron mobilization, siderophores also have the capacity to chelate other heavy metals, such as Al3+, Zn2+, Cu2+, Pb2+ and Cd2+, that can affect homeostasis and the heavy metal tolerance of microorganisms.
The main goal of our study was to select the most efficient siderophore-producing bacterial strains isolated from the roots (endophytes) and rhizosphere of Betula pendula L. and Alnus glutinosa L. growing at two heavy metal contaminated sites in southern Poland. Siderophore biosynthesis of these strains in the presence of increasing concentrations of Cd2+ (0, 0.5, 1, 2 and 3 mM) under iron-deficiency conditions was analysed using spectrophotometric chemical tests for hydroxamates, catecholates and phenolates, as well as the separation of bacterial siderophores by HPLC and characterization of their structure by UHPLC-QTOF/MS.
We proved that (i) siderophore-producing bacterial strains seems to be more abundant in the rhizosphere (47%) than in root endophytes (18%); (ii) the strains most effective at siderophore synthesis belonged to the genus Streptomyces and were able to secrete three types of siderophores under Cd2+ stress: hydroxamates, catecholates and phenolates; (iii) in general, the addition of Cd2+ enhanced siderophore synthesis, particularly ferrioxamine B synthesis, which may indicate that siderophores play a significant role in tolerance to Cd2+ in Streptomyces sp.
•Identification and selection of the most efficient siderophore-producing bacterial strains.•Siderophore biosynthesis in the presence of increasing concentrations of Cd2+.•Analysis of different types of siderophores: hydroxamates, catecholates and phenolates.•Separation of bacterial siderophores by HPLC and characterization of their structure by UHPLC-QTOF/MS.
The development of new techniques for the detection of carbapenemase activity is of great importance since the increased incident of resistance against carbapenems represents a serious threat to ...global public health. In this context, the matrix-assisted laser desorption/ionization approach already demonstrated to be a reliable tool for rapid carbapenemase detection. As a newly developed test, there is still a lack of in-depth analysis of its robustness and possible wider application. The main goal of this study was to evaluate the potential for using the design MBT STAR-Carba assay as the pre-characterization method for Enterobacterales and P. aeruginosa strains in terms of the produced classes of carbapenemases using modified procedure parameters-various suspension densities and incubation times. Moreover, its usefulness for the in-depth analysis and characterization of metallo-β-lactamases (MBL) was tested by applying inhibition assays. In this study, the designed assay proved to be a sensitive tool for the detection of carbapenemase hydrolytic activity, which can be successfully used to partially classify the class of carbapenemase present. Additionally, the use of defined high concentration suspensions would allow to shorten the incubation time to 1 minute for certain strains. Considering that the assay was also suitable to investigate the effect of different inhibitors on the MBL activity, it demonstrates far higher discriminatory potential than only a rapid routine carbapenemase detection tool and could be used as a susceptibility assay.
The main goal of the study was to evaluate the usefulness of the culturomics approach in the reflection of diabetic foot infections (DFIs) microbial compositions in Poland. Superficial swab samples ...of 16 diabetic foot infection patients (Provincial Polyclinical Hospital in Toruń, Poland) were subjected to culturing using 10 different types of media followed by the identification via the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and Biotyper platform. Identified 204 bacterial isolates representing 18 different species—mostly Enterococcus faecalis (63%) and Staphylococcus aureus (44%). Most of the infections (81%) demonstrated a polymicrobial character. Great differences in the species coverage, the number of isolated Gram-positive and Gram-negative bacteria, and the efficiency of the microbial composition reflection between the investigated media were revealed. The use of commonly recommended blood agar allowed to reveal only 53% of the entire microbial composition of the diabetic foot infection samples, which considerably improved when the chromagar orientation and vancomycin-resistant enterococi agar were applied. In general, efficiency increased in the following order: selective < universal < enriched < differential media. Performed analysis also revealed the impact of the culture media composition on the molecular profiles of some bacterial species, such as Corynebacterium striatum, Proteus mirabilis or Morganella morganii that contributed to the differences in the identification quality. Our results indicated that the culturomics approach can significantly improve the accuracy of the reflection of the diabetic foot infections microbial compositions as long as an appropriate media set is selected. The chromagar orientation and vancomycin-resistant enterococi agar media which were used for the first time to study diabetic foot infection microbial profiles demonstrate the highest utility in the culturomics approach and should be included in further studies directed to find a faster and more reliable diabetic foot infection diagnostic tool.
The bacterial infection of post-operative wounds is a common health problem. Therefore, it is important to investigate fast and accurate methods of identifying bacteria in clinical samples. The aim ...of the study was to analyse the use of the MALDI-TOF MS technique to identify microorganism wounds that are difficult to heal. The most common bacteria are Escherichia coli, Staphylococcus spp., and Enterococcus spp. We also demonstrate the effect of culture conditions, such as the used growth medium (solid: Brain Heart Infusion Agar, Mueller Hilton Agar, Glucose Bromocresol Purple Agar, and Vancomycin Resistance Enterococci Agar Base and liquid: Tryptic Soy Broth and BACTEC Lytic/10 Anaerobic/F), the incubation time (4, 6, and 24h), and the method of the preparation of bacterial protein extracts (the standard method based on the Bruker guideline, the Sepsityper method) to identify factors and the quality of the obtained mass spectra. By comparing the protein profiles of bacteria from patients not treated with antibiotics to those treated with antibiotics based on the presence/absence of specific signals and using the UniProt platform, it was possible to predict the probable mechanism of the action of the antibiotic used and the mechanism of drug resistance.
The study investigated the zearalenone (ZEA) neutralization process as a consequence of metabolization and binding process by the probiotic bacterial strain Lactobacillus paracasei using high ...performance liquid chromatography (HPLC). In order to determine the nature of the binding process the kinetic and spectroscopic approach were used. Moreover, the influence of ZEA on L. paracasei metabolism was examined by the determination of the proteome profile of cells and the profile of volatile compounds (VOCs) produced by bacteria cells. For this purpose the Matrix-Assisted Laser Desorption/Ionization-Time of Flight mass spectrometry (MALDI-TOF MS) and headspace solid-phase microextraction coupled to gas chromatography/mass spectrometry (HS-SPME/GC-MS) techniques were used. The obtained results indicate that in the mechanism of ZEA neutralization both – metabolization/biotransformation and binding/biosorption processes are involved. Furthermore, the biotransformation of ZEA to both α- and β-ZOL with a predominance of β-ZOL by lactic acid bacteria strain was recorded. The results suggest that the tested microorganism can be used as a potential detoxification agent for grain and feed.
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•L. paracasei effectively neutralize the zearalenone by both biosorption mechanism and metabolization to less toxic form.- Zearalenone has a significant impact on metabolism and viability of L. paracasei.•Zearalenone has a significant impact on metabolism and viability of L. paracasei.•L. paracasei cells adopt to the presence of ZEA by progressive shift in proteins composition within 48 h of incubation.
Analysis by MALDI-TOF mass spectrometry and gas chromatography-mass spectrometry was used to characterize the lipid profile of 3 lactic acid bacteria strains. By gas chromatography coupled with mass ...spectrometry, 23 fatty acids were identified. Dominant acids were palmitic (C16:0), oleic (C18:1), and α-linoleic acid (C18:3n-3) for Lactobacillus paracasei; for Lactococcus lactis they were palmitic (C16:0), gondoic (C20:1), myristoleic (C14:1), and eicosadienoic acid (C20:2), respectively; and in the case of Lactobacillus curvatus were C18:1, C18:2n-6, and C16:0, respectively. The effect of the medium on fatty acid composition was also determined. In addition, the fatty acid profile was also compared using MALDI MS analysis. The MALDI-TOF MS was used for qualitative analysis and identification of bacterial lipids. Phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylcholine, triacylglycerols, and ceramides were the most abundant species in lactic acid bacteria. One hundred different combinations of fatty acids in polar and nonpolar lipids have been identified, including 11 phospholipids (18 phosphatidylglycerol, 16 phosphatidylethanolamine, 10 phosphatidylinositol, 8 phosphatidylcholine, 4 lyso-phosphatidylethanolamine, 3 lyso-phosphatidylcholine, 3 phosphatidylserine, 1 lyso-phosphatidic acid, 1 lyso-phosphatidylglycerol, 1 lyso-phoshatidylinositol, and 1 phosphatidic acid), 23 triacylglycerols, 9 ceramides, and 2 sphingomyelin. The most abundant fatty acids identified were C16:0, C16:1, C18:0, and C18:3. Obtained lipid profiles allowed to distinguish the tested bacterial strains.
Phytoremediation is the bioremediation of contaminated soils and waters by using plants and their associated microorganisms. Phytoremediation of heavy metal (HM)-contaminated soils is based on ...immobilization of metals in rhizosphere soil and roots (phytostabilization) and on mobilization, uptake, and transfer of metals into the aboveground plant organs (phytoextraction). In this review, we aimed to (i) discuss the fundamentals, potential, and limitations of plant-associated microorganisms (bacteria and fungi) to increase the efficiency of phytostabilization and phytoextraction of HM-contaminated soils and (ii) describe promising developments and future challenges to expanding their use. Controlled inoculations of plants with growth-promoting microorganisms can significantly increase their root growth, biomass production, and stress tolerance in HM-contaminated soils. A serious weakness of phytoremediation in general is the usually high and difficult to measure expenditure of time for successful completion. The bioconcentration factors (BCFs) and the translocation factors (TFs) are among the most important measures of the efficiency of phytoremediation. However, an overview of BCFs and TFs for a variety of combinations of plants with defined associated microorganisms is lacking. Moreover, the joint evaluation of model systems would allow an improved cost–benefit calculation of microbial inoculations in phytoremediation systems. For this purpose, the use of in vitro model systems is considered to be preferable to field experiments due to the savings in time and costs and the control of environmental conditions. However, the transferability of in vitro data to field conditions is limited. Currently, attention is focused on the use of artificial neural networks, mainly to avoid formulating any complex relationships between soil inputs (e.g., soil amendments, pH, carbon, nitrogen and hydrogen contents, electrical conductivity, and dissolved organic carbon) and design outputs (e.g., BCFs and TFs) beforehand and because of the high accuracy of the obtained models. The controlled use of associated microorganisms to increase the efficiency of phytoremediation of HM, mainly using combinations of Brassica and Salix spp. and rhizobacteria at contaminated soils, is a promising possibility. A crucial future challenge for the expansion of their use will be to develop well-defined cost- and time-efficient tools for a credible prediction of their effectiveness on contaminated field sites.
La phytoremédiation est la bioremédiation de sols contaminés et d’eaux contaminées en utilisant des plantes et leurs micro-organismes associés. La phytoremédiation des sols contaminés par des métaux lourds (ML) est fondée sur l’immobilisation de métaux dans le sol et les racines de la rhizosphère (phytostabilisation) et sur la mobilisation, l’assimilation et le transfert de métaux jusqu’aux organes de plantes à la surface (phytoextraction). Dans cette revue, notre but était (i) de discuter des principes de base, des possibilités et des limitations de l’utilisaton des micro-organismes associés aux plantes (bactéries et champignons) afin d’augmenter l’efficacité de la phytostabilisation et de la phytoextraction de sols contaminés par les ML et (ii) de décrire les développements prometteurs et les défis futurs quant à l’augmentation de leur utilisation. Les inoculations contrôlées de plantes au moyen de micro-organismes favorisant la croissance peuvent significativement augmenter la croissance de racines des plantes, leur production de biomasse et leur résistance au stress causé par des sols contaminés de ML. Une grave lacune de la phytoremédiation est en général qu’habituellement les dépenses en temps nécessaire pour son achèvement réussi sont élevées et difficiles à mesurer. Les facteurs de bioconcentration (FBC) et les facteurs de translocation (FT) sont parmi les mesures les plus importantes de l’efficacité de la phytoremédiation. Cependant, il manque une synthèse des FBC et des FT pour une variété de combinaisons de plantes avec les micro-organismes associés définis. De plus, l’évaluation commune de systèmes modèles permettrait d’améliorer le calcul des coûts et des avantages d’inoculations microbiennes dans le cadre de systèmes de phytoremédiation. À cette fin, l’utilisation de systèmes modèles in vitro est jugée préférable aux expériences de terrain en raison de l’économie de temps et de frais et du contrôle des conditions du milieu. Cependant, la transférabilité de données in vitro aux conditions de terrain est limitée. Actuellement, l’attention se concentre sur l’utilisation de réseaux de neurones artificiels, principalement afin d’éviter de formuler n’importe quelles relations complexes entre les apports du sol (par exemple les amendements de sol, le pH, le carbone, le contenu en azote et en hydrogène, la conductivité électrique, le carbone organique dissous) et les extrants de conception (p. ex., FBC et FT) à l’avance et à cause de la haute exactitude des modèles obtenus. L’utilisation contrôlée de micro-organismes associés afin d’augmenter l’efficacité de la phytoremédiation des ML, utilisant principalement des combinaisons de Brassica et de Salix spp. et de rhizobactéries aux sols contaminés, est une possibilité prometteuse. Un défi d’avenir crucial pour l’augmentation de leur utilisation sera de développer des outils efficaces au point de vue des coûts et du temps et bien définis pour une prédiction crédible de leur efficacité sur des sites de terrains contaminés.
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