Fructobacillus, a Gram-positive, non-spore-forming, facultative anaerobic bacterium, belongs to the fructophilic lactic acid bacteria (FLAB) group. The group's name originates from fructose, the favored carbon source for its members. Fructobacillus spp. are noteworthy for their distinctive traits, captivating the interest of scientists. However, there have been relatively few publications regarding the isolation and potential utilization of these microorganisms in the industry. In recent years, F. tropaeoli has garnered interest for its promising role in the food and pharmaceutical sectors, although the availability of isolates is rather limited. A more comprehensive understanding of Fructobacillus is imperative to evaluate their functionality in the industry, given their unique and exceptional properties. Our in vitro study on Fructobacillus tropaeoli KKP 3032 confirmed its fructophilic nature and high osmotolerance. This strain thrives in a 30% sugar concentration, shows resistance to low pH and bile salts, and exhibits robust autoaggregation. Additionally, it displays significant antimicrobial activity against foodborne pathogens. Evaluating its probiotic potential, it aligns with EFSA recommendations in antibiotic resistance, except for kanamycin, to which it is resistant. Further research is necessary, but preliminary analyses confirm the high probiotic potential of F. tropaeoli KKP 3032 and its ability to thrive in the presence of high concentrations of fructose. The results indicate that the isolate F. tropaeoli KKP 3032 could potentially be used in the future as a fructophilic probiotic, protective culture, and/or active ingredient in fructose-rich food.

• MeSH
• Anti-Bacterial Agents pharmacology   MeSH
• Fructose metabolism   MeSH
• Hydrogen-Ion Concentration MeSH
• Fruit and Vegetable Juices * microbiology   MeSH
• Citrus sinensis microbiology   chemistry   MeSH
• Food Microbiology MeSH
• Probiotics * isolation & purification   MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Bile Acids and Salts metabolism   MeSH
• Publication type
• Journal Article MeSH

A novel Gram-stain-negative, strictly aerobic, rod-shaped, light-yellow-pigmented, and chemo-organoheterotrophic bacterium, designated DF-77T, was isolated from dense mats of filamentous algae collected in March 2004 at Okinawa in Japan. The microorganism grew at 0-2.0% NaCl concentrations (w/v), pH 6.0-9.0, and 20-30 °C. The 16S rRNA gene sequence-based phylogenetic tree demonstrated that the strain DF-77T is a novel member of the family Flavobacteriaceae and was greatly related to Flagellimonas nanhaiensis SM1704T with sequence similarity of 95.5%. The main fatty acids were iso-C15:1 G, iso-C15:0, and iso-C17:0 3-OH, and the only isoprenoid quinone was menaquinone-6. The dominant polar lipids were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phosphoaminolipid, and four unidentified lipids. The genome size of strain DF-77T was 3.60 Mbp with a DNA G + C content of 47.5%. The average nucleotide identity (ANI) value between the genomes of strain DF-77T and its closely related species was 69.8-70.7%. The digital DNA - DNA hybridization (dDDH) value of strain DF-77T with the strain of F. nanhaiensis SM1704T was 16.8%. The genome of the strain DF-77T revealed that it encoded several genes involved in bio-macromolecule degradation, indicating a high potential for producing industrially useful enzymes. Consequently, the strain is described as a new species in the genus Flagellimonas, for which the name Flagellimonas algarum sp. nov., is proposed with the type strain DF-77T (= KCTC 72791T = NBRC 114251T).

• MeSH
• DNA, Bacterial genetics   chemistry   MeSH
• Flavobacteriaceae * classification   isolation & purification   genetics   MeSH
• Phospholipids analysis   MeSH
• Phylogeny MeSH
• Genome, Bacterial MeSH
• Nucleic Acid Hybridization MeSH
• Fatty Acids analysis   MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Sequence Analysis, DNA MeSH
• Bacterial Typing Techniques MeSH
• Vitamin K 2 analysis   analogs & derivatives   MeSH
• Base Composition MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Japan MeSH

In this study, lactic acid bacteria (LAB) isolation from fermented foods and molecular identification using magnetic bead technology were performed. And then exopolysaccharide (EPS) production possibility was tested in agar medium, and the positive ones were selected for the next step. The bacteria that could produce higher carbohydrate level were grown in MRS medium fortified with whey and pumpkin waste. In our study, 19 different LAB species were identified from fermented products collected from different places in Hatay (Türkiye) province. In molecular identification, universal primer pairs, p806R/p8FPL, and PEU7/DG74 were used for PCR amplification. After that, PCR products purified using paramagnetic bead technology were sequenced by the Sanger sequencing method. The dominant species, 23.8% of the isolates, were identified as Lactiplantibacillus plantarum. As a technological property of LAB, exopolysaccharide production capability of forty-two LAB isolate was tested in agar medium, and after eleven isolates were selected as positive. Two LAB (Latilactobacillus curvatus SHA2-3B and Loigolactobacillus coryniformis SHA6-3B) had higher EPS production capability when they were grown in MRS broth fortified with pumpkin waste and whey. The highest EPS content (1750 mg/L glucose equivalent) was determined in Loigolactobacillus coryniformis SHA6-3B grown in MRS broth fortified with 10% pumpkin waste. Besides the produced EPS samples were validated with FTIR and SEM methods.

• MeSH
• Polysaccharides, Bacterial * biosynthesis   metabolism   MeSH
• Cucurbita microbiology   MeSH
• Fermentation MeSH
• Fermented Foods * microbiology   MeSH
• Phylogeny MeSH
• Culture Media chemistry   MeSH
• Lactobacillales * isolation & purification   classification   genetics   metabolism   MeSH
• Waste Products * analysis   MeSH
• Food Microbiology * MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Whey MeSH
• Publication type
• Journal Article MeSH

Halophilic bacteria are extremophiles that thrive in saline environment. Their ability to withstand such harsh conditions makes them an ideal choice for industrial applications such as lignocellulosic biomass degradation. In this study, a halophilic bacterium with the ability to produce extracellular cellulases and hemicellulases, designated as Nesterenkonia sp. CL21, was isolated from mangrove sediment in Tanjung Piai National Park, Malaysia. Thus far, studies on lignocellulolytic enzymes concerning bacterial species under this genus are limited. To gain a comprehensive understanding of its lignocellulose-degrading potential, the whole genome was sequenced using the Illumina NovaSeq 6000 platform. The genome of strain CL21 was assembled into 25 contigs with 3,744,449 bp and a 69.74% GC content and was predicted to contain 3,348 coding genes. Based on taxonomy analysis, strain CL21 shares 73.8 to 82.0% average nucleotide identity with its neighbouring species, below the 95% threshold, indicating its possible status as a distinct species in Nesterenkonia genus. Through in-depth genomic mining, a total of 81 carbohydrate-active enzymes were encoded. Among these, 24 encoded genes were identified to encompass diverse cellulases (GH3), xylanases (GH10, GH11, GH43, GH51, GH127 and CE4), mannanases (GH38 and GH106) and pectinases (PL1, PL9, and PL11). The production of lignocellulolytic enzymes was tested in the presence of several substrates. This study revealed that strain CL21 can produce a diverse array of enzymes which are active at different time points. By combining experimental data with genomic information, the ability of strain CL21 to produce lignocellulolytic enzymes has been elucidated, with potential applications in biorefinery industry.

• MeSH
• Bacterial Proteins genetics   metabolism   MeSH
• Cellulases genetics   metabolism   MeSH
• Phylogeny * MeSH
• Genome, Bacterial * MeSH
• Genomics * MeSH
• Geologic Sediments microbiology   MeSH
• Glycoside Hydrolases * genetics   metabolism   MeSH
• Lignin * metabolism   MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Whole Genome Sequencing MeSH
• Base Composition MeSH
• Publication type
• Journal Article MeSH

Interferon‐induced transmembrane proteins (IFITMs) are frequently overexpressed in cancer cells, including cervical carcinoma cells, and play a role in the progression of various cancer types. However, their mechanisms of action remain incompletely understood. In the present study, by employing a combination of surface membrane protein isolation and quantitative mass spectrometry, it was comprehensively described how the IFITM1 protein influences the composition of the cervical cancer cell surfaceome. Additionally, the effects of interferon‐γ on protein expression and cell surface exposure were evaluated in the presence and absence of IFITM1. The IFITM1‐regulated membrane and membrane‐associated proteins identified are involved mainly in processes such as endocytosis and lysosomal transport, cell‐cell and cell‐extracellular matrix adhesion, antigen presentation and the immune response. To complement the proteomic data, gene expression was analyzed using reverse transcription‐quantitative PCR to distinguish whether the observed changes in protein levels were attributable to transcriptional regulation or differential protein dynamics. Furthermore, the proteomic and gene expression data are supported by functional studies demonstrating the impact of the IFITM1 and IFITM3 proteins on the adhesive, migratory and invasive capabilities of cervical cancer cells, as well as their interactions with immune cells.

• MeSH
• Cell Adhesion MeSH
• Antigens, Differentiation * metabolism   genetics   MeSH
• Phenotype MeSH
• Interferon-gamma pharmacology   metabolism   MeSH
• Humans MeSH
• Membrane Proteins * metabolism   genetics   MeSH
• Cell Line, Tumor MeSH
• Uterine Cervical Neoplasms * pathology   genetics   metabolism   immunology   MeSH
• Cell Movement MeSH
• RNA-Binding Proteins * metabolism   genetics   MeSH
• Proteome * MeSH
• Proteomics methods   MeSH
• Gene Expression Regulation, Neoplastic MeSH
• Check Tag
• Humans MeSH
• Female MeSH
• Publication type
• Journal Article MeSH

Development of dentition is a commonly studied process as a representative of the development of ectodermal derivates. A key step is the formation of a signaling center called the enamel knot (EK), which organizes tooth crown formation. In the mouse lower jaw, the anterior part of the tooth-forming region undergoes a series of complex events before the first molar primary EK can form more posteriorly and the tooth can progress through the cap stage. Although much is known about the molecular factors involved in tooth development, disentangling their specific roles is difficult. In this study, we circumvented this problem by isolating the posterior part of the tooth-forming region at embryonic day 13.5 and cultivating it in vitro. By treating them with molecules activating or inhibiting Sonic hedgehog (Shh) and fibroblast growth factor (Fgf) pathways, we demonstrate that Shh plays the role of an inhibitor of EK formation, and we suggest that the FGF pathways may have both positive and negative roles, as seen in hair. By RNA-sequencing of the cultivated isolates after 0, 16, or 24 h in vitro, respectively, we screened for genes whose expression varies with EK and cap formation and pointed to Cdkn2b and Sema3b as 2 promising candidates in this process.

• MeSH
• Fibroblast Growth Factors physiology   MeSH
• Molar embryology   MeSH
• Mice MeSH
• Odontogenesis * physiology   genetics   MeSH
• Hedgehog Proteins physiology   metabolism   MeSH
• Signal Transduction MeSH
• Gene Expression Regulation, Developmental MeSH
• Tooth Crown * embryology   MeSH
• Dental Enamel * embryology   MeSH
• Animals MeSH
• Check Tag
• Mice MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH

Antisense transcripts play an important role in generating regulatory non-coding RNAs but whether these transcripts are also translated to generate functional peptides remains poorly understood. In this study, RNA sequencing and six-frame database generation were combined with mass spectrometry analysis of peptides isolated from polysomes to identify Nascent Pioneer Translation Products (Na-PTPs) originating from alternative reading frames of bi-directional transcripts. Two Na-PTP originating peptides derived from antisense strands stimulated CD8+ T cell proliferation when presented to peripheral blood mononuclear cells (PBMCs) from nine healthy donors. Importantly, an antigenic peptide derived from the reverse strand of two cDNA constructs was presented on MHC-I molecules and induced CD8+ T cell activation. The results demonstrate that three-frame translation of bi-directional transcripts generates antigenic peptide substrates for the immune system. This discovery holds significance for understanding the origin of self-discriminating peptide substrates for the major histocompatibility class I (MHC-I) pathway and for enhancing immune-based therapies against infected or transformed cells.

• MeSH
• Lymphocyte Activation immunology   MeSH
• RNA, Antisense * genetics   immunology   MeSH
• CD8-Positive T-Lymphocytes * immunology   MeSH
• Leukocytes, Mononuclear immunology   MeSH
• Humans MeSH
• Histocompatibility Antigens Class I * immunology   genetics   MeSH
• Peptides * immunology   genetics   MeSH
• Antigen Presentation MeSH
• Protein Biosynthesis * MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH

Background: Stenotrophomonas infections are becoming more widespread around the world and can be counted as a "newly emerging pathogen of concern". The present study aimed to detect a variety of Stenotrophomonas species (S. maltophilia) using specific 23S rRNA gene primers and investigate their multi-drug resistance potential.Methods: This study includes 375 clinical samples from different clinical sources 175 from males and 200 from females collected from Mosul City Hospital. Identification of Stenotrophomonas was conducted through multiple steps including culturing methods, molecular methods in addition to some biochemical tests 11(3%) of isolates belonged to Stenotrophomonas maltophilia. The isolates understudy were tested for their ability to resist 10 different antibiotics using the Kirby-Bauer disk diffusion method.Results: The resistance rate to amoxicillin, gentamicin, and amikacin (100%), cefixime (91%), imipenem (64%), meropenem(55%), Azithromycin (36%), nalidixic acid and trimethoprim (18%), ciprofloxacin(0%). The virulence factors of S. maltophilia siderophores were found in all (11) isolates belonging to S. maltophilia at a percentage (100%). The result of PCR assay using specific primers designed for detecting 23S rRNA genes of S. maltophilia gives amplification for 11 isolates from 14 suspected isolates. Nucleic acid sequencing for the 23S rRNA gene shows that all isolates belong to S. maltophilia with a similarity rate (91-99) in NCBI.Because the 23S rRNA gene sequence in Stenotrophomonas species shows more variety in this location this study used specific 23S rRNA gene primers to identify S. maltophilia.Conclusion: The study used phenotypic and molecular diagnostic techniques to isolate the bacteria, including the S rRNA23 gene. The results emphasize the need for increased vigilance in hospitals to prevent the spread of antibiotic-resistant bacteria and the development of new treatment strategies.

• MeSH
• Drug Resistance, Microbial genetics   MeSH
• Drug Resistance, Bacterial genetics   MeSH
• Cross Infection genetics   microbiology   MeSH
• Clinical Studies as Topic methods   MeSH
• Humans MeSH
• Microbiological Techniques methods   MeSH
• Polymerase Chain Reaction methods   MeSH
• RNA, Ribosomal, 23S * analysis   genetics   MeSH
• Siderophores analysis   genetics   MeSH
• Stenotrophomonas maltophilia * genetics   pathogenicity   MeSH
• Check Tag
• Humans MeSH

OBJECTIVES: While the reported incidence of non-tuberculous mycobacterial (NTM) infections is increasing, the true prevalence remains uncertain due to limitations in diagnostics and surveillance. The emergence of rare and novel species underscores the need for characterization to improve surveillance, detection, and management. METHODS: We performed whole-genome sequencing (WGS) and/or targeted deep-sequencing using the Deeplex Myc-TB assay on all NTM isolates collected in Slovakia and the Czech Republic between the years 2019 to 2023 that were unidentifiable at the species level by the routine diagnostic line probe assays (LPA) GenoType CM/AS and NTM-DR. Minimal inhibitory concentrations against amikacin, ciprofloxacin, moxifloxacin, clarithromycin, and linezolid were determined, and clinical data were collected. RESULTS: Twenty-eight cultures from different patients were included, of which 9 (32.1%) met the clinically relevant NTM disease criteria. The majority of those had pulmonary involvement, while two children presented with lymphadenitis. Antimycobacterial resistance rates were low. In total, 15 different NTM species were identified, predominantly rare NTM like M. neoaurum, M. kumamotonense and M. arupense. Notably, clinically relevant M. chimaera variants were also identified with WGS and Deeplex-Myc TB, which, unlike other M. chimaera strains, appeared to be undetectable by LPA assays. Deeplex detected four mixed infections that were missed by WGS analysis. In contrast, WGS identified two novel species, M. celatum and M. branderi, which were not detected by Deeplex-Myc TB. Importantly, one of these novel species strains was associated with clinically relevant pulmonary disease. DISCUSSION: Our study demonstrates the clinical relevance of uncommon NTM and the effectiveness of targeted deep-sequencing combined with WGS in identifying rare and novel NTM species.

• MeSH
• Anti-Bacterial Agents * pharmacology   MeSH
• Mycobacterium Infections, Nontuberculous * microbiology   diagnosis   MeSH
• Drug Resistance, Bacterial MeSH
• Child MeSH
• Adult MeSH
• Genotype MeSH
• Clinical Relevance MeSH
• Middle Aged MeSH
• Humans MeSH
• Microbial Sensitivity Tests * MeSH
• Adolescent MeSH
• Nontuberculous Mycobacteria * drug effects   genetics   isolation & purification   MeSH
• Child, Preschool MeSH
• Whole Genome Sequencing * MeSH
• Aged MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Check Tag
• Child MeSH
• Adult MeSH
• Middle Aged MeSH
• Humans MeSH
• Adolescent MeSH
• Male MeSH
• Child, Preschool MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Czech Republic MeSH
• Slovakia MeSH

Single-cell RNA-seq methods can be used to delineate cell types and states at unprecedented resolution but do little to explain why certain genes are expressed. Single-cell ATAC-seq and multiome (ATAC + RNA) have emerged to give a complementary view of the cell state. It is however unclear what additional information can be extracted from ATAC-seq data besides transcription factor binding sites. Here, we show that ATAC-seq telomere-like reads counter-inituively cannot be used to infer telomere length, as they mostly originate from the subtelomere, but can be used as a biomarker for chromatin condensation. Using long-read sequencing, we further show that modern hyperactive Tn5 does not duplicate 9 bp of its target sequence, contrary to common belief. We provide a new tool, Telomemore, which can quantify nonaligning subtelomeric reads. By analyzing several public datasets and generating new multiome fibroblast and B-cell atlases, we show how this new readout can aid single-cell data interpretation. We show how drivers of condensation processes can be inferred, and how it complements common RNA-seq-based cell cycle inference, which fails for monocytes. Telomemore-based analysis of the condensation state is thus a valuable complement to the single-cell analysis toolbox.

• MeSH
• Single-Cell Analysis * methods   MeSH
• B-Lymphocytes metabolism   cytology   MeSH
• Cell Cycle * genetics   MeSH
• Chromatin Immunoprecipitation Sequencing methods   MeSH
• Chromatin * metabolism   chemistry   genetics   MeSH
• Fibroblasts metabolism   cytology   MeSH
• Humans MeSH
• RNA-Seq methods   MeSH
• Telomere * genetics   MeSH
• Binding Sites MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH