Pseudonectria keratitis-emerging pathogenic fungi in the eye.

BACKGROUND: Infectious keratitis, a significant contributor to blindness, with fungal keratitis accounting for nearly half of cases, poses a formidable diagnostic and therapeutic challenge due to its delayed clinical presentation, prolonged culture times, and the limited availability of effective antifungal medications. Furthermore, infections caused by rare fungal strains warrant equal attention in the management of this condition. CASE PRESENTATION: A case of fungal keratitis was presented, where corneal scraping material culture yielded pink colonies. Lactophenol cotton blue staining revealed distinctive spore formation consistent with the Fusarium species. Further analysis using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) identified the causative agent as Fusarium proliferatum. However, definitive diagnosis of Pseudonectria foliicola infection was confirmed through ITS sequencing. The patient's recovery was achieved with a combination therapy of voriconazole eye drops and itraconazole systemic treatment. CONCLUSION: Pseudonectria foliicola is a plant pathogenic bacterium that has never been reported in human infections before. Therefore, ophthalmologists should consider Pseudonectria foliicola as a possible cause of fungal keratitis, as early identification and timely treatment can help improve vision in most eyes.

Molecular characterization of Bertiella studeri infecting a primate in South India.

Bertiella spp. is a mite-borne cestode parasite that inhabits the small intestine of wide range of mammals, including non-human primates. In the present study, the morphological and molecular analysis of Bertiella studeri recovered from the small intestine of a bonnet macaque (Macaca radiata) from Wayanad, Kerala (South India) was performed. Acetic alum carmine staining identified the cestode morphologically based on the characters like broader proglottids, which contain irregularly alternating genital pores, single set of reproductive organs, 280 testes and a tubular transverse uterus. Molecular characterization was done using 18SrRNA, ITS1-5.8S and COX1 genes. Phylogenetic trees were constructed using MEGA X based on the Maximum Likelihood (ML) method (Hasegawa-Kishino-Yano (HKY) model). Cytochrome oxidase I gene could detect the existence of genetic variation in the parasite from two different hosts viz., monkey (Kerala, Argentina, and Kenya) and human (Sri Lanka). A minimum spanning network of haplotypes was generated by the haplotype networking with the above sequences using the popARTv1.7. Haplotype analysis based on COX1 revealed that the parasite haplotype was different in each country with highest population frequency in Sri Lanka.

Morphological, ultrastructural, and phylogenetic analysis of Ascaridia columbae infecting domestic pigeons (Columba livia domestica).

Ascaridia species are the most common nematodes infecting pigeons. The current study investigated specific identity of nematode parasites collected from domestic pigeons (Columba livia domestica) in Al-Qassim Region, Saudi Arabia. Out of 354 pigeons, 13.3 % were infected with nematode parasites. The morphological structure and genetic relationship of nematode worms were studied using conventional methods (Light and scanning electron microscopes) coupled with the newly introduced molecular method. Microscopical and ultrastructure observations showed that the present nematode worms belong to the genus Ascaridia and have all the characteristic features of Ascaridia columbae. Moreover, Random Amplifier morphometric (RAPD) PCR analysis revealed that the present A. columbae had a close identity of up to 98.3 % to Ascaridia columbae JX624729 for Cox-1 gene regions, and up to 98.3 % to Ascaridia nymphii LC057210, and Ascaridia galli EF180058 for ITS1-5.8s- ITS2 rDNA gene regions. Phylogenetic analysis supported the placement of this Ascaridia species within Ascaridiidae family with close relationships to other nematode species obtained from GenBank. Finally, our study recommends using molecular analysis in helminths identification as the main methodology for correct identification especially in closely related species.

Exploring the feasibility of utilizing universal primers in detecting mucormycosis pathogens: An in-silico analysis.

This study aimed to design and evaluate a universal primer for Polymerase Chain Reaction (PCR)- based detection of mucormycosis-causing fungi by targeting their Internal Transcribed Spacer (ITS) sequences. In-silico analysis was conducted to assess primer suitability. Using Clustal Omega and Primer-BLAST, ITS sequences of 32 fungi species causing mucormycosis were aligned and subjected to primer design. Generated primers were sorted and in silico PCR simulations were performed to identify primers capable of amplifying all fungal species. Instead of identifying one pair of universal primer, in silico PCR analysis identified a panel of 14 primer pairs designed from full-length ITS sequences, and a panel of 12 primer pairs designed from conserved regions, that could detect 31 species. The study recommends a panel of 12 primers for multiplex-PCR to detect mucormycosis-causing fungi instead of a long list of PCR analyses for each fungus in diagnosing mucormycosis.

Evaluation of ITS1 rDNA primers for the detection and identification of African trypanosomes in mammalian hosts and tsetse flies.

Although several primers targeted to the internal transcribed-spacer 1 (ITS1) of the ribosomal DNA (rDNA) have been designed to improve the detection of African trypanosomes, no study tried to compare their agreement level and ability to amplify different trypanosome species in tsetse flies and mammals in various epidemiological settings. This study was designed to fill this gap, by targeting tsetse-infested areas of Cameroon. For this, archived DNA samples reporting at-least one trypanosome species with species-specific PCR primers were reviewed. Ten sets of primers targeting different ITS1 rDNA sequences of trypanosomes were selected for assessment using single-round and nested-PCR method. Amplification rates (sensitivity) and agreement level of different ITS1 assays were compared using Cohen's-Kappa and McNemar's x2 statistic. Little agreement level (k=0.05-0.52) were observed between different ITS1-primers PCRs detection of African trypanosome species despite significant (X2=54.3, p=0.0001) high amplification rate 91.6% (339/370). This sensitivity varied from quite low for T. simiae (11.9%) and T. vivax (27.3%) to fairly good for T. congolence (51.9%), Trypanozoon (32.4%) and T. theileri (40.3%). Primers set targeting ITS1-A sequence of trypanosome species recorded the highest sensitivity (50.5%) with fairly good agreement compared to 39.2% for ITS1-C (k=0.52), 32.4% for ITS1-R (k=0.47), 29.7% for ITS1-N (k=0.48) and 23.0% for ITS1-KIN (k=0.43) respectively. This study revealed a diversity in the sensitivity of different trypanosome species with different sets of ITS-primers enhancing the need to use the same sets of primers in different bio-ecological settings. The use of nested-PCR instead of single-round PCR enabled improvement of trypanosome infections detection in both tsetse and mammals. Among the sets of ITS1-primers tested, those designed by to amplify ITS1-A can be considered as the most appropriate for the detection of trypanosome infections in mammals and tsetse flies.

Three New Species of Tuber Discovered in Alpine Fir Forests in Yunnan, China.

Three new species of Tuber, T. albicavum, T. laojunshanense, and T. umbilicicavatum belonging to the Puberulum phylogroup, are described based on specimens collected in alpine Abies forests at 3600-4000 m, Northwest Yunnan, China. T. albicavum is distinguished by its ascomata with a single chamber of 0.5-1.8 cm diameter, with an apical opening of 0.2-0.6 cm in diameter, and light golden-brown alveolate reticulate ascospores up to 30 µm in length; T. laojunshanense is characterized by having ascomata with a slightly tomentose surface, sometimes with a white navel, a relatively thick peridium, up to 280 µm, and yellow-brown spores with alveolate reticulate ornamentation, up to 34 µm in length; T. umbilicicavatum is characterized by smooth ascomata with a distinct white navel, a relatively thin peridium, up to 110 µm, and golden or golden-brown alveolate reticulate ascospores, up to 40 µm in length. The molecular analysis of the internal transcribed spacer region also supports that these three new species differ from previously described Tuber species.

Phenotypical Differences at the Physiological and Clinical Level between Two Genetically Closely Related Clavispora lusitaniae Strains Isolated from Patients.

The occurrence of non-albicans species within the genus Candida poses a major challenge in the clinical setting. Clavispora lusitaniae, formerly known as Candida lusitaniae, has gained attention due to its potential multidrug resistance, particularly to amphotericin B (AmB). While intrinsic resistance to AmB is rare, secondary resistance may develop during treatment due to phenotypic rearrangement and the reorganization of the cell wall. Although there is evidence of genetic variability within C. lusitaniae, comprehensive genomic studies are lacking. This study examines the physiological differences within Candida species and focuses on the medical implications of this. Using two case reports, significant physiological and resistance differences between two strains of C. lusitaniae are demonstrated, highlighting the need for further research into genetic variability. While one strain showed higher resistance to antifungal drugs and slower growth compared to Strain 2, both strains showed minimal beta-D-glucan production, suggesting alternative pathogenic mechanisms. The study underlines the importance of understanding microbial adaptation and selection mechanisms, especially in the clinical setting, to effectively combat emerging drug resistance. Furthermore, research is needed to clarify the complex interplay between environmental causes, physiological traits, and the mechanisms of drug resistance in C. lusitaniae.

Phylogenetic and Pathogenic Evidence Reveals Novel Host-Pathogen Interactions between Species of Lasiodiplodia and Citrus latifolia Dieback Disease in Southern Mexico.

Mexico ranks second in the world for Persian lime (Citrus latifolia) exports, making it the principal citrus exporter within the national citrus industry, exporting over 600,000 tons per year. However, diseases are the main factor reducing production, resulting in significant economic losses. Among these diseases, fungal diseases like dieback, caused by species of Lasiodiplodia, are an emerging issue in Persian lime. Symptoms include gummosis, twig and branch dieback, cankers, the necrosis of bark and wood, fruit mummification, and tree decline. The aim of this study was to investigate the occurrence and pathogenicity of the fungal species associated with twig and branch dieback, cankers, and decline of Persian lime trees in southern Mexico, and to elucidate the current status of the Lasiodiplodia species causing the disease in Mexico. During June, July, and August of 2023, a total of the 9229 Persian lime trees were inspected across 230 hectares of Persian lime orchards in southern Mexico, and symptoms of the disease were detected in 48.78% of the trees. Branches from 30 of these Persian lime trees were collected. Fungal isolates were obtained, resulting in a collection of 40 strains. The isolates were characterized molecularly and phylogenetically through the partial regions of four loci: the internal transcribed spacer region (ITS), the ß-tubulin gene (tub2), the translation elongation factor 1-alpha gene (tef1-α), and the DNA-directed RNA polymerase II second largest subunit (rpb2). Additionally, pathogenicity was assessed, successfully completing Koch's postulates on both detached Persian lime branches and certified 18-month-old Persian lime plants. Through multilocus molecular phylogenetic identification, pathogenicity, and virulence tests, five species were identified as causal agents: L. iraniensis, L. lignicola, L. mexicanensis, L. pseudotheobromae, and L. theobromae. This study demonstrates that in southern Mexico, at least five species of the genus Lasiodiplodia are responsible for dieback in Persian lime. Additionally, this is the first report of L. lignicola and L. mexicanensis as causal agents of the disease in citrus, indicating novel host interactions between species of Lasiodiplodia and C. latifolia.

Exhaustive identification and characterization of Colletotrichum siamense and Colletotrichum fructicola as causative agents of circular leaf spot disease of rubber tree (Hevea brasiliensis) in India.

The rubber tree (Hevea brasiliensis) is one of the major domesticated crops planted commercially for the production of natural rubber (NR) worldwide. In recent years, rubber trees in the Southern states of India and other rubber-producing countries have experienced a severe leaf spot disease, characterized by the appearance of several brown circular spots in the initial stage, which later spread all over the lamina of fully matured leaves, leading to yellowing and defoliation. The causal organism of this Circular Leaf Spot (CLS) disease has not been conclusively identified in any previous studies. In this study, we collected infected leaf samples from various locations in the South Indian states. We aimed to identify the actual fungal pathogen that causes the CLS disease on rubber trees. Based on the morphological and molecular analysis of the most frequently isolated fungi from infected leaf samples were identified as Colletotrichum siamense and Colletotrichum fructicola. Pathogenicity tests also confirmed the involvement of isolated Colletotrichum spp. in the development of CLS disease. These findings provide valuable insights into understanding the CLS disease and its impact on rubber cultivation. To our knowledge, it is the first report of C. siamense and C. fructicola associated with CLS disease of rubber trees in India.

Genotypic Identification of Trees Using DNA Barcodes and Microbiome Analysis of Rhizosphere Microbial Communities.

DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. Two of the four trees were identified as Acer rubrum and Fagus sylvatica. However, Quercus was only identified at the genus level, and the fourth tree did not show similar identification between barcodes. Next-generation sequencing of 16S rRNA genes showed that the predominant bacterial communities in the rhizosphere mainly consisted of the Pseudomonadota, Actinomycetota, Bacteroidota, and Acidobacteriota. A. rubrum showed the most diverse bacterial community while F. sylvatica was less diverse. The genus Rhodoplanes showed the highest relative bacterial abundance in all trees. Fungal ITS sequence analysis demonstrated that the communities predominantly consisted of the Ascomycota and Basidiomycota. Quercus showed the highest fungi diversity while F. sylvatica showed the lowest. Russula showed the highest abundance of fungi genera. Average similarity values in the rhizosphere for fungi communities at the phylum level were higher than for bacteria. However, at the genus level, bacterial communities showed higher similarities than fungi. Similarity values decreased at lower taxonomical levels for both bacteria and fungi, indicating each tree has selected for specific bacterial and fungal communities. This study confirmed the distinctiveness of the microbial communities in the rhizosphere of each tree and their importance in sustaining and supporting viability and growth but also demonstrating the limitations of DNA barcoding with the primers used in this study to identify genus and species for some of the trees. The optimization of DNA barcoding will require additional DNA sequences to enhance the resolution and identification of trees at the study site.

18S and ITS2 rRNA gene sequence-structure phylogeny of the Phaeophyceae (SAR, Stramenopiles) with special reference to Laminariales.

The phylogeny of brown algae (Phaeophyceae) has undergone extensive changes in the recent past due to regular new scientific insights. We used nuclear 18S rDNA with an extensive dataset, aiming to increase the accuracy and robustness of the reconstructed phylogenetic trees using a simultaneous sequence-structure approach. Individual secondary structures were generated for all 18S rDNA sequences. The sequence-structure information was encoded and used for an automated simultaneous sequence-structure alignment. Neighbor-joining and profile neighbor-joining trees were calculated based on 186 phaeophycean sequence-structure pairs. Additionally, sequence-structure neighbor-joining, maximum parsimony and maximum likelihood trees were reconstructed on a representative subset. Using a similar approach, ITS2 rDNA sequence-structure information was used to reconstruct a neighbor-joining tree including 604 sequence-structure pairs of the Laminariales. Our study results are in significant agreement with previous single marker 18S and ITS2 rDNA analyses. Moreover, the 18S results are in wide agreement with recent multi-marker analyses. The bootstrap support was significantly higher for our sequence-structure analysis in comparison to sequence-only analyses in this study and the available literature. This study supports the simultaneous inclusion of sequence-structure data at least for 18S to obtain more accurate and robust phylogenetic trees compared to sequence-only analyses.

Occurrence and genotyping of Enterocytozoon bieneusi in flying squirrels (Trogopterus xanthipes) from China.

Enterocytozoon bieneusi is an obligate intracellular microsporidian parasite with a worldwide distribution. As a zoonotic pathogen, E. bieneusi can infect a wide range of wildlife hosts through the fecal-oral route. Although the feces of flying squirrels (Trogopterus xanthipes) are considered a traditional Chinese medicine (as "faeces trogopterori"), no literature is available on E. bieneusi infection in flying squirrels to date. In this study, a total of 340 fresh flying squirrel fecal specimens from two captive populations were collected in Pingdingshan city, China, to detect the prevalence of E. bieneusi and assess their zoonotic potential. By nested PCR amplification of the ITS gene, six specimens tested positive, with positive samples from each farm, with an overall low infection rate of 1.8%. The ITS sequences revealed three genotypes, including known genotype D and two novel genotypes, HNFS01 and HNFS02. Genotype HNFS01 was the most prevalent (4/6, 66.7%). Phylogenetic analysis showed that all genotypes clustered into zoonotic Group 1, with the novel genotypes clustering into different subgroups. To our knowledge, this is the first report of E. bieneusi infection in flying squirrels, suggesting that flying squirrels could act as a potential reservoir and zoonotic threat for E. bieneusi transmission to humans in China.

Title: Occurrence et génotypage d'Enterocytozoon bieneusi chez les écureuils volants (Trogopterus xanthipes) de Chine. Abstract: Enterocytozoon bieneusi est un parasite microsporidien intracellulaire obligatoire présent dans le monde entier. En tant qu'agent pathogène zoonotique, E. bieneusi peut infecter un large éventail d'hôtes sauvages par la voie fécale-orale. Bien que les excréments d'écureuils volants (Trogopterus xanthipes) soient considérés comme un ingrédient de médecine traditionnelle chinoise (comme « faeces trogopterori ¼), aucune littérature n'est disponible à ce jour sur l'infection par E. bieneusi chez les écureuils volants. Dans cette étude, un total de 340 spécimens fécaux frais d'écureuils volants provenant de deux populations captives ont été collectés dans la ville de Pingdingshan, en Chine, pour détecter la prévalence d'E. bieneusi et évaluer leur potentiel zoonotique. Par amplification PCR nichée du gène ITS, six échantillons se sont révélés positifs, avec des échantillons positifs dans chaque ferme, et un taux d'infection global faible, à 1,8 %. Les séquences ITS ont révélé trois génotypes, dont le génotype D connu et deux nouveaux génotypes, HNFS01 et HNFS02. Le génotype HNFS01 était le plus répandu (4/6, 66,7 %). L'analyse phylogénétique a montré que tous les génotypes se regroupaient dans le groupe zoonotique 1, les nouveaux génotypes se regroupant en différents sous-groupes. À notre connaissance, il s'agit du premier rapport d'infection par E. bieneusi chez des écureuils volants, ce qui suggère que les écureuils volants pourraient agir comme un réservoir potentiel et une menace zoonotique pour la transmission d'E. bieneusi aux humains en Chine.

Comparative microbiome diversity in root-nodules of three Desmodium species used in push-pull cropping system.

Background: Desmodium species used as intercrops in push-pull cropping systems are known to repel insect-pests, suppress Striga species weeds, and shift soil microbiome. However, the mechanisms through which Desmodium species impact the soil microbiome, either through its root exudates, changes in soil nutrition, or shading microbes from its nodules into the rhizosphere, are less understood. Here, we investigated the diversity of root-nodule microbial communities of three Desmodium species- Desmodium uncinatum (SLD), Desmodium intortum (GLD), and Desmodium incanum (AID) which are currently used in smallholder maize push-pull technology (PPT). Methods: Desmodium species root-nodule samples were collected from selected smallholder farms in western Kenya, and genomic DNA was extracted from the root-nodules. The amplicons underwent paired-end Illumina sequencing to assess bacterial and fungal populations. Results: We found no significant differences in composition and relative abundance of bacterial and fungal species within the root-nodules of the three Desmodium species. While a more pronounced shift was observed for fungal community compositions compared to bacteria, no significant differences were observed in the general diversity (evenness and richness) of fungal and bacterial populations among the three Desmodium species. Similarly, beta diversity was not significantly different among the three Desmodium species. The root-nodule microbiome of the three Desmodium species was dominated by Bradyrhizobium and Fusarium species. Nevertheless, there were significant differences in the proportion of marker gene sequences responsible for energy and amino acid biosynthesis among the three Desmodium species, with higher sequence proportions observed in SLD. Conclusion: There is no significant difference in the microbial community of the three Desmodium species used in PPT. However, root-nodule microbiome of SLD had significantly higher marker gene sequences responsible for energy and amino acid biosynthesis. Therefore, it is likely that the root-nodules of the three Desmodium species host similar microbiomes and influence soil health, consequently impacting plant growth and agroecosystem functioning.

Suggestions and Comparisons of Two Algorithms for the Simplification of Bluetooth Sensor Data in Traffic Cordons.

Bluetooth sensors in intelligent transportation systems possess extensive coverage and access to a large number of identity (ID) data, but they cannot distinguish between vehicles and persons. This study aims to classify and differentiate raw data collected from Bluetooth sensors positioned between various origin-destination (i-j) points into vehicles and persons and to determine their distribution ratios. To reduce data noise, two different filtering algorithms are proposed. The first algorithm employs time series simplification based on Simple Moving Average (SMA) and threshold models, which are tools of statistical analysis. The second algorithm is rule-based, using speed data of Bluetooth devices derived from sensor data to provide a simplification algorithm. The study area was the Historic Peninsula Traffic Cord Region of Istanbul, utilizing data from 39 sensors in the region. As a result of time-based filtering, the ratio of person ID addresses for Bluetooth devices participating in circulation in the region was found to be 65.57% (397,799 person IDs), while the ratio of vehicle ID addresses was 34.43% (208,941 vehicle IDs). In contrast, the rule-based algorithm based on speed data found that the ratio of vehicle ID addresses was 35.82% (389,392 vehicle IDs), while the ratio of person ID addresses was 64.17% (217,348 person IDs). The Jaccard similarity coefficient was utilized to identify similarities in the data obtained from the applied filtering approaches, yielding a coefficient (J) of 0.628. The identity addresses of the vehicles common throughout the two date sets which are obtained represent the sampling size for traffic measurements.

Study on the antidepressant activity of (2R,6R; 2S,6S)-Hydroxynorketamine (HNK) and its derivatives.

OBJECTIVE: This study mainly explores (2R,6R; 2S,6S)-HNK and its compounds whether there are antidepressant effects. METHODS: Four HNK compounds were obtained from 2-(Chlorophenyl) Cyclopentylmethanone. Forced swimming test, locomotor sensitization test, and conditioned location preference test were used to screen the antidepressant activity of the synthesized target compounds. RESULTS: In the case of 10 mg HNK treatment, compared with saline, the immobile time of mice in the HNK group, I5 group and I6 group at 1 h and 7 days had statistical significance. In the case of 10 mg HNK treatment, compared with saline, the immobile time of compound C and D groups in the glass cylinder area was significantly different. In the locomotor sensitization test, the movement distance of compound C and D groups on day 15 and day 7 mice increased significantly compared with the first day. In the conditioned place preference experiment, compound C and compound D induced conditioned place preference in mice compared with the Veh group. CONCLUSION: The results of the forced swimming test, locomotor sensitization test, and conditioned location preference test showed that compounds C and D may have certain anti-depressant activity. However, HNK exerts a rapid and significant antidepressant effect within 1 week, but the duration is short.

A case of Aspergillus quadrilineatus pulmonary infection in China.

A 91-year-old Chinese male was hospitalized on June 28, 2021, due to a sudden fever. The patient had a long history of smoking, a 10-year history of type 2 diabetes, a family history of hypertension, and a history of coronary heart disease and lower extremity arterial occlusive disease. He presented with cough, sputum, and dry and wet rales in both lungs. A computed tomography scan revealed multiple infectious lesions in both lungs and a small pleural effusion. His procalcitonin level was 1.75 ng/mL. Microscopic examination of the sputum revealed abundant fungal spores and hyphae. Sputum culture results revealed Aspergillus quadrilineatus, which was confirmed by matrix-assisted laser desorption/ionization time-of-flight and internal transcribed spacer gene sequencing. Fungal drug sensitivity testing revealed that azoles (excluding fluconazole) and echinocandins exhibited high activity against Aspergillus quadrilineatus. The patient's condition improved following intravenous voriconazole treatment for 2 weeks, after which he was discharged. Subsequently, the patient was hospitalized six times for pulmonary infections, with the most recent hospitalization being on March 8, 2024. The symptoms improved, and the patient was discharged on March 15, 2024.

Evolutionary unraveling: new insights into the Persicaria amphibia complex.

The Persicaria amphibia complex exhibits significant morphological variation depending on its habitat, existing in either aquatic or terrestrial forms. Traditionally, four distinct elements have been recognized based on morphological features along with their distinct geographical distributions. Recent studies suggest that the Asian element may be genetically distinct from the European and American elements. However, a comprehensive study on the genetic differentiation among all four elements remains lacking. This study aimed to leverage whole plastid genome sequences and ITS2 haplotypes to comprehensively assess the genomic diversity within the P. amphibia complex. Notably, we included multiple individuals from New York State to resolve the ongoing debate regarding the taxonomic status of two American elements - whether they represent a single species or distinct entities. Our analysis revealed a well-supported monophyletic clade encompassing all four elements, endorsing their own section, Amphibia. Notably, the terrestrial form of the American element is sister to all other elements, suggesting it deserves its own species status. This reinstates its historical name, P. coccinea, separating it from the broader P. amphibia. Furthermore, distinct compositions of the ITS2 haplotypes differentiated the four elements, although the European element should be further investigated with more sampling. The most intriguing discovery is the identification of putative hybrids between the two American elements. In one population out of four putative hybrid populations, all three entities - the two parent species and their hybrid offspring - thrive together, showcasing a fascinating microcosm of ongoing evolutionary processes. Unraveling the intricate genetic tapestry within each American species and their hybrid populations remains a compelling next step. By delving deeper into their genetic makeup, we can gain a richer understanding of their evolutionary trajectories and the intricacies of their interactions. Finally, it is estimated that the two species of sect. Amphibia diverged approximately 4.02 million years ago during the Pliocene epoch, when there was a significant global cooling and drying trend.

Diversity of fungi associated with petroglyph sites in the Negev Desert, Israel, and their potential role in bioweathering.

The petroglyphs of the Negev Desert, Israel, are famous and valuable archaeological remains. Previous studies have investigated the microbial communities associated with petroglyphs and their potential role in stone deterioration; nevertheless, the role of fungi remains unclear. In this study, the fungal communities present on the stone and, as a comparison, in the surrounding environment (soil and air) at Negev petroglyph sites were analyzed by means of culture-dependent and -independent (metagenomic) techniques. The metagenomic results showed a high fungal biodiversity in the soil, and both approaches highlighted the prevalence of species producing melanized, large, thick-walled spores (mainly Alternaria spp.). From the air sampling, mostly Cladosporium spp. were retrieved. On the other hand, on the rock, the results seem to indicate a low presence of fungi, but with a rock-specialized mycobiota consisting of extremotolerant microcolonial fungi (MCF) (e.g., Vermiconidia and Coniosporium) and lichens (Flavoplaca). In addition, low proportions of cosmopolitan fungi were detected on the stone, but the comparison of the data clearly indicates that they are transients from the surrounding environment. The ability of the isolated strains to dissolve CaCO3 and therefore be a potential threat to the petroglyphs (limestone substrate) was tested, but only one strain resulted in positive acid production under laboratory conditions. Nevertheless, both lichens and MCF detected in this study are well-known stone deteriogens, which may have a significant impact on the petroglyph's deterioration.

Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2.

BACKGROUND: Fungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human body and can be beneficial when administered as probiotics. In mycology, the internal transcribed spacer (ITS) region was adopted as the universal marker for classifying fungi. Hence, an accurate and robust method for ITS classification is not only desired for the purpose of better diversity estimation, but it can also help us gain a deeper insight into the dynamics of environmental communities and ultimately comprehend whether the abundance of certain species correlate with health and disease. Although many methods have been proposed for taxonomic classification, to the best of our knowledge, none of them fully explore the taxonomic tree hierarchy when building their models. This in turn, leads to lower generalization power and higher risk of committing classification errors. RESULTS: Here we introduce HiTaC, a robust hierarchical machine learning model for accurate ITS classification, which requires a small amount of data for training and can handle imbalanced datasets. HiTaC was thoroughly evaluated with the established TAXXI benchmark and could correctly classify fungal ITS sequences of varying lengths and a range of identity differences between the training and test data. HiTaC outperforms state-of-the-art methods when trained over noisy data, consistently achieving higher F1-score and sensitivity across different taxonomic ranks, improving sensitivity by 6.9 percentage points over top methods in the most noisy dataset available on TAXXI. CONCLUSIONS: HiTaC is publicly available at the Python package index, BIOCONDA and Docker Hub. It is released under the new BSD license, allowing free use in academia and industry. Source code and documentation, which includes installation and usage instructions, are available at https://gitlab.com/dacs-hpi/hitac .

Dysbiosis and interactions of the mycobiome and bacteriome in mucosal lesions of erosive and non-erosive oral lichen planus patients.

Background: Oral lichen planus (OLP) is a common oral mucosal disease, clinically categorized into erosive OLP (EOLP) and non-erosive OLP (NEOLP) based on symptoms, but its pathogenic mechanism remains unclear. This study aims to explore the relationship between OLP and the oral microbiome. Methods: We collected oral mucosal samples from 49 patients and 10 healthy individuals and conducted 16S rRNA and ITS gene sequencing to explore the oral fungal and bacterial communities. Results: We observed significantly lower α diversity of fungi in the EOLP group, with Candida being significantly enriched as the main dominant genus. In the NEOLP group, Aspergillaceae were significantly enriched. The EOLP group showed significant enrichment of Aggregatibacter and Lactobacillus, but the relative abundance of Streptococcus was notably lower than in the other two groups. In the NEOLP group, two species including Prevotella intermedia were significantly enriched. The microbial co-occurrence and co-exclusion networks display distinct characteristics across the three groups, with Lactobacillus assuming a significant bridging role in the ELOP group. Conclusions: Our study indicates that EOLP and NEOLP experience varying degrees of dysbiosis at both the fungal and bacterial levels. Therefore, the pathogenic mechanisms and interactive relationships of these microbiota associated with OLP merit further in-depth investigation.

The microbial community in the oral lesions of EOLP patients exhibits highly distinctive features, both in terms of bacteria and fungi.In NEOLP patients, the overall bacterial composition does not exhibit significant differences compared to the healthy population, but P. intermedia and Aspergillaceae are notably enriched.