Search Results (5,070)

Bioremediation induced by bacteria offers a promising alternative for the contamination of aromatic hydrocarbons due to their metabolic processes suitable for the removal of these pollutants, as many of them are carcinogenic molecules and dangerous to human health. Our research focused on isolating a bacterium from the rhizosphere of the tara tree with the ability to degrade polycyclic aromatic hydrocarbons, using draft genomic sequencing and computational analysis. Enterobacter sp. strain UNJFSC 003 possesses 4460 protein-coding genes, two rRNA genes, 77 tRNA genes, and a GC content of 54.38%. A taxonomic analysis of our strain revealed that it has an average nucleotide identity (ANI) of 87.8%, indicating that it is a new native Enterobacteria. Additionally, a pangenomic analysis with 15 strains demonstrated that our strain has a phylogenetic relationship with strain FDAARGOS 1428 (Enterobacter cancerogenus), with a total of 381 core genes and 4778 accessory genes. Orthologous methods predicted that strain UNJFSC 003 possesses genes with potential for use in hydrocarbon bioremediation. Genes were predicted in the sub-pathways for the degradation of homoprotocatechuate and phenylacetate, primarily located in the cytoplasm. Studies conducted through molecular modeling and docking revealed the affinity of the predicted proteins in the degradation of benzo[a]pyrene in the homoprotocatechuate sub-pathway, specifically hpcB, which has enzymatic activity as a dioxygenase, and hpcC, which functions as an aldehyde dehydrogenase. This study provides information on native strains from Lomas de Lachay with capabilities for the bioremediation of aromatic hydrocarbons and other compounds. Full article

Six novel Microbacterium phages belonging to the Tectiviridae family were isolated using Microbacterium testaceum as a host. Phages MuffinTheCat, Badulia, DesireeRose, Bee17, SCoupsA, and LuzDeMundo were purified from environmental samples by students participating in the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program at Alliance University, New York. The phages have linear dsDNA genomes 15,438–15,636 bp with 112–120 bp inverted terminal repeats. Transmission electron microscopy (TEM) imaging analysis revealed that the six novel phages have six-sided icosahedral double-layered capsids with an internal lipid membrane that occasionally forms protruding nanotubules. Annotation analysis determined that the novel Microbacterium phages all have 32–34 protein-coding genes and no tRNAs. Like other Tectiviridae, the phage genomes are arranged into two segments and include three highly conserved family genes that encode a DNA polymerase, double jelly-roll major capsid protein, and packaging ATPase. Although the novel bacteriophages have 91.6 to 97.5% nucleotide sequence similarity to each other, they are at most 58% similar to previously characterized Tectiviridae genera. Consequently, these novel Microbacterium phages expand the diversity of the Tectiviridae family, and we propose they form the sixth genus, Zetatectivirus. Full article

In nature, bacteria often form heterogeneous communities enclosed in a complex matrix known as biofilms. This extracellular matrix, produced by the microorganisms themselves, serves as the first barrier between the cells and the environment. It is composed mainly of water, extracellular polymeric substances (EPS), lipids, proteins, and DNA. Cyanobacteria form biofilms and have unique characteristics such as oxygenic photosynthesis, nitrogen fixation, excellent adaptability to various abiotic stress conditions, and the ability to secrete a variety of metabolites and hormones. This work focused on the characterization of the cyanobacterium Halomicronema sp. strain isolated from a brackish environment. This study included microscopic imaging, determination of phenolic content and antioxidant capacity, identification of chemicals interfering with biofilm formation, and transcriptomic analysis by RNA sequencing and real-time PCR. Gene expression analysis was centered on genes related to the production of EPS and biofilm-related transcription factors. This study led to the identification of wza1 and wzt as EPS biomarkers and luxR-05665, along with genes belonging to the TetR/AcrR and LysR families, as potential biomarkers useful for studying and monitoring biofilm formation under different environmental conditions. Moreover, this work revealed that Halomicronema sp. can grow even in the presence of strong abiotic stresses, such as high salt, and has good antioxidant properties. Full article

Cassava is an important staple food that contributes to the food security of small-scale Mozambican farmers. In southern Mozambique, cassava roots are usually processed into cassava roasted flour, locally known as “rale”. The handling and processing practices connected to “rale” production may introduce microbial contamination. We assessed the microbial contamination of “rale” processed in local farmers’ associations and consumed either locally or sold in rural markets. Microbial sampling was carried out both during the warmer rainy and cooler dry seasons, and microorganisms of relevance for food safety and fermentation were enumerated. The results revealed variation in terms of microbial diversity in all stages of cassava root processing. In samples collected in the warmer rainy season, molds, lactic acid bacteria, general aerobic bacteria and Bacillus spp. were isolated, whereas in samples collected in the cooler dry season, other groups of microorganisms such as yeasts and Staphylococcus aureus were present. Wickerhamomyces anomalus, Rhodotorula mucilaginosa, Pichia exigua, Meyerozyma caribbica and Torulaspora delbrueckii were the most frequent yeast species found within the cassava processing stages. Aflatoxin-producing molds were observed infrequently in this study, and only at low counts, thus, the risk for aflatoxin contamination appears to be low. The results obtained from the Illumina 16S rRNA gene sequencing can be considered a complementary technique to the plating methods relied on in this study. From a food quality and safety point of view, this staple food does not appear to pose a high risk for foodborne disease. Full article

Actinomycetes are known to produce a vast array of bioactive secondary metabolites with potential therapeutic applications, including antimicrobials, anticancer agents, and enzyme inhibitors. Among these, members of the genus Nonomuraea have received much attention due to their broad ecological importance in nutrient cycling in soil and their ability to produce new bioactive compounds. A novel actinomycetes, designated strain M3C6^T, was isolated from soil samples collected on Marmara Island, located in the Istanbul province, aiming to explore the microbial diversity of unexplored habitats, and characterized using a polyphasic approach. The isolate showed chemotaxonomic and morphological features consistent with members of the genus Nonomuraea. The 16S rRNA gene sequence analysis revealed that strain M3C6^T shared the highest similarity, at 98.7% sequence identity, to Nonomuraea basaltis 160415^T and Nonomuraea turkmeniaca DSM 43926^T. However, the ANI and dDDH values between strain M3C6^T and these reference strains were fairly low, ranging from 84.0 to 84.6% and 31.8 to 33.7%, respectively, below the generally accepted cutoffs for ANI and DDH that delineate different prokaryotic species. Genomic analysis of strain M3C6^T showed that it had a genome size of 10.38 Mbp and a DNA G+C content of 69.5 mol%. Based on these chemotaxonomic, phenotypic, and genomic data, strain M3C6^T is classified as a novel species within the genus Nonomuraea, for which the name Nonomuraea marmarensis sp. nov. is proposed. The type strain is M3C6^T (= KCTC 49983^T = CGMCC 4.8035^T). Genomic analyses confirmed the high potential of M3C6^T to produce specialized secondary metabolites. Full article

Methylsulfonylmethane (MSM) is a sulfur-containing molecule with reported anti-inflammatory and antioxidant activities. Exercise causes the formation of free radicals and stimulates inflammatory gene expression in leukocytes and skeletal muscle. The hypothesis that dietary supplementation with MSM alters the exercise-mediated inflammatory and oxidant response was assessed in unfit adult thoroughbred geldings. Ten geldings (6.7 ± 1.6 yr) were assigned to a diet supplemented without (CON, n = 5) or with 21 g of MSM (n = 5) for 30 days. Following the supplementation period, horses performed a standardized exercise test (SET) with blood collections before (t = 0), 10 min, 1 h, 4 h, and 24 h post-SET. Skeletal muscle biopsies were retrieved from the middle gluteus before and 1 h post-SET for total RNA isolation. All horses were rested for 120 days before the experiment was repeated in a cross-over design. Plasma total antioxidant capacity was unaffected (p > 0.05) by either exercise or MSM. Plasma glutathione peroxidase activity was less (p < 0.05) in MSM horses than in the CON. Plasma IL6, IL8, IL10, and TNFα were unaffected (p > 0.05) by either exercise or diet. Transcriptomic analysis of skeletal muscle revealed 35 genes were differentially expressed (DEG; p < 0.05) by 2-fold or more in response to exercise; no MSM DEGs were noted. A comparison of the exercise by diet contrasts revealed that horses supplemented with MSM contained a greater number of exercise-responsive genes (630; logFC > 0.2; q < 0.05) by comparison to the CON (237), with many of these mapping to the immune response (71) and cytokine signal transduction (60) pathways. These results suggest supplementation of MSM as a dietary aid for improved anti-inflammatory responses in skeletal muscle following exercise. Full article

Cryptostylis ovata is a terrestrial orchid endemic to southwestern Australia. The virus status of C. ovata has not been studied. Eighty-three C. ovata samples from 16 populations were collected, and sequencing was used to identify RNA viruses from them. In one population, all tested plants were co-infected with isolates of the exotic-to-Australia viruses Ornithogalum mosaic virus (OrMV) and bean yellow mosaic virus (BYMV). In another population, one plant was infected with BYMV. No viruses were detected in the remaining populations. The OrMV isolate shared 98–99% nucleotide identity with isolates identified from wild indigenous Lachenalia (Iridaceae) plants in South Africa. This suggests that the source of OrMV in C. ovata may be one or more bulbous iridaceous flowering plants of southern African origin that were introduced to Western Australia as ornamentals and that have since become invasive weeds. One BYMV isolate from C. ovata also exhibited 99% nucleotide identity with strains isolated from the exotic leguminous crop Lupinus angustifolius in Western Australia, suggesting possible spillover to indigenous species from this source. This study with C. ovata highlights the probable role of invasive weeds and exotic crops as sources of exotic virus spillovers to indigenous plants. Full article

The first marine pestivirus, Phocoena pestivirus (PhoPeV), isolated from harbor porpoise, has been recently described. To further characterize this unique pestivirus, its host cell tropism and growth kinetics were determined in different cell lines. In addition, the interaction of PhoPeV with innate immunity in porcine epithelial cells and the role of selected cellular factors involved in the viral entry and RNA replication of PhoPeV were investigated in comparison to closely and distantly related pestiviruses. While Bungowannah pestivirus (BuPV), a unique porcine pestivirus closely related to PhoPeV, exhibits a broad cell tropism, PhoPeV only infects cells from pigs, cattle, sheep, and cats, as has been described for classical swine fever virus (CSFV). Viral titers correlate with the amount of intracellular PhoPeV-specific RNA detected in the tested cell lines. PhoPeV replicates most efficiently in the porcine kidney cell line SK6. Pestiviruses generally counteract the cellular innate immune response by degradation of interferon regulatory factor 3 (IRF3) mediated by the viral N-terminal protease (N^pro). No degradation of IRF3 and an increased expression of the type 1 interferon-stimulated antiviral protein Mx1 was observed in porcine cells infected with PhoPeV whose genome lacks the N^pro encoding region. Infection of a CD46-deficient porcine cell line suggested that CD46, which is implicated in the viral entry of several pestiviruses, is not a major factor for the viral entry of PhoPeV. Moreover, the results of this study confirmed that the cellular factor DNAJC14 plays a crucial role in viral RNA replication of non-cytopathic pestiviruses, including PhoPeV. Full article

One of the major challenges of studying biomarkers in tumor samples is the low quantity and quality of isolated RNA, DNA, and proteins. Additionally, the extraction methods ideally should obtain macromolecules from the same tumor biopsy, allowing better-integrated data interpretation. In this work, an in-house, low-cost, mixed-type tissue crusher combining blade and beating principles was made and the simultaneous isolation of macromolecules from human cells and tissues was achieved using TRIzol. RT-qPCR, genotyping, SDS-PAGE, and Western blot analysis were used to validate the approach. For tissue samples, RNA, DNA, and proteins resulted in an average yield of 677 ng/mg, 225 ng/mg, and 1.4 µg/mg, respectively. The same approach was validated using cell lines. The isolated macromolecule validation included the detection of mRNA levels of ATP-binding cassette (ABC) transporters through RT-qPCR, genotyping of TNFR1 (rs767455), and protein visualization through SDS-PAGE following Coomassie blue staining and Western blot. This work contributed to filling a gap in knowledge about TRIzol efficiency for the simultaneous extraction of RNA, DNA, and proteins from a single human tissue sample. A low-cost, high yield, and quality method was validated using target biomarkers of multidrug resistance mechanisms. This approach might be advantageous for future biomarker studies using different tissue specimens. Full article

Inflammatory bowel disease (IBD) is increasing among mammals around the world, and domestic dogs are no exception. There is no approved cure for canine IBD with limited treatment options. Novel probiotic bacteria discovery from free-ranging animals for the treatment of IBD in domestic pets can likely yield promising probiotic candidates. Consequently, the overall aim was to isolate bacteria from free-ranging animals that could potentially be utilized as novel probiotics. Two bacteria identified as unique Paenibacillus spp. strains by small ribosomal RNA (16S) gene sequencing were isolated from the gastrointestinal tract of a North American Gray Wolf (Canis lupus). The bacteria were typed as Gram-variable, and both were catalase/oxidase positive as well as sensitive to commonly used antibiotics. The bacteria digested complex carbohydrates and lipids by standard assays. The isolated bacteria also inhibited the growth of Staphylococcus aureus and Micrococcus luteus. The whole genome sequence (WGS) length of bacterial isolate ClWae17B was 6,939,193 bp, while ClWae19 was 7,032,512 bp, both similar in size to other Paenibacillus spp. The genomes of both bacteria encoded enzymes involved with the metabolism of complex starches and lipids, such as lyases and pectinases, along with encoding antimicrobials such as lanthipeptides, lasso peptides, and cyclic-lactone-autoinducers. No pernicious virulence genes were identified in the WGS of either bacterial isolate. Phylogenetically, the most closely related bacteria based on 16S gene sequences and WGS were P. taichungensis for ClWae17B and P. amylolyticus for ClWae19. WGS analyses and phenotypic assays supported the hypothesis that the isolates described constitute two novel candidate probiotic bacteria for potential use in dogs. Full article

Asthma is a major non-communicable disease whose pathogenesis is still not fully elucidated. One of the asthma research models is precision-cut lung slices (PCLSs), and among the therapeutic options, miRNA molecules are of great interest. The aim of our study was to investigate whether inhibition of miR-223-3p and miR328a-3p affects the inflammatory response in PCLSs derived from a rat with HDM-induced allergic inflammation and a control rat. We generated rat PCLSs and transfected them with miR-223-3p and miR-328a-3p inhibitors. RNA was isolated from PCLSs and analyzed by qPCR. We also examined the proteins in the culture medium using the Magnetic Luminex Assay. The comparison between miRNA-transfected PCLSs and non-transfected controls showed significant differences in the expression of several genes associated with allergic inflammation, including Il-33, Ccl5, Prg2 and Tslp, in both the rat with allergic inflammation and the control rat. In the culture medium, we found no significant differences in protein levels between rat with allergic inflammation and the control. Our study highlighted some important issues: the need to extend the model by including more biological replicates, the need to standardize culture conditions, and the need to consider co-transfection with several miRNA inhibitors when modifying miRNAs expression in the PCLS model. Full article

Oral squamous cell carcinoma (OSCC) is a highly aggressive malignancy with poor prognosis, mainly due to the presence of cancer stem cells (CSCs), a small subpopulation of cells that contribute to therapy resistance and tumor progression. The principal objective of this study was to investigate the role of miRNA-21 in the maintenance of cancer cell stemness and the possibility of altering it. The CD44 antigen was used as a marker for CSC isolation from oral cancer cell cultures. CD44+ and CD44− populations were sorted via magnetic separation. miRNA-21 inhibition was performed in CD44+ cells via transfection. CD44+ cells possessed a significantly higher migration and invasion potential compared to CD44− cells, higher levels of miRNA-21 (p = 0.004) and β-catenin (p = 0.005), and lower levels of BAX (p = 0.015). miRNA-21 inhibition in CD44+ cells reduced migration, invasion, and colony formation while increasing apoptosis. Stemness markers were significantly downregulated following miRNA-21 inhibition: OCT4 (p = 0.013), SOX2 (p = 0.008), and NANOG (p = 0.0001), as well as β-catenin gene (CTNNB1) (p < 0.05), an important member of WNT signaling pathway. Apoptotic activity was enhanced, with a significant downregulation of the antiapoptotic Bcl-2 (p = 0.008) gene. In conclusion, miRNA-21 plays a critical role in the regulation of oral cancer CD44+ cells properties. Targeting and inhibiting miRNA-21 in CD44+ cells could represent a promising novel strategy in OSCC treatment. Full article

Hadal zones account for the deepest 45% of oceanic depth range and play an important role in ocean biogeochemical cycles. As the least-explored aquatic habitat on earth, further investigation is still required to fully elucidate the microbial taxonomy, ecological significance, metabolic diversity, and adaptation in hadal environments. In this study, a novel strain Lsc_1132^T was isolated from sediment of the Mariana Trench at 10,954 m in depth. Strain Lsc_1132^T contains heterogenous 16S rRNA genes, exhibiting the highest sequence similarities to the type strains of Neobacillus drentensis LMG 21831^T, Neobacillus dielmonensis, Neobacillus drentensis NBRC 102427^T, Neobacillus rhizosphaerae, and Neobacillus soli NBRC 102451^T, with a range of 98.60–99.10% identity. The highest average nucleotide identity (ANI), the highest digital DNA-DNA hybridization (DDH) values, and the average amino acid identity (AAI) with Neobacillus sp. PS3-40 reached 73.5%, 21.4%, and 75.54%, respectively. The major cellular fatty acids of strain Lsc_1132^T included iso-C_15:0, Summed Feature 3 (C_16:1ω6c and/or C_16:1ω7c), iso-C_17:0, anteiso-C_15:0, and iso-C_17:1ω5c. The respiratory quinone of strains Lsc_1132^T was MK-7. The G + C content of the genomic DNA was 40.9%. Based on the GTDB taxonomy and phenotypic data, strain Lsc_1132^T could represent a novel species of a novel genus, proposed as Aliineobacillus hadale gen. nov. sp. nov. (type strain Lsc_1132^T = MCCC 1K09620^T). Metabolically, strain Lsc_1132^T demonstrates a robust carbohydrate metabolism with many strain-specific sugar transporters. It also has a remarkable capacity for metabolizing amino acids and carboxylic acids. Genomic analysis reveals a streamlined genome in the organism, characterized by a significant loss of orthologous genes, including those involved in cytochrome c synthesis, aromatic compound degradation, and polyhydroxybutyrate (PHB) synthesis, which suggests its adaptation to low oxygen levels and oligotrophic conditions through alternative metabolic pathways. In addition, the reduced number of paralogous genes in strain Lsc_1132^T, together with its high protein-coding gene density, may further contribute to streamlining its genome and enhancing its genomic efficiency. This research expands our knowledge of hadal microorganisms and their metabolic strategies for surviving in extreme deep-sea environments. Full article

Glaesserella parasuis is the etiological agent of Glässer’s disease, which causes high morbidity and mortality in pigs worldwide. Macrolide resistance poses an urgent threat to their treatment, as macrolides are widely used for preventing and treating G. parasuis infections. Here, we determined the susceptibilities to five macrolides and characterized the genetic markers of macrolide resistance. The antimicrobial susceptibility of 117 G. parasuis isolates to erythromycin, tulathromycin, gamithromycin, tylosin, and tilmicosin was evaluated using broth microdilution method. Erythromycin-resistant isolates were sequenced using whole-genome sequencing. Further analysis of these sequences revealed the genetic basis of macrolide resistance in G. parasuis. Our results show that most G. parasuis isolates remained susceptible to the macrolide drugs. For commonly used agents (e.g., tylosin and tilmicosin), elevated minimum inhibitory concentrations (MICs) were observed, whereas for the newer macrolides (e.g., tulathromycin and gamithromycin), the MICs remained almost unchanged. The macrolide resistance gene erm(T) and the A2059G mutation in 23S rRNA were detected in the current study. To the best of our knowledge, integrative and conjugative element (ICE)-borne erm(T) in G. parasuis is reported for the first time in this study. Taken together, these results provide insights into the susceptibility of G. parasuis to macrolides. The presence of erm(T) on ICEs may facilitate its transfer, reducing the effectiveness of macrolide treatment. Full article

In 2020, severe diarrhea occurred in four-month-old fattening pigs from nine farms in Shandong Province, China. Fecal samples were collected from diseased pigs and tested by PCR for the presence of mammalian orthoreovirus (MRV), porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), porcine rotavirus A (PoRVA), transmissible gastroenteritis virus (TGEV), porcine kobuvirus (PKV), and pseudorabies virus (PRV). The viral RNA of MRV and PEDV was detected in the fecal samples. The genome sequences of MRV and PEDV were successfully amplified from the same fecal sample. Genomic and phylogenetic analysis showed that the MRV isolate named MRV2-SD/2020 belongs to serotype 2 MRV (MRV2) and may originate from the reassortment of human and porcine MRVs. Compared with other MRV2 strains, there were four other unique amino acid mutations (L274I, F302L, V347I, and T440M) in the receptor binding region. For the PEDV isolate named PEDV-SD/2020, the nearly complete genome was amplified from the positive fecal samples. Phylogenetic analysis showed that it was classified into the G2a genotype. Compared with CV777 and other PEDV variant strains, its spike (S) protein exhibited two unique mutations (S663T and L966M). This study first reports the co-infection of PEDV and MRV2 in the pigs and provides a new direction for the prevention and control of the diarrhea diseases. Full article