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Methods in Molecular Biology (Clifton,... 2024Soil metaproteomics could explore the proteins involved in life activities and their abundance in the soils to overcome the difficulty in pure cultures of soil...
Soil metaproteomics could explore the proteins involved in life activities and their abundance in the soils to overcome the difficulty in pure cultures of soil microorganisms and the limitations of proteomics of pure cultures. However, the complexity and heterogeneity of soil composition, the low abundance of soil proteins, and the presence of massive interfering substances (including humic compounds) generally lead to an extremely low extraction efficiency of soil proteins. Therefore, the efficient extraction of soil proteins is a prerequisite and bottleneck problem in soil metaproteomics. In this chapter, a soil protein extraction method suitable for most types of soils with low cost and enabling simple operation (about 150 μg protein can be extracted from 5.0 g soil) is described. The quantity and purity of the extracted soil proteins could meet the requirements for further analysis using routine mass spectrometry-based proteomics.
Topics: Soil; Proteomics; Proteins; Soil Microbiology; Mass Spectrometry
PubMed: 38941012
DOI: 10.1007/978-1-0716-3910-8_4 -
Methods in Molecular Biology (Clifton,... 2024The metaproteomic approach allows a deep microbiome characterization in different complex systems. Based on metaproteome data, microbial communities' composition,...
The metaproteomic approach allows a deep microbiome characterization in different complex systems. Based on metaproteome data, microbial communities' composition, succession, and functional role in different environmental conditions can be established.The main challenge in metaproteomic studies is protein extraction, and although many protocols have been developed, a few are focused on the protein extraction of fermented foods. In this chapter, a reproducible and efficient method for the extraction of proteins from a traditionally fermented starchy food is described. The method can be applied to any fermented food and aims to enrich the extraction of proteins from microorganisms for their subsequent characterization.
Topics: Fermented Foods; Proteomics; Fermentation; Proteins; Microbiota; Food Microbiology
PubMed: 38941011
DOI: 10.1007/978-1-0716-3910-8_3 -
Clinical Oral Investigations Jun 2024Evaluate the efficacy of denture cleaners on the adhesion of Candida albicans and their effects on the surface, optical, and mechanical properties of resins for...
OBJECTIVES
Evaluate the efficacy of denture cleaners on the adhesion of Candida albicans and their effects on the surface, optical, and mechanical properties of resins for conventional, milled, and 3D-printed denture bases.
MATERIALS AND METHODS
A total of 240 resin samples were made, 120 for testing Candida albicans adhesion, optical stabilities (ΔE), roughness (Ra), hydrophilicity (°), surface free energy (Owens-Wendt) and 120 samples for testing Candida albicans adhesion, surface microhardness (Knoop), flexural strength and modulus of elasticity in a three-point test, in which they were divided into 3 groups of denture resin (n = 40) and subdivided into 5 cleaners of dentures (n = 8). Data were evaluated by two-way ANOVA and Tukey's test for multiple comparisons (α = 0.05).
RESULTS
Denture cleaners with an alkaline solution and dilute acid composition were those that showed the greatest effectiveness in reducing Candida albicans (P < 0.001), however 1% NaOCl significantly affected the properties of the resins (P < 0.05). Denture 3D-printed showed that the surface microhardness was significantly lower for all cleansers (P < 0.05).
CONCLUSIONS
Listerine demonstrated superior efficacy in reducing Candida albicans with minimal effect on denture properties, whereas 1% NaOCl had a significant negative impact on the properties. The mechanical properties were significantly lower in 3D-printed resin than in other resins for all denture cleansers.
CLINICAL RELEVANCE
Denture base materials are being sold to adapt to the CAD/CAM system, increasing the number of users of dentures manufactured with this system. Despite this, there is little investigation into denture cleaners regarding the adhesion capacity of microorganisms and the optical, surface and mechanical properties of dentures, thus requiring further investigation.
Topics: Candida albicans; Denture Bases; Denture Cleansers; Surface Properties; Printing, Three-Dimensional; Materials Testing; Computer-Aided Design; Hardness; Flexural Strength; Dental Materials
PubMed: 38940942
DOI: 10.1007/s00784-024-05801-4 -
International Journal of Systematic and... Jun 2024
Topics: Bacteria; Terminology as Topic; Archaea
PubMed: 38940771
DOI: 10.1099/ijsem.0.006343 -
Microbiology Spectrum Jun 2024Many methods are being tried for rapid and accurate identification of sepsis-causing microorganisms. We analyzed the performance of three different preparation methods...
UNLABELLED
Many methods are being tried for rapid and accurate identification of sepsis-causing microorganisms. We analyzed the performance of three different preparation methods [MBT Sepsityper IVD Kit (Bruker Daltonics GmbH, Germany), sodium dodecyl sulfate (SDS) lysis, and differential centrifugation with protein extraction (Centrifugation +PE)] and compared in standard and Sepsityper modules of the Bruker Biotyper MALDI-TOF MS for direct identification of bacteria from 240 positive blood culture bottles of BACTEC FX (Becton Dickinson, USA). By using the standard module, correct identification at species level (score ≥2) was done in 46.7% of the samples with SDS lysis, 44.2% with centrifugation +PE, and 25.4% with the Sepsityper kit. These ratios at the genus level (score range 1.70-1.99) were 34.6%, 31.3%, and 32.5%, respectively. With SDS lysis (195), more bacteria were identified correctly than centrifugation +PE (181) and the Sepsityper kit (139). A statistically significant difference was found between SDS and the Sepsityper kit and Centrifugation +PE and the Sepsityper kit ( < 0.001, both). By using the Sepsityper module, correct identification at species level (score ≥1.8) was determined in 74.2% of the samples with SDS lysis and centrifugation +PE each and 55% with the Sepsityper kit. These ratios at the genus level (score range 1.60-1.79) were 16.3%, 10%, and 19.2%, respectively. SDS lysis (217) had significantly higher identification rates than centrifugation +PE (202) and the Sepsityper kit (178) ( = 0.028 and < 0.001). A statistically significant difference was also observed between centrifugation +PE and the Sepsityper kit ( < 0.001). Best performance was obtained with SDS lysis among the methods. Although better performance was achieved by using Sepsityper software module, risk of misidentification should not be ignored.
IMPORTANCE
Sepsis is a life-threatening condition, and rapid and accurate identification of the causative microorganisms from blood cultures is crucial for timely and effective treatment. Although there are many studies on direct identification from blood cultures with MALDI-TOF MS, further standardization is still needed. In our study, we analyzed the performance of three different preparation methods and compared by using two analysis modules of the Bruker Biotyper MALDI-TOF MS for direct identification of bacteria from numerous positive blood culture bottles. The literature reports a limited number of studies that compare different preparation methods for direct blood culture identification, processing a large number of blood samples concurrently and evaluating the same samples as in our study. Moreover, although SDS is used very frequently in medical laboratories, there are few studies on direct identification from blood culture bottles. In our study, the highest correct identification rate was observed with the SDS method.
PubMed: 38940589
DOI: 10.1128/spectrum.00638-24 -
Journal of the Science of Food and... Jun 2024Pomegranate peel waste is a valuable reservoir of heat-sensitive total hydrolysable tannins (THT), with potential applications in food and pharmaceuticals. Preserving...
BACKGROUND
Pomegranate peel waste is a valuable reservoir of heat-sensitive total hydrolysable tannins (THT), with potential applications in food and pharmaceuticals. Preserving THT is challenging due to degradation post-extraction. We explore ionic gelation as an encapsulation method to optimize THT utilization.
RESULTS
Through external gelation, we optimized the process variables using Box-Behnken design. At 40 g kg sodium alginate, 25 g kg calcium chloride, and 300 g kg pomegranate peel extract (PPE), we achieved an 83.65% encapsulation efficiency. Compared to spray drying, external gelation demonstrated superior performance, with enhanced release percentages and stability. Physical, phytochemical, and release profiles of encapsulates were extensively analysed. External gelation achieved an 87.5% release in 30 min, outperforming spray-dried counterparts (69.7% in 25 min). Encapsulated PPE exhibited robust antibacterial activity against Staphylococcus aureus (ATCC 25923) in powdered infant formula, with a 32 ± 0.01 mm zone of inhibition and 300 μg mL minimum inhibitory concentration. Insights into S. aureus growth curves underlined the mechanism of action via membrane potential alterations. The results of carried investigations also showed that the antibacterial activity of the encapsulated PPE extracts against the targeted organism was identical to the antibacterial activity exhibited by synthetic antibiotics used generally to kill microorganisms in food. Therefore, from the findings, it can be concluded that the PPE encapsulate produced using the external gelation technique at the optimized condition displayed superior storage stability possessing strong antimicrobial activity when compared to encapsulate produced using the spray drying technique.
CONCLUSIONS
External gelation emerges as a potent technique for developing effective encapsulates enriched with natural antimicrobials or antibiotics. This approach holds promise for applications in food, pharmaceuticals, and nutraceuticals, enhancing stability and efficacy while reducing reliance on synthetic antibiotics. © 2024 Society of Chemical Industry.
PubMed: 38940545
DOI: 10.1002/jsfa.13698 -
MSystems Jun 2024The Mariana Trench (MT) is the deepest part of the ocean on Earth. Previous studies have described the microbial community structures and functional potential in the...
UNLABELLED
The Mariana Trench (MT) is the deepest part of the ocean on Earth. Previous studies have described the microbial community structures and functional potential in the seawater and surface sediment of MT. Still, the metabolic features and adaptation strategies of the microorganisms involved in nitrogen cycling processes are poorly understood. In this study, comparative metagenomic approaches were used to study microbial nitrogen cycling in three MT habitats, including hadal seawater [9,600-10,500 m below sea level (mbsl)], surface sediments [0-46 cm below seafloor (cmbsf) at a water depth between 7,143 and 8,638 mbsl], and deep sediments (200-306 cmbsf at a water depth of 8,300 mbsl). We identified five new nitrite-oxidizing bacteria (NOB) lineages that had adapted to the oligotrophic MT slope sediment, their CO fixation capability through the reductive tricarboxylic acid (rTCA) or Calvin-Benson-Bassham (CBB) cycle; an anammox bacterium might perform aerobic respiration and utilize sedimentary carbohydrates for energy generation because it contains genes encoding type A cytochrome oxidase and complete glycolysis pathway. In seawater, abundant alkane-oxidizing species can fix inert N released from other denitrifying and/or anammox bacteria. This study further expands our understanding of microbial life in the largely unexplored deepest part of the ocean.
IMPORTANCE
The metabolic features and adaptation strategies of the nitrogen cycling microorganisms in the deepest part of the ocean are largely unknown. This study revealed that anammox bacteria might perform aerobic respiration in response to nutrient limitation or O fluctuations in the Mariana Trench sediments. Meanwhile, an abundant alkane-oxidizing species could fix N in hadal seawater. This study provides new insights into the roles of hadal microorganisms in global nitrogen biogeochemical cycles. It substantially expands our understanding of the microbial life in the largely unexplored deepest part of the ocean.
PubMed: 38940525
DOI: 10.1128/msystems.00243-24 -
MSystems Jun 2024We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain...
Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA.
We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs ( = 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (, , and ), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea ( Methanoperedens) in anoxic depths and uncultured bacteria (. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot. . Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the . Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured archaea in the . Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.IMPORTANCEThe cycling of carbon by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high organic carbon that can be degraded into C1 compounds such as methane, methanol, and methylamines, the fate of which depends on the microbial metabolisms present as well as the hydrological conditions and availability of oxygen. In the present study, we generated over 1,000 MAGs from subsurface sediments from a montane river floodplain and recovered genomes for microorganisms that are capable of producing and consuming methane and other C1 compounds, highlighting a robust potential for C1 cycling in subsurface sediments both with and without oxygen. Archaea from the . Methanoperedens genus were exceptionally abundant in one sample, indicating a potential C1/methane-cycling hotspot in the Slate River floodplain system.
PubMed: 38940520
DOI: 10.1128/msystems.00314-24 -
Annals of Agricultural and... Jun 2024Ultraviolet light in the UV-C band is known as germicidal radiation and was widely used for both sterilization of the equipment and creation of a sterile environment....
INTRODUCTION AND OBJECTIVE
Ultraviolet light in the UV-C band is known as germicidal radiation and was widely used for both sterilization of the equipment and creation of a sterile environment. The aim of the study is to assess the effectiveness of inactivation of microorganisms deposited on surfaces with various textures by UV-C radiation disinfection devices.
MATERIAL AND METHODS
Five microorganisms (3 bacteria, virus, and fungus) deposited on metal, plastic, and glass surfaces with smooth and rough textures were irradiated with UV-C light emitted by low-pressure mercury lamp and ultraviolet emitting diodes (LEDs), from a distance of 0.5 m, 1 m, and 1.5 m to check their survivability after 20-minute exposure.
RESULTS AND CONCLUSIONS
Both tested UV-C sources were effective in inactivation of microorganisms; however, LED emitter was more efficient in this respect than the mercury lamp. The survival rate of microorganisms depended on the UV-C dose, conditioned by the distance from UV-C source being the highest at 0.5 m and the lowest at 1.5 m. For the tested microorganisms, the highest survival rate after UV-C irradiation was usually visible on glass and plastic surfaces. This observation should be considered in all environments where the type of material (from which the elements of technical equipment are manufactured and may be contaminated by specific activities) is important for maintaining the proper level of hygiene and avoiding the unwanted and uncontrolled spread of microbiological pollution.
Topics: Ultraviolet Rays; Disinfection; Fungi; Bacteria; Viruses; Surface Properties; Microbial Viability; Plastics; Glass
PubMed: 38940114
DOI: 10.26444/aaem/189695 -
Annals of Agricultural and... Jun 2024Correlations between the number of milk somatic cells (SCC), the number of microorganisms, and the content of basic components of milk were studied on five farms (F1-F5)...
INTRODUCTION AND OBJECTIVE
Correlations between the number of milk somatic cells (SCC), the number of microorganisms, and the content of basic components of milk were studied on five farms (F1-F5) with cows of the same breed, but with different milking systems.
MATERIAL AND METHODS
From each farm, 50 Holstein Friesien milk samples were collected once a month (250 samples/month; n=3,000) during March 2022 - February 2023. Samples from farms F1 and F5 were tested for fat, protein, lactose, no fat dry matter content (FTIR spectroscopy), for the SCC (Fossomatic 7), and for the differential cells (Vetscan DC-Q).
RESULTS
The highest fat content was confirmed on farm F5 (3.85 ± 1.70%) and F4 (3.82 ± 0.21%) with automatic milking system (AMS). However, from the point of view of protein content, these farms showed slightly lower values (<0.05). F1 did not meet the minimum required amount for fat content (2.84 ± 0.81%) set by the legislation of the Slovakia. The comparison shows that there is not much difference in cell size between healthy cells and mastitis cells. The average size of healthy cells was approximately 8.77 ± 0.49 μm. In the monitored period, the average values determined were at the level of 292,000/mL (5.46 ± 0.72 log10 SCC) in cow milk samples, while for the rest of the year, the values remained at 256,000/mL (5.40 ± 0.80 log10 SCC). F1 was categorized as a positive farm with a high TLC (total milk leucocyte count) concentration (5.58 log10 cells/mL, 406.65 ± 53.80 × 10 cells/mL) and a predominant NEU fraction (61%). Farms F2, F4, and F5 were classified as negative farms (TLC was 4.70 ± 0.26 log10 cells/ml).
CONCLUSIONS
According to the results, the size of SCCs in healthy milk does not differ from SCCs found in mastitis milk. From the results, it can be concluded that the transition to the latest generation of robotic milking method can positively affect milk production and its quality.
Topics: Animals; Milk; Dairying; Female; Cell Count; Cattle; Lactose; Slovakia; Milk Proteins; Lactation
PubMed: 38940103
DOI: 10.26444/aaem/187170