Bacterial DNA Research Articles

Deletion of mitochondrial DNA methyltransferase 1 contributes the development of murine heart failure under pressure overloaded

Abstract Background Mitochondrial DNA (mitDNA) has similarities to bacterial DNA, which contains inflammatogenic unmethylated CpG motifs. We found that mitDNA that escapes from autophagy causes inflammatory response and heart failure under pressure overload. DNA methyltransferase 1 (DNMT1) maintains methylation patterns in somatic cells. Deletion of DNMT1 results in embryonic lethality in mice and mitotic catastrophe in cultured cells. Additional possible translational start sites (ATG1, ATG2) are located upstream of the commonly accepted nuclear DNMT1 translational start site (ATG3) and there is a conserved mitochondrial translocation signal sequence between ATG1 and ATG3. The role of mitochondrial DNMT1 in the development of heart failure remains to be elucidated. Purpose The purpose of this study is to examine the in vivo role of mitochondrial DNMT1 in the heart under pressure overload. Methods We generated HA-tagged DNMT1 constructs, 1) starting from ATG1 (termed as whole) 2) from ATG3 (nuclear) and 3) from ATG3 and mutated in the nuclear translocation sequence (mitochondrial) and transfected HEK293 cells with the constructs. Localization of HA-tagged proteins was assessed by immunocytochemistry. We also generated mitochondrial DNMT1-deficient mice by inserting mutations into the ATG1 and ATG2. The mice were subjected to pressure overload by means of transverse aortic constriction (TAC) to induce heart failure. Cardiac remodelling was assessed by echocardiography as well as histological analyses 4 weeks after operation. Results Whole, nuclear and mitochondrial DMNT1 translocated to both mitochondria and nuclei, only nucleus and only mitochondria, respectively. Mitochondrial DNMT1-deficient mice were born at Mendelian frequency and grew to adulthood. Those showed no cardiac phenotypes under baseline conditions. However, the mice exhibited severe systolic dysfunction, indicated by left ventricular fractional shortening, 2 weeks after surgery compared with control littermates (control littermates 47.9% versus Mitochondrial DNMT1-deficient mice 32.3%, p<0.05). Intermuscular cell infiltration was observed in TAC-operated mitochondrial DNMT1-deficient hearts. Conclusions Mitochondrial DNA methyltransferase 1 plays a protective role in failing hearts and mitDNA methylation might be a therapeutic target to treat patients with heart failure.

Characteristics of the Gut Microbiota Composition of the Arctic Zone Residents in the Far Eastern Region

Background. In many studies over the past decade, scientists have made a connection between the composition of gut microbiota and human health. A number of publications have shown that gut bacteria are involved in many metabolic and physiological processes of the organism. The composition of the gut microbiome is unique for each person and is formed under the influence of various factors associated with both the individual characteristics of the body and the characteristics of the environment. Different regional characteristics make it necessary for the body to adapt to certain conditions, including temperature fluctuations. Living in areas with low temperatures, such as the Arctic zone, dictates the need for increased energy consumption, which affects the composition of the gut microbiome. Methods. In our study, an extensive questionnaire was conducted among the participants, where many questions were included about the dietary preferences of the study participants, which allowed them us to further divide them into groups according to their diets. Stool samples were collected from participants from 3 groups: Arctic native, Arctic newcomer and the control group. The next step was the isolation of bacterial DNA and sequencing the 16S rRNA gene. The analysis of the results of the diversity of the intestinal microbiota was carried out both with and without taking into account the dietary preferences of the participants. Results. As a result of comparing the intestinal microbiota obtained from residents of the Arctic zone with the gut microbiota of residents of other regions with a milder climate, significant differences are found. These differences may be related to limited food resources and a reduction in the variety of food products characteristic of this Arctic region. t was also found that representatives of the bacterial families Christensenellaceae and Muribaculaceae dominated the control group, both with traditional nutrition and with a dairy-free diet in comparison with the Arctic groups. The control group was dominated by representatives of the Prevotellaceae, Enterobacteriaceae and Comamonadaceae families compared to the Arctic group (with a traditional diet). The results also show that the number of representatives of the families Desulfovibrionaceae (with traditional diet) and Enterobacteriaceae (with milk-free diet) is growing in the Arctic group. Conclusions. In the course of this work, bacterial families characteristic of people living in the Arc-tic zone of the Far Eastern region of the Russian Federation were identified. Poor diet, difficult climatic conditions, and problems with logistics and medical care can have a strong impact on the health of this population. The main type of diet for the inhabitants of the Arctic is the traditional type of diet. They consume a large number of low-cost products, obtainget animal protein from poultry and canned food, and also eat a small number of fresh vegetables and fruits. Such a diet is due to the social status of the study participants and the climatic and geographical features of the region (difficulties in agriculture). With such a diet, we observe a decrease in representatives of the Christensenellaceae, Muribaculaceae, Eubacteriaceae, and Prevotellaceae families and an increase in representatives of the Enterobacteriaceae and Desulfovibrionaceae families among Arctic residents. This imbalance in the futuremay cause, this population may to develop various diseases in the future, including chronic diseases such as obesity, intestinal dysbiosis, inflammatory bowel diseases, and type 2 diabetes.

Isolation and degradation characterization of a 1, 4-dioxane-degrading bacterial strain

To address the potential pollution caused by the carcinogen 1, 4-dioxane in aquatic environments, we isolated a highly efficient 1, 4-dioxane-degrading bacterial strain, designated as DXTK-010, from the groundwater contaminated by 1, 4-dioxane. According to the morphological characteristics, the phylogenetic tree established based on the 16S rRNA gene sequence, and the whole genome sequence, we identified DXTK-010 as Aminobacter aminovorans. This strain demonstrated robust degradation capacity within a temperature range of 20 ℃ to 37 ℃ and a pH range of 5.0 to 8.0. Furthermore, single-factor experiments indicated the optimal degradation conditions at 30 ℃ and pH 7.5. Under the optimal conditions, the strain completely degraded 200 mg/L of 1, 4-dioxane within 24 h, achieving a maximum degradation rate of 9.367 mg/(L·h). The Monod equation was adopted to fit the degradation kinetics of 1, 4-dioxane at different initial concentrations, which revealed a maximum specific degradation rate of 0.224 mg 1, 4-dioxane/(mg protein·h), a half-saturation constant (Ks) of 41.350 mg/L, and a cell yield of 0.130 mg protein/(mg 1, 4-dioxane). Whole genome sequencing revealed a circular chromosome and three plasmids within DXTK-010. Functional gene annotation and analysis underscored the significance of the propane monooxygenase gene cluster and alcohol dehydrogenase gene in facilitating the efficient degradation of 1, 4-dioxane by this strain. DXTK-010 outperformed the existing degraders for 1, 4-dioxane, expanding the strain resources for the bioremediation of 1, 4-dioxane pollution. This study provides a theoretical basis for the practical application of DXTK-010 in the remediation of 1, 4-dioxane pollution.

Illumina Sequencing in Conjunction with Propidium Monoazide to Identify Live Bacteria After Antiseptic Treatment in a Complex Oral Biofilm: A Study Using an Ex Vivo Supragingival Biofilm Model

Background/Objectives: The evaluation of the efficacy of antibacterial treatments in complex oral ecosystems is limited by the inability to differentiate live from dead bacteria using omic techniques. The objective of this study was therefore to assess the ability of the combination of the 16S rRNA Illumina sequencing methodology and the action of propidium monoazide (PMA) to study viable bacterial profiles in oral biofilms after exposure to an antiseptic compound. Methods: Cariogenic supragingival biofilms were developed in an ex vivo model for 96 h, using saliva from healthy volunteers. The biofilms were treated with 0.12% chlorhexidine (CHX) combined with 0.05% cetylpyridinium chloride (CPC), for 60 s, using phosphate buffered saline as a control. After exposure, each biofilm was treated or not with PMA to then extract the bacterial DNA, quantify it by Qubit, quantify the bacterial population using qPCR, and perform the metataxonomic study of the samples using Illumina 16S rRNA sequencing. Results: A significantly lower DNA concentration in the PMA-treated biofilms (p < 0.05 compared with those not exposed to PMA) was observed. The viable bacterial count obtained by qPCR differed significantly from the total bacterial count in the biofilm samples exposed to the antiseptic (p < 0.05). The viable microbiome differed significantly from the total bacterial profile of the samples treated with CHX/CPC after exposure to PMA (p < 0.05 at the α- and β-diversity levels). Conclusions: The combination of Illumina 16S rRNA sequencing and PMA helps solve the inability to evaluate the efficacy of antibacterial treatments in the bacterial profile of complex ecosystems such as oral biofilms.

Complete genome sequence of the Sphingobacterium bambusae type strain KACC 22910T.

We report the whole genome sequence of Sphingobacterium bambusae KACC 22910T. The complete genome consists of a 5.6 Mb circular chromosome with a G + C content of 44.4 % and 4,526 predicted coding genes.

Pseudomonas koreensis AB36 from a gold mine: genomic insights into adaptation to extreme conditions and potential plant growth promotion

AbstractThe genus Pseudomonas is one of the most varied and widespread bacterial genera, with species found in most environment. They are known to degrade organic and inorganic compounds, produce secondary metabolites, and enhance plant growth. The genome of Pseudomonas koreensis AB36, a heavy metal resistant organism isolated from a gold mine was sequenced to unveil the versatile metabolic potential of the organism. The genome is a single circular chromosome of 5,902,614 bp, with G + C content of 60.1%. There are 4154 similar orthologous gene clusters shared among strain AB36 and other sequenced P. koreensis strains with 7 clusters found alone in the genome of strain AB36. Genome mining of the organism predicted 8 biosynthetic gene clusters using antiSMASH including three non-ribosomal peptide synthethase (NRPS) clusters, arylpolyene and bacteriocin. The genome contains putative genes for heavy metal transport/resistance. These results show the heavy metal resistance ability and degradation of xenobiotic compounds of strain AB36 as well as its potential to adapt to various environments.

Association of WNT Gene Polymorphism with Frequency of Cytogenetic Disorders under the Action of Ionizing Radiation

The paper presents the results of a study of the association of single nucleotide polymorphisms of the WNT genes with an increased frequency of cytogenetic disorders in the blood lymphocytes of workers at an ionizing radiation facility exposed to long-term radiation exposure at doses of 100–500 mGy.The object of the study was the blood of 95 apparently healthy workers who were subjected to long-term technogenic external exposure to γ-radiation in doses from 100 to 500 mGy in the course of their professional activities. For all examined individuals, a standard cytogenetic analysis of blood lymphocytes was performed. Genomic DNA was isolated from workers’ blood lymphocytes using a “QIAamp DNA Blood mini Kit” (Qiagen, Germany). DNA was genotyped for 116 single nucleotide polymorphisms of the WNT genes using high-density “CytoScan™ HD Array” (Affymetrix, USA) chips (DNA chips). Taking into account the Bonferroni correction, an association of single nucleotide polymorphisms of the WNT genes with a high frequency of circular chromosomes in blood lymphocytes was established, all other types of cytogenetic disorders did not show statistical significance. As a result of the study, a single nucleotide polymorphism of the WNT9B gene rs1530364 was identified, which can be considered as a potential marker of individual radiosensitivity.

Enhancing antibacterial efficacy through macrocyclic host complexation of fluoroquinolone antibiotics for overcoming resistance

The use of supramolecular assemblies in pharmaceuticals has garnered significant interest. Recent studies have shown that the activities of antibacterial agents can be enhanced through complexation with cyclic oligomers and metal ions. Notably, these complexes sometimes possess greater therapeutic properties than the parent drugs. To develop microbiologically potent supramolecular drugs, the complexation of macrocyclic hosts with fluoroquinolone (FQ) antibiotics was investigated. FQs are a successful family of antibiotics that target the bacterial enzymes DNA gyrase and DNA topoisomerase IV, leading to bacterial cell death through the inhibition of DNA synthesis. However, antibiotic resistance resulting from the repeated use of FQs over time has limited their effectiveness against resistant pathogens. To overcome this issue, the encapsulation of FQs in polyphenolic macrocycles was investigated. This study highlights resorcinarene, a polyphenolic host with antibacterial properties, and its ability to chemically interact with FQs. The inclusion complexation process was analyzed using NMR and FTIR techniques. The binding constants determined by 1H-NMR titration revealed that levofloxacin forms more stable complexes with resorcinarene than with β-cyclodextrin, which aligned with MD simulations. Assessment of the geometric characteristics of the inclusion complexes using 2D NMR analysis confirmed that different moieties of various FQs can fit into a single host cavity and improve activity against gram-negative bacteria. Overall, these findings suggest that encapsulation in polyphenolic macrocycles is a promising strategy for utilizing FQs against antibiotic-resistant bacteria.

Identification of pathogenic bacteria from eggshell of leatherback sea turtle (Dermochelys coriacea) in Lampuuk Beach, Aceh Besar using 16S rRNA gene

Currently, the leatherback turtle population in Indonesia tends to decline. One of the factors that cause turtles' existence is the turtle eggs that fail to hatch because bacteria contaminate them, 80% of the reasons turtle eggs fail to hatch are due to infection by microorganisms found on the eggshell. Turtle eggs have a soft structure and there are pores that function for gas exchange and water absorption. Microorganisms in sand can infect turtle eggs through the pores and cause hatching failure. This study aims to isolate and identify pathogenic bacteria found in leatherback turtle eggshell (Dermochelys coriacea) from Lampuuk Beach, Aceh Besar, based on the 16S rRNA gene analysis. Eight eggshell samples from leatherback turtle eggs that failed and hatched were cultured on Nutrient Agar (NA) medium. Then, the samples were inoculated on a blood agar medium for haemolysis test. Molecular identification of the 16S rRNA gene was also carried out to determine bacterial species. A total of five bacterial colonies from leatherback turtle eggshells were successfully isolated consisting of two Gram-negative bacteria (Penyu Belimbing Aceh (PBA) = PBA-1 and PBA-2 and three Gram-positive bacteria (PBA-3, PBA-4, and PBA-5). Based on the haemolysis test, the five bacterial isolates were unable to haemolyze blood. Bacterial DNA of PBA-1 and PBA-2 were successfully isolated and amplified using polymerase chain reaction (PCR) with a DNA target of ~1500 bp. Analysis using BLASTN and phylogenetic tree construction showed that PBA-1 isolate had 98.64% similarity with Acinetobacter baumannii, while PBA-2 isolate had 97.82% similarity with Enterobacter kobei. Both bacteria are members of the Enterobacteriaceae family. It can be concluded that, there were two pathogenic bacteria can potentially be opportunistic pathogens found in leatherback turtle eggshells that failed or succeeded in hatching, namely A. baumannii and E. Kobei

Exploiting β-Lactams-Induced Lysis and DNA Fragmentation for Rapid Molecular Antimicrobial Susceptibility Testing of Neisseria Gonorrhoeae via Dual-Digital PCR.

The evolution of antimicrobial resistance (AMR) presents substantial challenges to global medical health systems. Neisseria gonorrhoeae (N. gonorrhoeae), in particular, has developed resistance to all currently available antimicrobials. Addressing this issue necessitates not only discovering new antimicrobials but also deepening the understanding of bacterial responses to these agents, which can lead to new markers for rapid antimicrobial susceptibility testing (AST). Such advancements can enhance treatment outcomes and promote antimicrobial stewardship. In this study, single-cell techniques, including live-cell imaging, flow cytometry, and digital polymerase chain reaction (PCR) are utilized, to investigate the lysis dynamics and molecular features of N. gonorrhoeae upon exposure to β-lactam antimicrobials. Distinct patterns of bacterial lysis and DNA fragmentation are uncovered in susceptible strains. Leveraging these discoveries, A microfluidic dual-digital PCR approach that combines single-cell and single-molecule analyses, facilitating rapid and efficient phenotypic molecular AST for N. gonorrhoeae against β-lactams is developed. This proof-of-concept validation demonstrates the effectiveness of the method in accessing antimicrobial susceptibility across a range of bacterial strains, contributing valuable insights for advancing the battle against AMR.

Halosquirtibacter laminarini gen. nov., sp. nov. and Halosquirtibacter xylanolyticus sp. nov., marine anaerobic laminarin and xylan degraders in the phylum Bacteroidota

The bacterial group of the phylum Bacteroidota greatly contributes to the global carbon cycle in marine ecosystems through its specialized ability to degrade marine polysaccharides. In this study, it is proposed that two novel facultative anaerobic strains, DS1-an-13321T and DS1-an-2312T, which were isolated from a sea squirt, represent a novel genus, Halosquirtibacter, with two novel species in the family Prolixibacteraceae. The 16S rRNA sequence similarities of these two strains were 91.26% and 91.37%, respectively, against Puteibacter caeruleilacunae JC036T, which is the closest recognized neighbor. The complete genomes of strains DS1-an-13321T and DS1-an-2312T each consisted of a single circular chromosome with a size of 4.47 and 5.19 Mb, respectively. The average amino acid identity and the percentage of conserved proteins against the type species of the genera in the family Prolixibacteraceae ranged from 48.33 to 52.35% and 28.34–37.37%, respectively, which are lower than the threshold for genus demarcation. Strains DS1-an-13321T and DS1-an-2312T could grow on galactose, glucose, maltose, lactose, sucrose, laminarin, and starch, and only DS1-an-2312T could grow on xylose and xylan under fermentation conditions. These strains produced acetic acid and propionic acid as the major fermentation products. Genome mining of the genomes of the two strains revealed 27 and 34 polysaccharide utilization loci, which included 155 and 249 carbohydrate-active enzymes (CAZymes), covering 57 and 65 CAZymes families, respectively. The laminarin-degrading enzymes in both strains were cell-associated, and showed exo-hydrolytic activity releasing glucose as a major product. The xylan-degrading enzymes of strain DS1-an-2312T was also cell-associated, and had endo-hydrolytic activities, releasing xylotriose and xylotetraose as major products. The evidence from phenotypic, biochemical, chemotaxonomic, and genomic characteristics supported the proposal of a novel genus with two novel species in the family Prolixibacteraceae, for which the names Halosquirtibacter laminarini gen. nov., sp. nov. and Halosquirtibacter xylanolyticus sp. nov. are proposed. The type strain of Halosquirtibacter laminarini is DS1-an-13321T (= KCTC 25031T = DSM 115329T) and the type strain of Halosquirtibacter xylanolyticus is DS1-an-2312T (= KCTC 25032T = DSM 115328T).

Complete Genome Sequence and Probiotic Characterization of Lactobacillus delbrueckii subsp. Indicus DC-3 Isolated from Traditional Indigenous Fermented Milk.

In this study, Lactobacillus delbrueckii subsp. indicus DC-3 was isolated from Indian traditional indigenous fermented milk Dahi and identified using whole genome sequencing. The safety of the strain was evaluated using genetic and phenotypic analyses, such as the presence of virulence factors, mobile and insertion elements, plasmids, antibiotic resistance, etc. Besides this, the strain was comprehensively investigated for in vitro probiotic traits, biofilm formation, antibacterials, and exopolysaccharide (EPS) production. In results, the strain showed a single circular chromosome (3,145,837bp) with a GC content of 56.73%, a higher number of accessory and unique genes, an open pan-genome, and the absence of mobile and insertion elements, plasmids, virulence, and transmissible antibiotic resistance genes. The strain was capable of surviving in gastric juice (83% viability at 3h) and intestinal juice (71% viability at 6h) and showed 42.5% autoaggregation, adhesion to mucin, 8.7% adhesion to xylene, and 8.3% adhesion to Caco-2 cells. The γ-hemolytic nature, usual antibiotic susceptibility profile, and negative results for mucin and gelatin degradation ensure the safety of the strain. The strain produced 10.5g/L of D-lactic acid and hydrogen peroxide, capable of inhibiting and co-aggregating Escherichia coli MTCC 1687, Proteus mirabilis MTCC 425, and Candida albicans ATCC 14,053. In addition, the strain showed 90mg/L EPS (48h) and biofilm formation. In conclusion, this study demonstrates that L. delbrueckii subsp. indicus DC-3 is unique and different than previously reported L. delbrueckii subsp. indicus strains and is a safe potential probiotic candidate.

SUPREM: an engineered non-site-specific m6A RNA methyltransferase with highly improved efficiency.

N 6-Methyladenine(m6A) RNA methylation plays a key role in RNA processing and translational regulation, influencing both normal physiological and pathological processes. Yet, current techniques for studying RNA methylation struggle to isolate the effects of individual m6A modifications. Engineering of RNA methyltransferases (RNA MTases) could enable development of improved synthetic biology tools to manipulate RNA methylation, but it is challenging due to limited understanding of structure-function relationships in RNA MTases. Herein, using ancestral sequence reconstruction, we explore the sequence space of the bacterial DNA methyltransferase EcoGII (M.EcoGII), a promising target for protein engineering due to its lack of sequence specificity and its residual activity on RNA. We thereby created an efficient non-specific RNA MTase termed SUPer RNA EcoGII Methyltransferase (SUPREM), which exhibits 8-fold higher expression levels, 7°C higher thermostability and 12-fold greater m6A RNA methylation activity compared with M.EcoGII. Immunofluorescent staining and quantitativeliquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis confirmed SUPREM's higher RNA methylation activity compared with M.EcoGII in mammalian cells. Additionally, Nanopore direct RNA sequencing highlighted that SUPREM is capable of methylating a larger number of RNA methylation sites than M.EcoGII. Through phylogenetic and mutational analysis, we identified a critical residue for the enhanced RNA methylation activity of SUPREM. Collectively, our findings indicate that SUPREM holds promise as a versatile tool for in vivo RNA methylation and labeling.

Revolutionizing Quinolone Development for DNA Gyrase Targeting; Discovering the Promising Approach to Fighting Microbial Infections

Abstract: DNA gyrase is a type II topoisomerase enzyme that can cause negative supercoiling in DNA by using the energy produced by ATP hydrolysis. There are two main types of topoi-somerases: type I and type II. Type I enzymes cut a single strand of DNA and are further clas-sified as type IA if they connect to a 5′ phosphate of DNA, or type IB if they link to a 3′ phos-phate. Type II topoisomerases break both strands, creating a staggered double-strand break. Antimicrobial resistance is a major concern for the global healthcare system. Resistance is the ability of microorganisms to neutralize and withstand antimicrobial drugs previously used to treat microbial infections. Some known classes of DNA gyrase inhibitors are coumarins, cyclo-thialidines, and quinolones. Antimicrobial medicines such as quinolones have been widely used to treat microbiological diseases. However, the increased use of quinolones has led to the emer-gence of quinolone-resistant bacteria, which poses a serious risk to public health. Microorgan-isms can cause resistance due to changes in the target enzymes, DNA gyrase, and topoisomerase IV, which are responsible for transcription and DNA replication. Additionally, differences in drug entry and efflux may also play a role in resistance. Plasmids that produce the Qnr protein can mediate resistance to quinolones by protecting the quinolone targets from inhibition. This review aims to revolutionize the discovery of quinolone-based antibiotics, specifically targeting DNA gyrase, a critical enzyme in bacterial DNA replication, to enhance the efficacy and spec-ificity of anti-microbail agents against microbial infections.

Mycobacterium terrae Complex Associated Lymphadenitis: Negative AFB PCR

Abstract Introduction/Objective Nontuberculous mycobacteria included with the Mycobacterium terrae complex (MTC) include a ubiquitous, slow-growing collection of mycobacteria known for causing severe resistant skin, joint, and bone infections. There are limited reports of M. Arupensis, included under MTC, causing human infections despite environmental ubiquity. Low sequencing sensitivity for species such as M. Arupensis may result in negative preliminary PCR speciation thus influencing the negative predictive value of this method of organism detection. No prior case reports have described MTC infection presenting as subacute lymphadenitis. Methods/Case Report A 48 year old El Salvadorian male with known diagnosis of HIV presented with oral thrush and significant left-sided lymphadenopathy. He was initially diagnosed with HIV in El Salvador and on ART until immigrating to the US six months prior. HIV antigen and antibody was positive with positive reflex viral PCR. QuantiFERON-TB Gold resulted positive, but CXR was without evidence of pulmonary TB. TB1, TB2, and mitogen minus NIL were negative. He was referred for fine needle aspiration and core needle biopsy of the left cervical lymph node. AFB and AFB FITE stains were performed, but no definitive mycobacteria were identified. GMS was performed and negative for fungal elements. A final histological diagnosis of necrotizing granuloma was given and the tissue was sent for bacterial, AFB, and fungal DNA PCR; no organisms were detected. A sputum sample was obtained and cultured four months after initial presentation and was positive for acid fast bacilli: Mycobacterium terrae complex, most closely resembling Mycobacterium arupensis. The Fite and AFB stains were again reviewed, revealing one single acid fast bacilli organism identified on Fite stain in the necrotizing granuloma. Results (if a Case Study enter NA) N/A Conclusion The negative AFB DNA PCR result may have been a false negative result due to poor sensitivity or selectivity for M. arupensis. There are no former reported cases of M. Arupensis associated necrotizing granulomas in lymph node. This unusual MTC infection presenting as chronic unilateral lymphadenitis underscores the importance of broadening clinical laboratory AFB DNA PCR sensitivity especially in cases of suspected AFB or modified AFB associated necrotizing granulomas.

Safety Assessment and Evaluation of Probiotic Potential of Lactobacillus bulgaricus IDCC 3601 for Human Use

Lactic acid bacteria (LAB) are probiotic microorganisms widely used for their health benefits in the food industry. However, recent concerns regarding their safety have highlighted the need for comprehensive safety assessments. In this study, we aimed to evaluate the safety of L. bulgaricus IDCC 3601, isolated from homemade plain yogurt, via genomic, phenotypic, and toxicity-based analyses. L. bulgaricus IDCC 3601 possessed a single circular chromosome of 1,865,001 bp, with a GC content of 49.72%, and 1910 predicted coding sequences. No virulence or antibiotic resistance genes were detected. Although L. bulgaricus IDCC 3601 exhibited antibiotic resistance to gentamicin and kanamycin, this resistance is an intrinsic feature of this species. L. bulgaricus IDCC 3601 did not produce biogenic amines and did not exhibit hemolytic activity. Phenotypic analysis of enzyme activity and carbohydrate fermentation profiles revealed the metabolic features of L. bulgaricus IDCC 3601. Moreover, no deaths or abnormalities were observed in single-dose oral toxicity tests, suggesting that L. bulgaricus IDCC 3601 has no adverse effect on human health. Finally, L. bulgaricus IDCC 3601 inhibited the growth of potential carbapenem-resistant Enterobacteriaceae. Therefore, our results suggest that L. bulgaricus IDCC 3601 is a safe probiotic strain for human consumption.

Complete genome sequence of Sphingobacterium thalpophilum BAA-1094.

We report the complete genome of Sphingobacterium thalpophilum BAA-1094 obtained from the American Type Culture Collection. The genome has one circular chromosome (5.7 Mbp). The rather low average nucleotide identity of 76.5% to the type strain Sphingobacterium thalpophilum DSM 11723 suggests the need for reclassification.

Application of Drug Delivery System Based on Nanozyme Cascade Technology in Chronic Wound.

Chronic wounds are characterized by long-term inflammation, including diabetic ulcers, traumatic ulcers, etc., which provide an optimal environment for bacterial proliferation. At present, antibiotics are the main clinical treatment method for chronic wound infections. However, the overuse of antibiotics may accelerate the emergence of drug-resistant bacteria, which poses a significant threat to human health. Therefore, there is an urgent need to develop new therapeutic strategies for bacterial infections. Nanozyme-based antimicrobial therapy (NABT) is an emerging antimicrobial strategy with broad-spectrum activity and low drug resistance compared to traditional antibiotics. NABT has shown great potential as an emerging antimicrobial strategy by catalyzing the generation of reactive oxygen species (ROS) with its enzyme-like catalytic properties, producing a powerful bactericidal effect without developing drug resistance. Nanozyme-based cascade antimicrobial technology offers a new approach to infection control, effectively improving antimicrobial efficacy by activating cascades against bacterial cell membranes and intracellular DNA while minimizing potential side effects. However, it is worth noting that this technology is still in the early stages of research. This article comprehensively reviews wound classification, current methods for the treatment of wound infection, different types of nanozymes, the application of nanozyme cascade reaction technology in antimicrobial therapy, and future challenges and prospects.

Complete genome sequence of Serratia plymuthica SWSY-3.47.

Serratia plymuthica strain SWSY-3.47 is a Gram-negative, rod-shaped bacteria isolated for its high chitinolytic activity. Here, we report the complete genome of this strain comprised of a single circular chromosome of 5,636,345 bp with a G + C content of 56.0%.

Metagenomic Analysis of Bacterial Communities in Bee Bread in Türkiye

This study aims to investigate the bacterial community structure in bee bread samples collected from 10 provinces of Türkiye using next-generation sequencing (NGS) and metagenomic analysis. Bacterial genomic DNA was extracted and sequenced using Illumina MiSeq. Bioinformatic analysis involved quality assessment, OTU classification, principal coordinate analysis (PCoA), and diversity index calculations. Heatmap and PCoA were utilized to explore the impact of locality and ecological zones on microbial diversity. Metagenomic analysis of 12 bee bread samples revealed 276,583 high-quality sequencing reads. The dominant bacterial phyla identified were Proteobacteria, Actinobacteria, Cyanobacteria, and Firmicutes. At the genus level, Streptomyces, Streptococcus, Bacillus, and Synechococcus were the most abundant, with Streptomyces and Bacillus playing key roles in the fermentation process of bee bread. The Shannon diversity index (ranging from 2.92 to 4.26) and Simpson's index (0.83 to 0.95) indicated high species diversity and relative abundance in bee bread. The study underscores the need for locality-specific approaches in beekeeping management and highlights the potential significance of beneficial bacterial taxa, particularly those involved in fermentation, in contributing to the nutritional and health properties of bee bread. These findings provide a foundation for further research on the microbial dynamics that support bee colony health.