Species Of Microorganisms Research Articles

Decoding the Genetic Code: Scientific Exploration of the Telomere-totelomere (T2T) Genome

Abstract: With the development of third-generation sequencing technology, genome assembly has entered a new era. The combination of multiple sequencing methods can combine the strengths of each, resulting in higher-quality assembly results. Telomere-to-Telomere (T2T) genome refers to a zero gap genome that is assembled at the T2T level of one or more chromosomes through the combination of multiple sequencing technologies, such as Pacific Biosciences High-Fidelity (PacBio HiFi), Oxford Nanopore Technologies (ONT) Ultra-long, High-throughput Chromosome Conformation Capture (Hi-C), and others. High-quality reference genomes are the basis for genomics research, and the T2T genome has enabled the exploration of unknown areas of the genome, such as telomeres and centromeres, which has provided a more in-depth direction for research. This review provides a comprehensive overview of the T2T genome, reviewing the development of sequencing technologies and then outlining sequencing strategies, assembly methods, quality assessment processes, and analysis software for the T2T genome with practical examples. Representative T2T genomic species of plants, animals, and microorganisms (e.g., human, Arabidopsis, brewer's yeast, and so on) are presented separately. A summary of the potential and challenges of current T2T genomic applications is provided, along with an outlook for future developments.

Profiling The Growth Conditions and Persistent Organic Pollutants (POPS) Tolerance of Phenoliferia glacialis USM-PSY62

Antarctica is characterized by extreme cold, isolated, and unique ecosystems. Nevertheless, Antarctica harbors diverse species of microorganisms, particularly in its ice-covered lakes and subglacial environments. These microorganisms have special adaptations to extreme cold and low-nutrient conditions. Some extremophiles, like psychrophiles can thrive in these harsh environments. Phenoliferia glacialis USM-PSY62, previously identified as Rhodotorula sp. USM-PSY62 is a psychrophilic yeast isolated from the ice brine of Antarctica. However, there is very little information on this psychrophilic yeast. This study aims to characterize the P. glacialis USM-PSY62 through the identification of the optimum growth parameters in different media (Yeast Peptone Dextrose, YPD & Yeast Malt, YM), temperature (4°C, 15°C, 20°C) and pH (6, 7, 8, 9) as well as their ability in carbon assimilation and extracellular enzyme production. It has an optimal growth in YPD compared to YM broth media. P. glacialis USM-PSY62 grows optimally at 15°C and pH 7.0. This Antarctic yeast enters the stationary phase on day six of incubation under optimum conditions. It appeared mainly as elongated-shape and oval-shaped with budding formation and was found to produce extracellular enzymes such as protease and amylase in the presence of 2% glucose concentration in YM media. P. glacialis USM-PSY62 also can assimilate various types of carbon sources including raffinose, arabinose, and maltose. Interestingly, the psychrophilic yeast presented growth in media supplemented with Persistent Organic Pollutants (POPs) such as dichlorophenyldichloroethylene (DDE) and polychlorinated biphenyl (PCB). These preliminary findings suggest that P. glacialis USM-PSY62 has tremendous potential for bioremediation application in polluted cold regions, as well as deepening our knowledge of its optimal growth conditions.

Synthesis, Antibacterial, Anti-Biofilm Properties, and Docking Study of Indeno[1,2-b]Pyridin-5-One Derivatives

In this context, we designed and synthesized a series of hydrazonal and their related indeno[1,2-b]pyridin-5-one derivatives to investigate their antibacterial and anti-biofilm properties. Several of the synthesized compounds exhibited significant efficacy against all microorganism species tested. Most of the compounds demonstrated favorable results when tested against Gram-positive bacteria. The derivatives 4a, 4f, 6c, and 6f exhibit the highest antimicrobial efficacy, as indicated by their minimum inhibitory concentration (MIC) values ranging from 4 to 512 μg/mL. We conducted additional investigations on 4a, 6c, and 6f for the purpose of examining their synergy using Checkerboard assay. Compound 6c demonstrated a synergistic impact against methicillin-sensitive Staphylococcus aureus (MSSA) and Pseudomonas aeruginosa, while exhibiting moderate synergistic activity against methicillin-resistant Staphylococcus aureus (MRSA). In addition, the simultaneous use of gentamycin with compounds 4a and 6f demonstrates a synergistic impact in fighting against methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa, respectively. Three chosen compounds were evaluated for their antibiofilm efficacy. Application of 4a, 6c, and 6f effectively reduced the production of biofilms in MRSA, MSSA, and Pseudomonas aeruginosa, resulting in a significant decrease compared to the untreated samples. In addition, ADME and pharmacokinetic analyses were conducted for the three most potent derivatives, namely 4a, 6c, and 6f. Compounds 4a and 6c were subjected to docking in the LasR Quorum-Sensing Receptor, whereas compounds 6c and 6f were docked in the sortase enzyme.

Analysis of the hard rennet cheese microbiota at different stages of the technological process

The purpose of the research was microbiological screening using MALDI-TOF technology starting from bulk raw milk to the finished dairy product and analyzing microorganisms that were being detected during the technological process of production of Ukrainskyi hard rennet cheese and which were clinically significant for human and animal health. Methods. Microbial detection was performed by accumulation and inoculation using the sector inoculation method on differential media for aerobic and anaerobic microorganisms with further MALDI-TOF identification. Sampling was carried out at 7 stages of cheese production: starting from bulk raw milk to bactofugation, after bactofugation to a mixture normalized in fat content, a pasteurized mixture, a mixture prepared for coagulation, cheese after pressing, and cheese after maturation. Microflora studies were repeated three times, with 405 samples examined. Microbiological studies of Ukrainskyi hard rennet cheese using Maldi TOF technology starting from raw materials to finished dairy products showed the presence of microorganisms at all stages of production – from bulk milk to the finished product. During the entire period of experiments, 43 species of various microorganisms have been isolated and identified. However, the number and individual types of microorganisms differed at different stages of production. Some microorganisms that have been isolated in raw milk are also found in the final product, such as Acinetobacter baumannii and Escherichia coli. In total, 18 types of microorganisms have been isolated and identified in the final product – hard rennet cheese, including Acinetobacter baumannii, Klebsiella pneumoniae, and Escherichia coli, which are of particular concern in the context of safe consumption of this cheese.

Cultural Perspectives on the Sustainable Use and Added Value of Plant-Based Food Dyes—A Case Study from Bulgaria

Raised personal health awareness and social environmental responsibility put pressure on the agri-food industry to adopt more sustainable ways of production, including the use of more natural ingredients, reducing waste, conservation and the regeneration of resources and energy. Plant-based colorants are ecologically friendly alternatives to artificial food dyes, especially with regards to the current reports on the adverse effects of some of the latter on human health. Various plants are traditionally used by many cultures to obtain vivid food coloration; however, the knowledge and means to produce them becomes less and less accessible to urbanized societies, and affordable organic alternatives are not always available on the market. An online questionnaire was performed to explore the awareness on plant-based dyes and pro-environmental attitudes of Bulgarian customers through the lens of Orthodox Easter eggs dyeing and the obtaining of plant dyes. From a total of 294 adult participants, only 5% reported a strict preference for natural dyes, while more than half of them (54%) were found to use natural and artificial ones concomitantly or switching between both. Of 45 plant taxa used for egg coloration, 12 were most frequently cited with many new additions of imported plants. Most of the used plant-based dyes were common fruits, spices, herbal infusions and even food waste like onion peels and avocado pits that were readily available from home gardens, markets and food shops. Additionally, we made a review of the scientific literature regarding their antioxidant and antimicrobial activity against food spoilage bacteria and foodborne pathogens isolated from eggs. All frequently used taxa were reported to exhibit antibacterial activities against Gram-positive and Gram-negative bacteria and possess antioxidant activity due to the presence of various polyphenols, essential oils and other compounds. Grape and red wine, roselle and stinging nettle are the species with the most diverse antibacterial activity, effective against 15 out of the 16 bacterial species of spoilage and foodbourn microorganisms included in our focus. The antimicrobial activities, however, were found mostly tested against bacterial strains in vitro, and further studies are needed to confirm their potential antibacterial activity when applied to Easter/boiled eggs or other food products. Our findings suggest that traditional cultural practices, as a multifaceted and engaging phenomenon, have the potential to promote environmental responsibility and a healthy lifestyle using both contemporary and traditional knowledge.

The relationship between metabolic syndrome and intestinal microbiota: a review of the literature

Metabolic syndrome is a pathological condition that includes obesity, elevated blood glucose levels, hypertension and dyslipidemia. This comorbid condition is a global problem of our time. According to the INTERHEART study, metabolic syndrome occurs in more than 26% of the world’s population. In the Russian Federation, 40% of residents have 2 components of the metabolic syndrome, 11% have 3 or more of its components. In addition to well-known risk factors for the development of metabolic syndrome, such as genetic predisposition, overeating, physical inactivity, hormonal disorders and others, in recent years, increasing attention has been paid to the study of the intestinal microbiota and its effect on the metabolic syndrome. For example, a comparison of the intestinal microbiota of people with normal BMI and obesity showed different species of microorganisms inhabiting our gastrointestinal tract. Analyzing patients diagnosed with type 2 diabetes mellitus we can note a decrease in butyrate-producing bacteria (Faecalibacterium prausnitzii and Roseburia) that modify insulin sensitivity to body tissues. Some species of Lactobacillus are able to normalize lipid metabolism, reduce the number of adipocytes, reduce the absorption of cholesterol by converting it into insoluble coprostanol. In patients with arterial hypertension there is dysbacteriosis of I and II degree, in arterial hypertension with metabolic syndrome – absence of dysbacteriosis of I degree and presence of dysbacteriosis of II and III degrees, with prevalence of opportunistic forms. Understanding the role of intestinal microbiota becomes a key element not only in diagnosis, but also in the development of effective treatment methods and their application in complex treatment of metabolic syndrome.

Fabrication and evaluation of a biodegradable electrospun chip loaded with chlorhexidine for periodontal disease

Electrospinning technique is used for the manufacturing matrices of drug delivery systems. This study aimed at fabricating and evaluating an electrospun chip for prolonged retention and controlled drug release at the lesion site. A biodegradable electrospun chip loaded with chlorhexidine (BESC-CHX) was manufactured to treat periodontal diseases. Then, physicochemical properties and efficacy of BESC-CHXs were investigated. The CHX content of BESC was analyzed using high-performance liquid chromatography. The antimicrobial activity and anti-inflammation effects of BESC-CHX were assessed using a disc diffusion assay and a periodontal disease model. BESC-CHX, which is composed of 700 nm fibers, was observed by scanning electron microscopy. Many BESC-CHX batches maintained consistent CHX levels, with a drug entrapment efficiency of 83.3 %. The chip released CHX for seven days and was completely degraded in artificial saliva. BESC-CHX exhibited 99.99 % antimicrobial activity against 11 species of microorganisms. In a beagle periodontal disease model, BESC-CHX demonstrated improvements in periodontal probing depth and clinical attachment level, but these changes were not statistically significant. However, alveolar bone regeneration was observed in cementoenamel junction-alveolar bone crest measurements. The lowest inflammation scores were observed in this group. These findings suggest that BESC-CHXs may be beneficial for the treatment of periodontal disease.

Cytotoxicity and Microbiological Properties of Ceramic CAD/CAM Materials Subjected to Surface Treatment with Nanometric Copper Layer

The aim of this study is to present the characteristics and a comparison of four different commercial materials dedicated to the CAD/CAM technique in dentistry, all of which can be classified as ceramic materials. Its purpose is also to evaluate the impact of surface treatment on the cytotoxicity and microbiological properties of the materials. The CAD/CAM technique has a perpetually growing role in modern reconstructive dentistry. It requires a material’s possession of peculiar characteristics, such as mechanical resistance, durability, functionality (similar to natural tissues), good aesthetics and biocompatibility. To critically evaluate a biomaterial, both manufacturer claims and in vitro tests should be considered. Further steps of evaluation may include animal tests and clinical trials. There are certain attributes of biomaterials that may be modified by surface treatment that can be crucial to the clinical success of the material. The evaluated materials were Vita Suprinity (VITA-Zahnfabrik, Germany), Vita Mark II (VITA-Zahnfabrik, Germany), Celtra Duo (Dentsply Sirona, USA) and Empress Cad (Ivoclar Vivadent, Liechtenstein). They are available in the form of prefabricated blocks of various diameters and are popular among operators performing clinical procedures using CAD/CAM. Standardized blocks of each material were prepared. Half of them had their surface polished. Further, half of all the samples were covered by a nano-copper layer. The samples were evaluated for cytotoxicity, presented on a 0–4 scale, adhesion susceptibility and potential of forming a biofilm on their surface. Physicochemical properties such as the water contact angle (WCA) were evaluated for the tested materials. The influence of copper coating on cytotoxicity cannot be unequivocally stated or denied. Surface polishing did not affect the materials’ cytotoxicity, but it increased the WCA of all materials and, therefore, their hydrophobicity. Different degrees of adhesion ability and biofilm formation were dependent on the species of microorganisms and properties of the dental materials.

Oral microbiome in the development of oral cancer

Oral cancer is an aggressive and rapidly progressive disease. The oral cavity is home to over 700 species of microorganisms which regulate metabolism, immune function and health. There are 3 types of mechanisms by which bacteria may participate in carcinogenesis. First, bacteria cause chronic inflammation, which stimulates the production of cytokines, including interleukins, interferons, and tumor necrosis factor. Second, bacteria can interact directly with host cells by secreting toxins or by binding to membrane receptors. Finally, the production of metabolites by bacteria may also contribute to carcinogenesis. The importance of bacteria level and composition in the transition of oral precancerous lesions to cancer has been demonstrated. The relationship of changes in microbiome composition with smoking, inflammation in healthy individuals, as well as with the development of oral cancer in patients has been studied.

RGeasy: a reference gene analysis tool for gene expression studies via RT-qPCR

Gene expression through RT-qPCR can be performed by the relative quantification method, which requires the expression normalization through reference genes. Therefore, it is essential to validate, experimentally, the candidate reference genes. Thus, although there are several studies that are performed to identify the most stable reference genes, most them validate genes for very specific conditions, not exploring the whole potential of the research since not all possible combinations of treatments and/or conditions of the study are explored. For this reason, new experiments must be conducted by researchers that have interest in analyzing gene expression of treatments and/or conditions present, but not explored, in these studies. Here, we present the RGeasy tool, which aims to facilitate the selection of reference genes, allowing the user to choose genes for a greater number of combinations of treatments/conditions, compared to the ones present in the original articles, through just a few clicks. RGeasy was validated with RT-qPCR data from gene expression studies performed in two coffee species, Coffea arabica and Coffea canephora, and it can be used for any animal, plant or microorganism species. In addition to displaying a rank of the most stable reference genes for each condition or treatment, the user also has access to the primer pairs for the selected reference genes.

Stand age-related effects of mangrove on archaeal methanogenesis in sediments: Community assembly and co-occurrence patterns

Mangrove sediment is a key source of methane emissions; however, archaea community structure dynamics and methanogenesis activities during long-term mangrove restoration remain unclear. In this study, microcosm incubations revealed a substantial reduction in microbial-mediated methane production potential from mangrove sediments with increasing stand age; methane production rates decreased from 0.42 ng g−1 d−1 in 6-year-old stands to 0.23 ng g−1 d−1 in 64-year-old stands. High-throughput sequencing revealed a reduction in community diversity because of specific microorganism colonization and species loss, notably a decline in the relative abundance of Bathyarchaeia in sediments of 64-year-old stands. In addition, mangrove sediments, especially those in older stands (20- and 64-year-old), had more complex and stable co-occurrence microbial networks than mudflats. Furthermore, archaea community assembly in older stands was dominated by stochastic processes wherein dispersal limitation was prominent, and that in younger stands (6- and 12-year-old) was driven by deterministic processes. The proportion of dispersal limitation of Bathyarchaeia and traditional methanogens in sediment decreased with an increase in stand age. Quantitative polymerase chain reaction analysis confirmed a decrease in Bathyarchaeia (from 3.50 to 0.54 copies g−1) and mcrA gene (from 3.83 to 0.25 copies g−1) abundance in mangrove sediments with an increase in stand age. These findings demonstrate the critical role of Bathyarchaeia in methanogenesis; the decline in microbial interactions and abundance, and the reduced proportion of dispersal limitation of Bathyarchaeia and traditional methanogens collectively contributed to the mitigation of microbial-mediated methane production potential in older mangrove stands.

Review of Antimicrobial Properties of Titanium Dioxide Nanoparticles

There is a growing interest in the utilization of metal oxide nanoparticles as antimicrobial agents. This review will focus on titanium dioxide nanoparticles (TiO2 NPs), which have been demonstrated to exhibit high antimicrobial activity against bacteria and fungi, chemical stability, low toxicity to eukaryotic cells, and therefore high biocompatibility. Despite the extensive research conducted in this field, there is currently no consensus on how to enhance the antimicrobial efficacy of TiO2 NPs. The aim of this review is to evaluate the influence of various factors, including particle size, shape, composition, and synthesis parameters, as well as microbial type, on the antibacterial activity of TiO2 NPs against bacteria and fungi. Furthermore, the review offers a comprehensive overview of the methodologies employed in the synthesis and characterization of TiO2 NPs. The antimicrobial activity of TiO2 exhibits a weak dependence on the microorganism species. A tendency towards increased antibacterial activity is observed with decreasing TiO2 NP size. The dependence on the shape and composition is more pronounced. The most pronounced antimicrobial potential is exhibited by amorphous NPs and NPs doped with inorganic compounds. This review may be of interest to specialists in biology, medicine, chemistry, and other related fields.

Influence of a synthetic analogue of the active center of GM-CSF – peptide ZP2 on the growth and biofilm formation of gram-negative bacteria – causes of surgical infections

The aim is to analyze the nature of the effect of the synthetic analogue of the active center of GM- CSF – peptide ZP2 on the growth and biofilm formation (BPO) of gram–negative bacteria – pathogens of surgical infections. The study used 18 clinical isolates of gram-negative bacteria of different species (Klebsiella pneumoniae, Citrobacter freundii, Stenotrophamonas maltophilia) isolated from purulent wounds in patients with surgical pathology and showing pronounced resistance to many antibiotics used in clinical practice. The isolation of pure cultures of microorganisms was carried out by conventional methods; species were assessed by direct protein profiling using a MALDI TOF mass spectrometer. To study the effect of ZP2 peptide on bacterial growth and BPO, isolates were co-cultured with a solution of ZP2 peptide in meat-peptone broth (MPB) at a concentration of 5 micrograms/ml at 37°C for 24-48 hours. The effect of the ZP2 peptide was studied both on emerging biofilms and on those formed, according to the degree of binding of crystalline violet in sterile 96-well polystyrene plates. Next, Growth inhibition indices and coefficients of BPO of microorganisms were determined. It was found that the synthetic analogue of the active center of granulocyte-macrophage colony stimulating factor (GM-CSF) – peptide ZP2 inhibited the growth of the studied bacterial strains, reducing the biomass of experimental cultures during the development of bacterial populations. At the same time, the species-specific effect of the ZP2 peptide on the ability of surgical strains of the studied bacteria to form biofilms has been shown. It was experimentally established that all the studied surgical strains of microorganisms were capable of biofilm formation, and the maximum severity of the trait was characteristic of S. maltophilia isolates. The synthetic analogue of the active center of granulocyte-macrophage colony stimulating factor (GM-CSF) – peptide ZP2 caused a decrease in the ability to form biofilms in isolates S. maltophilia and destroyed already formed biofilms in all studied species of microorganisms. The experimental data obtained expand the range of potential clinical applications of the synthetic analogue of the active center of granulocyte-macrophage colony stimulating factor (GM-CSF) – peptide ZP2, and its use in new medicines can be effective in combating antibiotic-resistant pathogens of surgical infections.

Research on the Biogas Production Mechanism of Mudstone in the Qaidam Basin under Different CO2 Pressures.

Mudstone, a class of sedimentary rocks rich in organic matter, possesses considerable potential for biogas production. Mudstones possess a rich biological origin, which is conducive to refining the mechanisms and enrichment patterns of biogenic gas reservoirs. This has significant theoretical and practical implications for guiding the exploration and development of Quaternary mudstone gas reservoirs. Furthermore, the Qaidam Basin is an excellent place for the geological storage of CO2 due to its rich petroleum reservoir conditions. Experimental research on biogas production under diverse CO2 pressure-mudstone-microorganism-water interactions is conducted to determine the biogas production mechanism of mudstone under different CO2 pressures during sequestration circumstances. According to the results: (1) under supercritical carbon dioxide conditions, there is a slight initial increase in biogas production, followed by a gradual decrease. The periods and peaks of gas production vary among the different reaction groups. As carbon dioxide pressure increases, the gas production cycle lengthens significantly, while the gas yield declines. (2) Siderite and secondary carbonate minerals have increased in the mudstone's mineral fraction both before and after biogas production, while clay mineral groups have decreased. Specifically, there was a notable drop in chlorite and kaolinite. (3) Microorganism species in the system were analyzed, and the results showed that there was a gap in each microorganism's ability to adapt to its surroundings, and the diversity and quantity of bacteria declined with increasing pressure. After carbon dioxide was fluxed, there was a considerable shift in the pattern of biogas generation, which consequently had a major impact on the alterations in mineral fractions.

KEANEKARAGAMAN JENIS-JENIS LABA-LABA (Arachnida) DI HUTAN PETUANAN DESA RUMAH TIGA KOTA AMBON DAN IMPLEMENTASINYA SEBAGAI BAHAN AJAR MATA KULIAH ZOOLOGI INVERTEBRATA

Background: The diversity of spider species is greatly influenced by the stability of the community of a spider species in a forest ecosystem and the presence of plant vegetation as spider habitat. Forest damage will have an impact on spider diversity which affects the cycle of nutrients and materials in the ecosystem. Biodiversity is a term that includes genes, plant, animal and microorganism species as well as ecosystems and ecological processes Methods: This research is a quantitative descriptive research, namely to calculate the diversity of spider types (Arachnida) in the petuanan forest of Rumah Tiga Village, Ambon Island. Results: There were 6 species of spiders (Arachnida) found in the forests of Taeno, Air Ali and Kranjang hamlets, including P. phalangioides, T. extensa, Araneus diadematus, Menemerus bivittatus, N. pilipes, and C. mildei. Conclusion: The level of diversity (Arachnida) at the research location located in the Taeno hamlet forest is H' 0.68, Air Ali is H' 0.64 and Kranjang is H' 0.60. Judging from the Shannon-Wiener criteria, if the diversity result = <1, diversity is classified as low.

Assessment of the Environmental Safety of the Ship Ballast Water Treated by Ozone

The aspects of purification of discharged ballast water from non-indigenous species of microorganisms in ballast water by the ballast water management systems (BWMS) installed on ships are considered. As a method of water treatment, the technology chosen is to influence the microorganisms with gaseous ozone introduced into the flow of ballast water when it is received onto the ship. A design diagram for a prototype BWMS unit for treating the ballast water during intake and deballasting has been developed. The results of studies of the prototype on the inactivation of microorganisms in water of various salinities (0, 18 and 36‰) are presented and its effectiveness is shown. Biotesting methods were used to assess the toxicity of ozone-treated waters. Using organisms of three trophic levels, it was shown that water neutralized using this technology is not toxic and can be discharged into a receiving reservoir.

Unveiling the relationship of volatile compounds and microbial communities in light-struck taste rice wine: A comprehensive analysis

Light-struck taste rice wine (LST-RW) is the most popular new rice wine at present, which is brewed by a variety of microorganisms. However, the relationship between microorganisms and flavor substances in light-struck taste rice wine is still unexplored. In this study, high-throughput sequencing, high-performance liquid chromatography (HPLC), headspace solid-phase microextraction (HS-SPME), and gas chromatography–mass spectrometry (GC–MS) were used to prove that microbial community had significant influence on flavor substances during light-struck taste rice wine fermentation. The results indicated a consistent increase in the majority of amino acids and organic acids within LST-RW with extended fermentation duration. A total of 49 volatile flavor compounds, including alcohols, esters, and aldehydes, were identified. In the brewing process of LST-RW, Bacillus (17.13 %) and Saccharopolyspora (15.55 %) emerge as the predominant bacterial genera; Aspergillus (83.34 %) and Saccharomyces (15.21 %) emerged as the dominant fungal genera. A notable correlation was observed between fermentation microorganisms and flavor substances. Microorganism species exhibiting strong co-exclusion or symbiotic relationships were also identified. The research findings offer a theoretical reference for optimizing and innovating the fermentation process of LST-RW.

Enhancing the Shelf Life of Sous-Vide Red Deer Meat with Piper nigrum Essential Oil: A Study on Antimicrobial Efficacy against Listeria monocytogenes.

Using sous-vide technology in combination with essential oils offers the potential to extend the preservation of food items while preserving their original quality. This method aligns with the growing consumer demand for safer and healthier food production practices. This study aimed to assess the suitability of minimal processing of game meat and the effectiveness of vacuum packaging in combination with Piper nigrum essential oil (PNEO) treatment to preserve red deer meat samples inoculated with Listeria monocytogenes. Microbial analyses, including total viable count (TVC) for 48 h at 30 °C, coliform bacteria (CB) for 24 h at 37 °C, and L. monocytogenes count for 24 h at 37 °C, were conducted. The cooking temperature of the sous-vide was from 50 to 65 °C and the cooking time from 5 to 20 min. Additionally, the study monitored the representation of microorganism species identified through mass spectrometry. The microbiological quality of red deer meat processed using the sous-vide method was monitored over 14 days of storage at 4 °C. The results indicated that the TVC, CB, and L. monocytogenes counts decreased with the temperature and processing time of the sous-vide method. The lowest counts of individual microorganism groups were observed in samples treated with 1% PNEO. The analysis revealed that PNEO, in combination with the sous-vide method, effectively reduced L. monocytogenes counts and extended the shelf life of red deer meat. Kocuria salsicia, Pseudomonas taetrolens, and Pseudomonas fragi were the most frequently isolated microorganism species during the 14-day period of red deer meat storage prepared using the sous-vide method.

Efficiency of Microorganisms and Effectiveness of Biodegradation Techniques on LDPE Plastics: A Systematic Review

Introduction The aim of the research was to demonstrate the efficiency of microorganisms and the effectiveness of biodegradation techniques on Low-density polyethylene (LDPE) plastics. The research question was: What is the efficiency of LDPE-degrading microorganisms and the effectiveness of biodegradation techniques? Methods The systematic review was based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Articles were obtained from Scopus, Web of Science (WOS), Embase, and Google Scholar. The DeCS/Mesh search terms were: Low-density polyethylene, efficiency, biodegradation, microbial consortia, fungi, bacteria. Inclusion criteria were: scientific articles that included bacteria, fungi, and microbial consortia reported as LDPE degraders that report the percentage of weight loss; articles published from January 2010 to October 2022, and publications in Spanish and English with open access. Exclusion criteria were: studies that do not report gravimetry, the biodegradation time of LDPE, and the genus or species of the polyethylene-degrading microorganism. Results Out of 483 studies found, 50 were included in this Systematic Review (SR). The most frequent study techniques were scanning electron microscopy (SEM), gravimetry, and fourier transform infrared spectroscopy (FTIR), and in the case of microorganisms, the most studied belonged to the genus Pseudomonas, Bacillus, and Aspergillus. Regarding the isolation place, the most frequent mentioned in the reviewed articles were landfill soil and sanitary landfill soil. The efficiency of LDPE-degrading microorganisms was higher in bacteria such as Enterobacter spp., Pantoea spp., Pseudomonas spp., Escherichia coli, and Bacillus spp., which obtained a range of DE of 9.00-70.00%, 24.00-64%, 1.15 – 61.00%, 45.00%, and 1.5-40% with DT of 4-150, 120, 4-150, 30, and 30-120 days, respectively; in the case of fungi, the main microorganisms are Neopestalotiopsis phangngaensis, Colletotrichum fructicola, and Thyrostroma jaczewskii with efficiencies of 54.34, 48.78, and 46.34%, in 90 days, respectively; and the most efficient microbial consortia were from Enterobacter spp. and Pantoea sp. with 38.00 – 81.00%, in 120 days; and, Pseudomonas protegens, Stenotrophomonas sp., B. vallismortis and Paenibacillus sp. with 55. 00 – 75.00% in 120 days. Conclusions The most efficient microorganisms in LDPE degradation are Enterobacter spp., Pantoea spp., Pseudomonas spp., Escherichia coli, and Bacillus spp.; in fungi Neopestalotiopsis phangngaensis, Colletotrichum fructicola, and Thyrostroma jaczewskii; and in microbial consortia, those formed by Enterobacter spp. and Pantoea sp., and that of P. protegens, Stenotrophomonas sp., B. vallismortis and Paenibacillus sp.; and the most effective techniques used in LDPE biodegradation are SEM, gravimetry, and FTIR.

Microbiology testing capacity and antimicrobial drug resistance in surgical-site infections: a post-hoc, prospective, secondary analysis of the FALCON randomised trial in seven low-income and middle-income countries

Surgical-site infection (SSI) is one of the most common health-care-associated infections, substantially contributing to antibiotic use. Targeted antibiotic prophylaxis to prevent SSIs and effective treatment are crucial to controlling antimicrobial resistance (AMR). This study aimed to describe the testing capacity and multidrug resistance (MDR) of SSI microorganisms in low-income and middle-income countries (LMICs). This analysis included patients undergoing abdominal surgery in seven LMICs (Benin, Ghana, India, Mexico, Nigeria, Rwanda, and South Africa) as part of the FALCON randomised controlled trial. Wound swabs were collected from patients diagnosed with SSI, as per US Centers for Disease Control and Prevention (CDC) definition. Data on microorganism species and MDR, as per CDC and European Centre for Disease Prevention and Control definitions, were analysed alongside hospital-level data on local microbiological practices. An adjusted analysis was performed to identify perioperative factors associated with MDR. Testing capacity was assessed by the completion of swab testing in positively diagnosed SSIs. Between Dec 10, 2018, and Sept 7, 2020, 5788 patients were recruited to the FALCON trial. 1163 patients were diagnosed with an SSI, of whom 905 (77·8%) received prophylactic antibiotics before surgery. In patients with SSIs, 935 of 1163 (80·4%) did not have a wound swab; 195 were from hospitals not performing swabs (15 hospitals) and 740 were from hospitals with capacity but no swab performed (35 hospitals). Of 228 patients swabbed, 200 (88·5%) had microorganisms detected. Escherichia coli (89 of 200, 37·9%) was the most common microorganism and 116 of 200 (58·0%) patients were not covered by the perioperative prophylactic antibiotic. MDR was found in 102 of 147 (69·4%) patients for whom data were available to determine MDR status. Adjusted analysis found that appropriate prophylactic antibiotic coverage (adjusted odds ratio 0·43, 95% CI 0·19-0·96) and regular availability of infection control teams (0·32, 0·11-0·93) were associated with a significant reduction in MDR. Targeted perioperative antibiotic prophylaxis during contaminated abdominal surgery is insufficient in LMICs, with very few SSI organisms undergoing formal diagnosis. Expansion of testing capacity, development of local guidelines, and implementation of infection control teams could support the prevention of SSI through directed antibiotic prophylaxis, subsequently reducing the burden of MDR. National Institute for Health and Care Research. For the French and Spanish translations of the abstract see Supplementary Materials section.