Search Results (23)

Background/Objectives: Meningitis due to the species Streptococcus is a severe central nervous system infection caused by various microorganisms belonging to Streptococcus spp. Its accurate identification is critical for effective clinical management. This study aimed to identify Streptococcus spp. causing meningitis in Greece over a nine-year period using PCR and sequencing-based methods. Methods: A total of 189 clinical samples, collected between 2015 and 2024 from patients suffering from meningitis and/or septicemia, were analyzed by the use of a combination of multiplex polymerase chain reaction (PCR) assays and tuf gene sequencing for further species identification. Results: Sample analysis identified 70 samples as S. pyogenes (18.52%) (GAS) and S. agalactiae (18.52%) (GBS), while 119 (62.96%) were recorded as non-typable Streptococcus spp. Further analysis using sequencing methods revealed that the most frequent Streptococcus spp. belonged to the mitis group (42.86%) and the pyogenic group (20.17%). A higher prevalence was observed in children aged 0–14 years old and adults over 50 years old. Conclusions: This study highlights the use of molecular diagnostics in identifying other Streptococcus spp., providing insights into age-related susceptibility and epidemiological trends. Future studies are needed to explore the pathogenic role of the identified Lactococcus spp. Full article

The taxonomic position of the green alga Capsosiphon fulvescens was first reported from Northern Europe and has since been reported from all over the world, including Korea. In Korea, C. fulvescens has been used as an essential edible economic alga for approximately 570 years, from the time of the Joseon Dynasty to the present, and is currently under development as a new aquaculture strain. Therefore, examining the taxonomic relationships between the European and Korean C. fulvescens is important. In this study, we analyzed nuclear 18S rDNA and ITS regions and compared them with the DNA sequences of authentic materials of North Atlantic C. fulvescens. Additionally, rbcL and tufA genes were sequenced to analyze genetic variations among populations. The results showed that the Korean and European C. fulvescens were different species. Moreover, the Korean C. fulvescens was distantly related to the North Atlantic C. fulvescens at the order level. Moreover, the Korean C. fulvescens formed a sister group with the North Pacific Pseudothrix borealis. Cryptic genetic diversity was observed at the intraspecific level among the Korean populations. These findings will help in tracing the origin of the Korean C. fulvescens and provide new genetic insights into this species. Full article

The development of biological pesticides is rapidly becoming an integral aspect of pest management in sustainable agriculture. This study was conducted to evaluate the effectiveness of Bacillus halotolerans strain B33 against three common seedborne fungal pathogens—Fusarium graminearum, Alternaria alternata, and Aspergillus flavus. B33 strain identity was determined using the 16S rRNA and tuf gene sequences. Commercial wheat, barley, oat, and rye seeds were artificially infected by fungal isolates and then treated with B33 overnight culture in Nutrient Broth. The obtained results indicate high efficacy against F. graminearum (83.55–94.38%) and A. alternata (85.05–96.70%), whereby the highest efficacy was noted on wheat seed and the lowest was detected on rye seed. On the other hand, B33 achieved 100% efficacy against A. flavus on barley, rye, and oat seeds, while being 96.24% effective against this pathogen on wheat. Principal component analysis indicated the highest treatment influence on A. flavus. The effect of all tested treatments on seed germination was statistically significant compared to the controls, whereby the number of germinated seeds declined as the seed infection rate increased. B. halotolerans strain B33 effectively managed seedborne fungal pathogens, thereby enhancing seed germination. Full article

The genus Borodinellopsis is extremely rare and is the subject of limited research and reports. It currently comprises only two species, Borodinellopsis texensis and Borodinellopsis oleifera, which differ from other globose algae due to their unique centrally radiating chloroplasts. In this study, we describe a new specimen in detail based on morphological data and phylogenetic analysis and identify it as B. insignis. B. insignis and B. texensis exhibit a high degree of similarity, likely due to their shared characteristics of centrally radiating chloroplasts and flagella that are significantly longer than the cell body. A phylogenetic tree constructed based on the 18S rDNA sequence indicates that B. insignis and B. texensis form a branch that is distinct from other genera, such as Tetracystis, Spongiococcum, and Chlorococcum. Phylogenetic analysis of the ITS sequence, the rbcL gene, and the tufA gene reveals that B. insignis is significantly different from B. texensis, in that it has oil droplets, smaller vegetative cells and zoospores, and distinct habitats. It is also different from B.oleifera as it has smaller vegetative cells and zoospores, turns red after cultivation, has longer flagella, and resides in different habitats. The chloroplast genomes of B. texensis and B. insignis further show significant differences, with the phylogenetic tree constructed based on the analysis of 49 protein-coding genes forming two separate branches. The collinearity of the chloroplast genomes in B. texensis and B. insignis is poor, with 15 out of the 31 homologous modules displaying inversions and complex rearrangements. Given these differences, we classify this alga as a new species and named it Borodinellopsis insignis sp. nov. Full article

Traditionally, the order Ulotrichales comprised green algae of an unbranched, uniseriate, filamentous morphology. However, since the establishment of ultrastructural features, the circumscription of this order has dramatically changed. Some genera and species have been excluded from this order and others with different morphologies (sarcinoid, branched filaments or even parenchymatous taxa) have been included. Phylogenetic analyses have confirmed the monophyly of this order, but its differentiation from the Ulvales and Acrosiphoniales remains difficult because of the lack of synapomorphies at every level (morphology, molecular signatures). To demonstrate the difficulties of placement into genera and orders, we investigated two sarcinoid taxa with the absence of zoospore formation. SSU and ITS rDNA tree topology and the ITS-2/CBC approach revealed that both strains SAG 2661 and CCAP 312/1 belong to Ulosarcina terrestrica and the newly erected genus Caulinema, respectively. The species conception using this approach was evaluated by sequencing the plastid-coding gene tufA, a commonly used barcode marker for green algae. All three molecular markers resulted in similar topologies at the generic and species levels, which is consistent with the ITS-2/CBC approach and tufA for barcoding. The reevaluation of the ultrastructural features revealed that the presence of organic scales on the surfaces of motile cells is characteristic for the order Ulotrichales and can be used for separation from the closely related orders. As a consequence of our study, we propose the new genus Caulinema for strain CCAP 312/1. Full article

Tamarisk witches’ broom, yellowing, and little leaf symptoms were observed during 2018–2023 surveys of rural deserts in central regions of Iran with the highest disease incidence up to 72% in Chah Afzal (Yazd province). A verification of the presence and identity of phytoplasmas associated with these symptoms was then performed. Tamarisk tree branch cuttings obtained from symptomatic plants sprouted up to 90.3% but with 15–25 days’ delay compared to the asymptomatic ones and showed internode shortening and witches’ broom, while the branch cuttings from asymptomatic plants had normal growth and sprouted up to 97.8%. Phytoplasma transmission by dodder bridges to periwinkle did not succeed, while nested polymerase chain reaction on the phytoplasma ribosomal gene followed by RFLP and phylogenetic analyses revealed the presence of ‘Candidatus Phytoplasma asteris’, ‘Ca. P. australasiae=australasiaticum’, and ‘Ca. P. trifolii’ (ribosomal subgroups 16SrI-B, 16SrII-D, and 16SrVI-A, respectively) in the samples from symptomatic plants only. Further amplifications were performed on selected phytoplasma-positive samples on tuf and secA genes, and the produced sequences indicated the presence of mixed phytoplasma infection in some of the samples. In particular, in the tuf gene, a mixed infection of ‘Ca. P. australasiae=australasiaticum’ and ‘Ca. P. trifolii’ was detected, while in the secA gene, the presence of ‘Ca. P. asteris’ or ‘Ca. P. tritici’ strains was identified. The first-time detection of diverse phytoplasma strains in symptomatic T. aphylla suggests that this species represent a relevant source of infection for the agricultural crops and for landscape plants especially when temperature allows insect vector transmission, and therefore, it represents a risk in every environment especially in the frame of climatic changes. Full article

Ivory shell (Babylonia areolata) is a commercially important aquaculture species mainly found on the southeast coast of China. However, it has been greatly affected by vibriosis in recent years. In this study, FP17 (a potential pathogen) was isolated from a dying ivory shell with “acute death syndrome” and confirmed as a pathogen via infectious experiment. Furthermore, phylogenetic analysis based on the average nucleotide identity (ANI) sequencing of the 16S rRNA gene and housekeeping genes (ftsz, gapA, gyrB, mreB, pyrH, rpoA, and topA) indicated that FP17 was identical to Vibrio tubiashii. Transmission electron microscopy showed that FP17 is curved and has a short rod shape, with a single flagellum. Besides, the calculated LD₅₀ after the intramuscular injection of FP17 was 2.11 × 10⁶ CFU/g at 14 d. The genome of the FP17 strain consists of two chromosomes and one plasmid with 5,261,336 bp and 45.08% GC content, including 4824 open reading frames (ORFs) and 150 non-coding RNAs (ncRNA). Genome mining revealed that 120 candidate gene clusters, including vibrioferrin and flagellum-related proteins, are responsible for virulence. Comparative genomic analysis showed that vibrioferrin genes, such as pvs and type Ⅵ secretion system protein genes (vas), are specific in V. tubiashii FP17 but not in the ATCC19109 strain. Furthermore, 92 antimicrobial resistance (AMR) genes, such as tufA, tet(35), crp, etc., were mapped within the genome as the potential candidate for virulence, consistent with antibiotic susceptibility assay. This is the first study to describe the complete genome sequence of V. tubiashii infecting ivory shell. The genetic characteristics, virulence factors, and antimicrobial resistance of the V. tubiashii strain FP17 were also explored. Full article

Green tides are a serious global ecological disaster; the largest occur in the Southern Yellow Sea (SYS). Early-stage green tides in the SYS are composed of four species (Ulva prolifera, Ulva flexuosa, Ulva linza, and Ulva compressa). We found that U. aragoensis is a constituent species of green tides in the SYS based on molecular data. Furthermore, this study re-evaluated the proportion of U. aragoensis in green tides and found that it was more prevalent in micro-propagules cultured from surface seawater during an early-stage green tide in 2021. The internal transcribed spacers, tufA, 18S, rbcL, large subunit, psbA, and rps2-trnL gene sequences were compared; the tufA and rbcL gene sequences were the most suitable DNA barcodes for distinguishing U. aragoensis. A haplotype analysis of the sequences of floating U. aragoensis and its micro-propagules was performed to study the correlation between green tide macroalgae and micro-propagules; close haplotype similarities occurred between them. This study further clarified the species composition of SYS green tides and provided a reference for assessing the relationship between micro-propagules and green tide macroalgae. Full article

To reveal the distribution and transmission pathway of Paulownia witches’-broom (PaWB) disease, which is caused by phytoplasmas related to genetic variation, and the adaptability to the hosts and environments of the pathogenic population in different geographical regions in China, in this study, we used ten housekeeping gene fragments, including rp, fusA, secY, tuf, secA, dnaK, rpoB, pyrG, gyrB, and ipt, for multilocus sequence typing (MLST). A total of 142 PaWB phytoplasma strains were collected from 18 provinces or municipalities. The results showed that the genetic diversity was comparatively higher among the PaWB phytoplasma strains, and substantially different from that of the other 16SrI subgroup strains. The number of gene variation sites for different housekeeping genes in the PaWB phytoplasma strains ranged from 1 to 14 SNPs. Among them, rpoB (1.47%) and dnaK (1.12%) had higher genetic variation, and rp (0.20%) had the least genetic variation. The tuf and rpoB genes showed the fixation of positively selected beneficial mutations in the PaWB phytoplasma populations, and all housekeeping genes except tuf followed the neutral evolutionary model. We found an absence of recombination among PaWB phytoplasma sequence types (STs) for each housekeeping gene except dnaK, and no evidence for such recombination events for concatenated sequences of PaWB phytoplasma strains. The 22 sequence types were identified among the concatenated sequences of seven housekeeping genes (rp, fusA, secY, secA, tuf, dnaK, and rpoB) from 105 representative strains. We analyzed all 22 STs by goeBURST algorithm, forming two clonal complexes (CCs) and three singletons. Among them, ST1, as the primary founder of CC1, had the widest geographical distribution, accounting for 72.38% of all strains, with a high frequency of shared sequence type. The results of phylogenetic analysis of the concatenated sequences further revealed that the 105 strains were clustered into two representative lineages of PaWB phytoplasma, with obvious geographical differentiation. The ST1 strains of highly homogeneous lineage-1 were a widespread and predominant population in diseased areas. Lineage-2 contained strains from Jiangxi, Fujian, and Shaanxi provinces, highlighting the close genetic relatedness of the strains in these regions, which was also consistent with the results of most single-gene phylogenetic analysis of each gene. We also found that the variability in the northwest China population was higher than in other geographical populations; the range of genetic differentiation between the south of the Yangtze River population and the Huang-huai-hai Plain (or southwest China) population was relatively large. The achieved diversity and evolution data, as well as the MLST technique, are helpful for epidemiological studies and guiding PaWB disease control decisions. Full article

‘Candidatus Phytoplasma solani’ (‘Ca. P. solani’) is a crop pathogen that is a member of the 16SrXII-A ribosomal subgroup. It is also known as stolbur phytoplasma and causes yield losses in several important crops, especially in Solanaceous crops. Different strains of the pathogen are regularly reported all over the world, particularly in the Mediterranean region. In this study, the determination of genetic diversity for the pathogen infecting tomatoes and potatoes was carried out by using multilocus sequence typing analysis for the Tuf, SecY, and Vmp1 genes to gain insight into the epidemiology of ‘Ca. P. solani’ in Turkey. Genetic diversity of the phytoplasmas was investigated by sequence-based phylogenetic analyses and in silico RFLP analysis of related genes. It was determined that all ‘Ca. P. solani’-related strains infecting tomatoes and potatoes were tuf-b, which is linked to field bindweed (Convolvulus arvensis L.). Tomato or potato-infecting ‘Ca. P. solani’-related strains showed similarities with each other; however, the isolates collected from different plants showed genetic differences in terms of the SecY gene. This study indicates that the highest genetic variability of collected samples was found in the Vmp1 gene. RsaI-RFLP analysis of TYPH10F/R amplicons showed that potato-infecting ‘Ca. P. solani’-related strains were found to be similar to some existing V types. However, the V-type of tomato-infecting isolates is not similar to any previously reported V-type. The results indicate that there could be an important genetic diversity of ‘Ca. P. solani’-related phytoplasmas in Turkey. This could indicate various ways in which the pathogen has adapted to the two host plants as a consequence of the various Vmp1 gene rearrangements seen in these two plant hosts. Obtained results also indicate that the epidemiology of ‘Ca. P. solani’-related phytoplasmas in the tomato and potato agroecosystem may be better understood with the use of molecular data on the complex of vmp-types. Full article

Turfgrass landscapes have expanded rapidly in recent decades and are a major vegetation type in urbanizing ecosystems. While turfgrass areas provide numerous ecosystem services in urban environments, ecological side effects from intensive management are raising concerns regarding their sustainability. One potentially promising approach to ameliorate the ecological impact and decrease the use of agricultural chemicals is to take advantage of naturally evolved turfgrass-associated microbes by harnessing beneficial services provided by microbiomes. Unfortunately, especially compared to agricultural crops, the microbiomes of turfgrasses are not well understood. Here, we analyzed microbial communities inhabiting the leaf and root endospheres as well as soil in two bermudagrass cultivars, ‘Latitude 36’ and ‘TifTuf’, which exhibit distinct tolerance to nematode damage, with the goal of identifying potential differences in the microbiomes that might explain their distinct phenotype. We used 16S rRNA gene V4 and ITS2 amplicon sequencing to characterize the microbiomes in combination with microbial cultivation efforts to identify potentially beneficial endophytic fungi and bacteria. Our results show that Latitude 36 and TifTuf showed markedly different fungal microbiomes, each harboring unique taxa from Ascomycota and Glomeromycota, respectively. In contrast, less difference was observed from bacterial and archaeal microbiomes, which were dominated by Bacteroidetes and Thaumarchaeota, respectively. The TifTuf microbiomes exhibited lower microbial diversity compared to Latitude 36. Many sequences could not be classified to a higher taxonomic resolution, indicating a relatively high abundance of hitherto undescribed microorganisms. Our results provide new insights into the structure and composition of turfgrass microbiomes but also raise important questions regarding the functional attributes of key taxa. Full article

The knowledge of phytoplasma genetic variability is a tool to study their epidemiology and to implement an effective monitoring and management of their associated diseases. ‘Candidatus Phytoplasma solani’ is associated with “bois noir” disease in grapevines, and yellowing and decline symptoms in many plant species, causing serious damages during the epidemic outbreaks. The epidemiology of the diseases associated with this phytoplasma is complex and related to numerous factors, such as interactions of the host plant and insect vectors and spreading through infected plant propagation material. The genetic variability of ‘Ca. P. solani’ strains in different host species and in different geographic areas during the last two decades was studied by RFLP analyses coupled with sequencing on vmp1, stamp, and tuf genes. A total of 119 strains were examined, 25 molecular variants were identified, and the variability of the studied genes was linked to both geographic distribution and year of infection. The crucial question in ‘Ca. P. solani’ epidemiology is to trace back the epidemic cycle of the infections. This study presents some relevant features about differential strain distribution useful for disease monitoring and forecasting, illustrating and comparing the phytoplasma molecular variants identified in various regions, host species, and time periods. Full article

Rubbery taproot disease of sugar beet (RTD), associated with ‘Candidatus Phytoplasma solani’, appeared in 2020 on an epidemic scale in northern Serbia and southern Slovakia, situated at opposite edges of the Pannonian Plain. In the affected locations where the disease was assessed, symptomatic sugar beets were analysed for phytoplasma infection. Additionally, multilocus sequence analyses of ‘Ca. P. solani’ strains on epidemiologically informative marker genes (tuf, stamp and vmp1) were performed. Symptomatic sugar beets from other countries of the Pannonian Plain (Croatia, Hungary and Austria), one sample from Germany, and red beets from Serbia were included in the analyses. ‘Ca. P. solani’ was detected in sugar beet in all assessed countries, as well as in red beet. Molecular analyses revealed the high genetic variability of ‘Ca. P. solani’ with the presence of all four tuf-types (a, b1, b2 and d), 14 stamp genotypes (seven new) and five vmp1 profiles (one new). The most common multilocus genotype in Serbia, Slovakia, Croatia, and Hungary was dSTOLg (tuf-d/STOL/V2-TA). It was dominant on sites with epidemic RTD outbreaks in the Pannonian Plain and in several sugar beet fields with non-epidemic RTD occurrence suggesting the prevalence of a particular epidemiological pathway during the epidemic’s phases. Full article

Investigation of changes in the skin microbiome following treatment of atopic dermatitis (AD) with dupilumab may provide valuable insights into the skin microbiome as a therapeutic target. The aim of this study is to assess changes in the AD skin microbiome following treatment of AD with dupilumab (n = 27). E-swabs were collected from nose, lesional, and nonlesional skin before and after 16 weeks of dupilumab therapy, and the microbiome was analyzed by 16S rRNA and tuf gene sequencing. Data for 17 patients with milder disease receiving treatment with non-targeted therapies are also presented. The results show that both groups experienced clinical improvement (p < 0.001) following dupilumab therapy and that Shannon diversity increased and bacterial community structure changed. The relative abundance of the genus Staphylococcus (S.) and S. aureus decreased, while that of S. epidermidis and S. hominis increased. No significant changes were observed for patients receiving non-targeted treatments. The increases in S. epidermidis and S. hominis and the decrease in S. aureus correlated with clinical improvement. Furthermore, changes in S. hominis and S. epidermidis correlated inversely with S. aureus. In conclusion, treatment with dupilumab significantly changed the skin microbiome and decreased S. aureus. Our results suggest a favorable role of commensal staphylococci in AD. Full article

The skin microbiota of atopic dermatitis (AD) patients is characterized by increased Staphylococcus aureus colonization, which exacerbates disease symptoms and has been linked to reduced bacterial diversity. Skin bacterial communities in AD patients have mostly been described at family and genus levels, while species-level characterization has been limited. In this study, we investigated the role of the bacteria belonging to the Staphylococcus genus using targeted sequencing of the tuf gene with genus-specific primers. We compared staphylococcal communities on lesional and non-lesional skin of AD patients, as well as AD patients with healthy controls, and determined the absolute abundance of bacteria present at each site. We observed that the staphylococcal community, bacterial alpha diversity, and bacterial densities were similar on lesional and non-lesional skin, whereas AD severity was associated with significant changes in staphylococcal composition. Increased S. aureus, Staphylococcus capitis, and Staphylococcus lugdunensis abundances were correlated with increased severity. Conversely, Staphylococcus hominis abundance was negatively correlated with severity. Furthermore, S. hominis relative abundance was reduced on AD skin compared to healthy skin. In conclusion, various staphylococcal species appear to be important for skin health. Full article