Unclassified Group Research Articles

Comparative study of the gut microbiota in three captive Rhinopithecus species

BackgroundSnub-nosed monkeys are highly endangered primates and their population continues to decline with the habitat fragmentation. Artificial feeding and breeding is an important auxiliary conservation strategy. Studies have shown that changes and imbalances in the gut microbiota often cause gastrointestinal problems in captive snub-nosed monkeys. Here, we compare the gut microbiota composition, diversity, and predicted metabolic function of three endangered species of snub-nosed monkeys (Rhinopithecus bieti, R. brelichi, and R. roxellana) under the same captive conditions to further our understanding of the microbiota of these endangered primates and inform captive conservation strategies. 16 S rRNA gene sequencing was performed on fecal samples from 15 individuals (R. bieti N = 5, R. brelichi N = 5, R. roxellana N = 5).ResultsThe results showed that the three Rhinopithecus species shared 24.70% of their amplicon sequence variants (ASVs), indicating that the composition of the gut microbiota varied among the three Rhinopithecus species. The phyla Firmicutes and Bacteroidetes represented 69.74% and 18.45% of the core microbiota. In particular, analysis of microbiota diversity and predicted metabolic function revealed a profound impact of host species on the gut microbiota. At the genus level, significant enrichment of cellulolytic genera including Rikenellaceae RC9 gut group, Ruminococcus, Christensenellaceae R7 group, UCG 004 from Erysipelatoclostridiaceae, and UCG 002 and UCG 005 from Oscillospiraceae, and carbohydrate metabolism including propionate and butyrate metabolic pathways in the gut of R. bieti indicated that R. bieti potentially has a stronger ability to use plant fibers as energy substances. Bacteroides, unclassified Muribaculaceae, Treponema, and unclassified Eubacterium coprostanoligenes group were significantly enriched in R. brelichi. Prevotella 9, unclassified Lachnospiraceae, and unclassified UCG 010 from Oscillospirales UCG 010 were significantly enriched in R. roxellana. Among the predicted secondary metabolic pathways, the glycan biosynthesis and metabolism had significantly higher relative abundance in the gut of R. brelichi and R. roxellana than in the gut of R. bieti. The above results suggest that different Rhinopithecus species may have different strategies for carbohydrate metabolism. The Principal coordinate analysis (PCoA) and Unweighted pair-group method with arithmetic mean (UPGMA) clustering tree revealed fewer differences between the gut microbiota of R. brelichi and R. roxellana. Correspondingly, no differences were detected in the relative abundances of functional genes between the two Rhinopithecus species.ConclusionTaken together, the study highlights that host species have an effect on the composition and function of the gut microbiota of snub-nosed monkeys. Therefore, the host species should be considered when developing nutritional strategies and investigating the effects of niche on the gut microbiota of snub-nosed monkeys.

621-P: Subphenotyping of Type 2 Diabetes Based on Pathophysiology and Its Association with Diabetes Remission in Urban Indians

Background and Aim: Sub-classification of type 2 diabetes (T2D) based on pathophysiological abnormalities is documented to facilitate better T2D management. Aim of the study was to classify 270 Indian patients with recently diagnosed T2D based on phenotype and the impact of each phenotype on the rate of remission, after a structured diabetes remission program. Methods: We retrospectively extracted and analyzed baseline data of patients with T2D (diagnosed as per WHO criteria) enrolled for a one-year diabetes management program at the Freedom from Diabetes Clinic, India. Inclusion criteria included a recent diagnosis of T2D (<2 years). Using the homeostatic assessment model, patients were categorized into 3 sub-phenotypes: insulinopenic (high insulin sensitivity (IS) and low beta cell function (BCF)), classical (low IS and low BCF), and hyperinsulinemic (low IS and high BCF) T2D. Post-intervention, remission was defined as maintaining HbA1c<48 mmol/mol without the use of glucose-lowering medications for at least 3 months. Results: Of the 270 patients, the majority were hyperinsulinemic (35.9%) followed by insulinopenic 17.4% and classical (13.3%) T2D. Additionally, a novel category of patients with both high IS and high BCF was observed (labeled ‘Unclassified’-33%). Hyperinsulinemic patients had the highest BMI (median 28 kg/m2), dyslipidemia, hypertension, and history of heart disease with the lowest remission rate (14.4%). One in four classical patients was on oral hypoglycemic agents and showed poor glycemic control but 25% remission. Unclassified patients showed the highest remission (28.1%). Conclusion: Pathophysiological sub-phenotyping could assist caregivers in better management of T2D through targeted treatment options. Remission rates were observed to be better in classical and unclassified (high insulin sensitivity and beta function) T2D. Further large-scale studies to understand the unclassified group are warranted. Disclosure P.Tripathi: Board Member; Freedom from Diabetes Clinic. A.R.Vyawahare: Research Support; Freedom From Diabetes. N.S.Kadam: Research Support; Freedom from Diabetes Clinic. B.Sharma: Research Support; Freedom From Diabetes clinic. M.H.Ganla: Employee; Freedom from Diabetes Clinic. M.Das biswas: Employee; Freedom from Diabetes Clinic. B.D.Saboo: None.

Performance of 11 Host Biomarkers Alone or in Combination in the Diagnosis of Late-Onset Sepsis in Hospitalized Neonates: The Prospective EMERAUDE Study.

Despite the high prevalence of late-onset sepsis (LOS) in neonatal intensive care units, a reliable diagnosis remains difficult. This prospective, multicenter cohort study aimed to identify biomarkers early to rule out the diagnosis of LOS in 230 neonates ≥7 days of life with signs of suspected LOS. Blood levels of eleven protein biomarkers (PCT, IL-10, IL-6, NGAL, IP-10, PTX3, CD14, LBP, IL-27, gelsolin, and calprotectin) were measured. Patients received standard of care blinded to biomarker results, and an independent adjudication committee blinded to biomarker results assigned each patient to either infected, not infected, or unclassified groups. Performances of biomarkers were assessed considering a sensitivity of at least 0.898. The adjudication committee classified 22% of patients as infected and all of these received antibiotics. A total of 27% of the not infected group also received antibiotics. The best biomarkers alone were IL-6, IL-10, and NGAL with an area under the curve (95% confidence interval) of 0.864 (0.798-0.929), 0.845 (0.777-0.914), and 0.829 (0.760-0.898), respectively. The best combinations of up to four biomarkers were PCT/IL-10, PTX3/NGAL, and PTX3/NGAL/gelsolin. The best models of biomarkers could have identified not infected patients early on and avoided up to 64% of unjustified antibiotics. At the onset of clinical suspicion of LOS, additional biomarkers could help the clinician in identifying non-infected patients.

Practice of IDH1, ATRX, and P53 Immunohistochemistry in Integrated Diagnosis of Adult Diffuse Gliomas: Single Center Study.

Diffuse gliomas exhibit different molecular and genetic profiles with a wide range of heterogeneity and prognosis. Recently, molecular parameters including ATRX, P53, and IDH mutation status or absence or presence of 1p/19q co-deletion have become a crucial part of the diagnosis of diffuse glioma. In the present study, we tried to analyze the routine practice of the above-mentioned molecular markers focusing on the IHC method in cases of adult diffuse gliomas to evaluate their utility in the integrated diagnosis of adult diffuse gliomas. In total, 134 cases of adult diffuse glioma were evaluated. Using the IHC method, 33,12, and 12 cases of IDH mutant Astrocytoma grade 2, 3, 4, and 45 cases of gliobalstoma, IDH wild type, were molecularly diagnosed. By adding the FISH study for 1p/19q co-deletion, 9 and 8 cases of oligodendroglioma grade 2 and 3 also were included. Two IDH mutant cases were negative for IDH1 in IHC but revealed a positive mutation in further molecular testing. Finally, we were not able to incorporate a complete integrated diagnosis in 16/134(11.94%) of cases. The main molecularly unclassified group was histologically high-grade diffuse glial tumors in patients less than 55 years old and negative IDH1 immunostaining. P53 was positive in 23/33 grade 2, 4/12 grade 3, and 7/12 grade 4 astrocytomas, respectively. Four out of 45 glioblastomas showed positive immunostain, and all oligodendrogliomas were negative. In conclusion, a panel of IHC markers for IDH1 R132H, P53, and ATRX significantly improves the molecular classification of adult diffuse gliomas in daily practice and can be used as a tool to select limited cases for co-deletion testing in the low resources area.

Clinical characteristics and short-term prognosis of 22 cases with SARS-CoV-2 infection associated acute encephalopathy

Objective: To investigate the clinical features and short-term prognosis of patients with SARS-CoV-2 infection associated acute encephalopathy (AE). Methods: Retrospective cohort study. The clinical data, radiological features and short-term follow-up of 22 cases diagnosed with SARS-CoV-2 infection associated AE in the Department of Neurology, Beijing Children's Hospital from December 2022 to January 2023 were retrospectively analyzed. The patients were divided into cytokine storm group, excitotoxic brain damage group and unclassified encephalopathy group according to the the clinicopathological features and the imaging features. The clinical characteristics of each group were analyzed descriptively. Patients were divided into good prognosis group (≤2 scores) and poor prognosis group (>2 scores) based on the modified Rankin scale (mRS) score of the last follow-up. Fisher exact test or Mann-Whitney U test was used to compare the two groups. Results: A total of 22 cases (12 females, 10 males) were included. The age of onset was 3.3 (1.7, 8.6) years. There were 11 cases (50%) with abnormal medical history, and 4 cases with abnormal family history. All the enrolled patients had fever as the initial clinical symptom, and 21 cases (95%) developed neurological symptoms within 24 hours after fever. The onset of neurological symptoms included convulsions (17 cases) and disturbance of consciousness (5 cases). There were 22 cases of encephalopathy, 20 cases of convulsions, 14 cases of speech disorders, 8 cases of involuntary movements and 3 cases of ataxia during the course of the disease. Clinical classification included 3 cases in the cytokine storm group, all with acute necrotizing encephalopathy (ANE); 9 cases in the excitotoxicity group, 8 cases with acute encephalopathy with biphasic seizures and late reduced diffusion (AESD) and 1 case with hemiconvulsion-hemiplegia syndrome; and 10 cases of unclassified encephalopathy. Laboratory studies revealed elevated glutathione transaminase in 9 cases, elevated glutamic alanine transaminase in 4 cases, elevated blood glucose in 3 cases, and elevated D-dimer in 3 cases. Serum ferritin was elevated in 3 of 5 cases, serum and cerebrospinal fluid (CSF) neurofilament light chain protein was elevated in 5 of 9 cases, serum cytokines were elevated in 7 of 18 cases, and CSF cytokines were elevated in 7 of 8 cases. Cranial imaging abnormalities were noted in 18 cases, including bilateral symmetric lesions in 3 ANE cases and "bright tree appearance" in 8 AESD cases. All 22 cases received symptomatic treatment and immunotherapy (intravenous immunoglobulin or glucocorticosteroids), and 1 ANE patient received tocilizumab. The follow-up time was 50 (43, 53) d, and 10 patients had a good prognosis and 12 patients had a poor prognosis. No statistically significant differences were found between the two groups in terms of epidemiology, clinical manifestations, biochemical indices, and duration of illness to initiate immunotherapy (all P>0.05). Conclusions: SARS-CoV-2 infection is also a major cause of AE. AESD and ANE are the common AE syndromes. Therefore, it is crucial to identify AE patients with fever, convulsions, and impaired consciousness, and apply aggressive therapy as early as possible.

Compositional alterations of the gut microbiota in acute myocardial infarction patients with type 2 diabetes mellitus.

Type 2 diabetes mellitus (T2DM) is a risk factor for acute myocardial infarction (AMI) and a common comorbidity in patients with AMI. T2DM doubles the fatality rate of patients with AMI in the acute phase of AMI and the follow-up period. However, the mechanisms by which T2DM increases the fatality rate remain unknown. This study sought to investigate changes in the gut microbiota of patients with AMI and T2DM (AMIDM) to extend understandings of the relative mechanisms from the aspects of gut microbiota. Patients were recruited and divided into 2 groups comprising 15 patients with AMIDM and 15 patients with AMI but without T2DM (AMINDM). Their stool samples and clinical information were collected. 16S ribosomal DNA sequencing was used to analyze the structure and composition of the gut microbiota based on the operational taxonomic units. A significant difference was observed in the gut microbiota β diversity between the 2 groups. At the phylum level, the AMIDM patients showed an increase in the abundance of Firmicutes and a decrease in the abundance of Bacteroidetes compared to the AMINDM patients. At the genus level, the AMIDM patients showed an increase in the abundance of Companilactobacillus, Defluvitaleaceae UCG-011 and UCG-009, and a decrease in the abundance of Phascolarctobacterium and CAG 56 compared to the AMINDM patients. At the species level, the AMIDM patients showed an increase in the abundance of species unclassified NK4A214 group, Bacteroides clarus, Coprococcus comes, unclassified Defluviltaleaceae UCG-011, uncultured rumen bacterium, unclassified CAG 56, Barnesiella intestinihominis, Lachnospiraceae bacterium, Bacteroides nordii, unclassified UCG-009, and the Family XIII AD3011 group compared to the AMINDM patients. The gut microbiota function predictions indicated that the nucleotide metabolism-related pathway was significantly more increase in the patients with AMIDM than those with AMINDM. Additionally, the patients with AMIDM showed an increase in gram-positive bacteria and a decrease in the proportion of gram-negative bacteria. Our correlation analysis results on the gut microbiota and clinical parameters might extend understandings of the progression of AMI. Changes in the gut microbiota composition of patients with AMIDM affect the severity of the metabolic disturbance and may be responsible for poorer clinical outcomes and worse disease progression in patients with AMIDM compared to those with AMINDM.

Long-term consumption of different doses of Grifola frondosa affects immunity and metabolism: correlation with intestinal mucosal microbiota and blood lipids.

Grifola frondosa (GF) is an edible mushroom with hypoglycemic and hypolipidemic effects. In this study, the specific pathogen-free male mice were randomized into the normal (NM), low-dose GF (LGF), medium-dose GF (MGF), and high-dose GF (HGF) groups. The LGF, MGF, and HGF groups were fed with 1.425g/(kgd), 2.85g/(kgd), and 5.735g/(kgd) of GF solution for 8weeks. After feeding with GF solution, compared with the NM group, the thymus index was significantly increased in the LGF group, and TC, TG, and LDL of mice were significantly increased in the HGF group, while HDL was significantly decreased. Compared with the NM group, the uncultured Bacteroidales bacterium, Ligilactobacillus increased in the LGF group, and Candidatus Arthromitus increased in the MGF group. The characteristic bacteria of the HGF group included Christensenellaceae R7, unclassified Clostridia UCG 014, unclassified Eubacteria coprostanoligenes, and Prevotellaceae Ga6A1. Among them, Ligilactobacillus showed a negative correlation with HDL. Unclassified Eubacterium coprostanoligenes group and Ligilactobacillus showed a positive correlation with TG. In summary, our experiments evidenced that GF improves lipid metabolism disorders by regulating the intestinal microbiota, providing a new pathway for hypolipidemic using GF dietary.

Application of Mendelian randomization to explore the causal role of the human gut microbiome in colorectal cancer

The role of the human gut microbiome in colorectal cancer (CRC) is unclear as most studies on the topic are unable to discern correlation from causation. We apply two-sample Mendelian randomization (MR) to estimate the causal relationship between the gut microbiome and CRC. We used summary-level data from independent genome-wide association studies to estimate the causal effect of 14 microbial traits (n = 3890 individuals) on overall CRC (55,168 cases, 65,160 controls) and site-specific CRC risk, conducting several sensitivity analyses to understand the nature of results. Initial MR analysis suggested that a higher abundance of Bifidobacterium and presence of an unclassified group of bacteria within the Bacteroidales order in the gut increased overall and site-specific CRC risk. However, sensitivity analyses suggested that instruments used to estimate relationships were likely complex and involved in many potential horizontal pleiotropic pathways, demonstrating that caution is needed when interpreting MR analyses with gut microbiome exposures. In assessing reverse causality, we did not find strong evidence that CRC causally affected these microbial traits. Whilst our study initially identified potential causal roles for two microbial traits in CRC, importantly, further exploration of these relationships highlighted that these were unlikely to reflect causality.

Red clover root-associated microbiota is shaped by geographic location and choice of farming system.

This study evaluated the red clover (Trifolium pratense) root-associated microbiota to clarify the presence of pathogenic and beneficial microorganisms in 89 Swedish field sites. 16S rRNA and ITS amplicon sequencing analysis were performed on DNA extracted from the red clover root samples collected to determine the composition of the prokaryotic and eukaryotic root-associated microbe communities. Alpha and beta diversities were calculated and relative abundance of various microbial taxa and their co-occurrence were analyzed. Rhizobium was the most prevalent bacterial genus, followed by Sphingomonas, Mucilaginibacter, Flavobacterium, and the unclassified Chloroflexi group KD4-96. The Leptodontidium, Cladosporium, Clonostachys, and Tetracladium fungal genera known for endophytic, saprotrophic, and mycoparasitic lifestyles were also frequently observed in all samples. Sixty-two potential pathogenic fungi were identified with a bias toward grass pathogens and a higher abundance in samples from conventional farms. We showed that the microbial community was mainly shaped by geographic location and management procedures. Co-occurrence networks revealed that the Rhizobiumleguminosarum bv. trifolii was negatively associated with all fungal pathogenic taxa recognized in this study.

Amendments of nitrogen and sulfur mitigate carbon-promoting effect on microbial mercury methylation in paddy soils

The imbalance of nutrient elements in paddy soil could affect biogeochemical processes; however, how the key elements input influence microbially-driven conversion of mercury (Hg) to neurotoxic methylmercury (MeHg) remains virtually unknown. Herein, we conducted a series of microcosm experiments to explore the effects of certain species of carbon (C), nitrogen (N) and sulfur (S) on microbial MeHg production in two typical paddy soils (yellow and black soil). Results showed that the addition of C alone into the soils increased MeHg production approximately 2–13 times in the yellow and black soils; while the combined addition of N and C mitigated the C- promoting effect significantly. Added S also had a buffering effect on C-facilitated MeHg production in the yellow soil despite the extent being lower than that of N addition, whereas this effect was not obvious for the black soil. MeHg production was positively correlated with the abundance of Deltaproteobactera-hgcA in both soils, and the changes in MeHg production were related to the shifts of Hg methylating community resulting from C, N, and S imbalance. We further found that the changes in the proportions of dominant Hg methylators such as Geobacter and some unclassified groups could contribute to the variations in MeHg production under different treatments. Moreover, the enhanced microbial syntrophy with adding N and S might contribute to the reduced C-promoting effect on MeHg production. This study has important implications for better understanding of microbes-driven Hg conversion in paddies and wetlands with nutrient elements input.

RNA virus discoveries in the electric ant, Wasmannia auropunctata

Despite being one of the most destructive invasive species of ants, only two natural enemies are known currently for Wasmannia auropunctata, commonly known as the electric ant or little fire ant. Because viruses can be effective biological control agents against many insect pests, including ants, a metagenomics/next-generation sequencing approach was used to facilitate discovery of virus sequences from the transcriptomes of W. auropunctata. Five new and complete positive sense, single-stranded RNA virus genomes, and one new negative sense, single-stranded RNA virus genome were identified, sequenced, and characterized from W. auropunctata collected in Argentina by this approach, including a dicistrovirus (Electric ant dicistrovirus), two polycipiviruses (Electric ant polycipivirus 1; Electric ant polycipivirus 2), a solinvivirus (Electric ant solinvivirus), a divergent genome with similarity to an unclassified group in the Picornavirales (Electric ant virus 1), and a rhabdovirus (Electric ant rhabdovirus). An additional virus genome was detected that is likely Solenopsis invicta virus 10 (MH727527). The virus genome sequences were absent from the transcriptomes of W. auropunctata collected in the USA (Hawaii and Florida). Additional limited field surveys corroborated the absence of these viruses in regions where the electric ant is invasive (the USA and Australia). The replicative genome strand of four of the viruses (Electric ant polycipivirus 2, Electric ant solinvivirus, Electric ant virus 1, and Solenopsis invicta virus 10 (in the electric ant) was detected in Argentinean-collected W. auropunctata indicating that the ant is a host for these viruses. These are the first virus discoveries to be made from W. auropunctata.

Antimicrobial profile of coagulase-negative staphylococcus isolates from categories of individuals at a neonatal intensive care unit of a tertiary hospital, Ghana.

we compared the antimicrobial resistance profile of young infants' clinical isolates (from blood samples) of Staphylococcus epidermidis and haemolyticus with those colonizing mothers, clinical staff, and students. Also, screened for resistance to the watch and reserve classified groups, antibiotics not prescribed in the Ho Teaching Hospital (HTH), Ghana. a cross-sectional study was conducted from March to June 2018 to determine the antimicrobial susceptibility of twenty-one antimicrobials for 123 isolates consisting of 54 S. epidermidis and 69 S. haemolyticus cultured from the participants. VITEK 2 was used for antimicrobial susceptibility testing. Staphylococcal species were identified using matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF). Statistical analysis was done with Grad-Pad prism. for S. epidermidis, clinical staff isolates have the highest methicillin-resistant (65%), followed by young infants' (50%) and mothers' and students' twenty-five percent each. Both young infants and clinical staff's Staphylococcus haemolyticus isolates have 100% methicillin-resistant, while mothers' and students' ones have 82% and 63%, respectively. We have identified resistance to one watch (teicoplanin), two reserves (tigecycline and fosfomycin) antimicrobial groups, and mupirocin, an unclassified group. identifying coagulase-negative staphylococci (CoNS) resistance to watch and reserve groups of antimicrobials in a non-previously exposed hospital calls for further studies to determine molecular mechanisms of resistance to these antimicrobials.

Expanding known viral diversity in plants: virome of 161 species alongside an ancient canal

BackgroundSince viral metagenomic approach was applied to discover plant viruses for the first time in 2006, many plant viruses had been identified from cultivated and non-cultivated plants. These previous researches exposed that the viral communities (virome) of plants have still largely uncharacterized. Here, we investigated the virome in 161 species belonging to 38 plant orders found in a riverside ecosystem.ResultsWe identified 245 distinct plant-associated virus genomes (88 DNA and 157 RNA viruses) belonging to 27 known viral families, orders, or unclassified virus groups. Some viral genomes were sufficiently divergent to comprise new species, genera, families, or even orders. Some groups of viruses were detected that currently are only known to infect organisms other than plants. It indicates a wider host range for members of these clades than previously recognized theoretically. We cannot rule out that some viruses could be from plant contaminating organisms, although some methods were taken to get rid of them as much as possible. The same viral species could be found in different plants and co-infections were common.ConclusionsOur data describe a complex viral community within a single plant ecosystem and expand our understanding of plant-associated viral diversity and their possible host ranges.

Bioinformatics Analysis of WRKY Family Genes in Erianthus fulvus Ness.

One of the most prominent transcription factors in higher plants, the WRKY gene family, is crucial for secondary metabolism, phytohormone signaling, plant defense responses, and plant responses to abiotic stresses. It can control the expression of a wide range of target genes by coordinating with other DNA-binding or non-DNA-binding interacting proteins. In this study, we performed a genome-wide analysis of the EfWRKY genes and initially identified 89 members of the EfWRKY transcription factor family. Using some members of the OsWRKY transcription factor family, an evolutionary tree was built using the neighbor-joining (NJ) method to classify the 89 members of the EfWRKY transcription factor family into three major taxa and one unclassified group. Molecular weights ranged from 22,614.82 to 303,622.06 Da; hydrophilicity ranged from (-0.983)-(0.159); instability coefficients ranged from 40.97-81.30; lipid coefficients ranged from 38.54-91.89; amino acid numbers ranged from 213-2738 bp; isoelectric points ranged from 4.85-10.06. A signal peptide was present in EfWRKY41 but not in the other proteins, and EfWRK85 was subcellularly localized to the cell membrane. Chromosome localization revealed that the WRKY gene was present on each chromosome, proving that the conserved pattern WRKYGQK is the family's central conserved motif. Conserved motif analysis showed that practically all members have this motif. Analysis of the cis-acting elements indicated that, in addition to the fundamental TATA-box, CAAT-box, and light-responsive features (GT1-box), there are response elements implicated in numerous hormones, growth regulation, secondary metabolism, and abiotic stressors. These results inform further studies on the function of EfWRKY genes and will lead to the improvement of sugarcane.

Application of NGS molecular classification in the diagnosis of endometrial carcinoma: A supplement to traditional pathological diagnosis.

This study aims to demonstrate the advantages of NGS molecular classification in EC diagnosis and to assess whether molecular classification could be performed on curettage specimens and its concordance with subsequent hysterectomy specimens. 80 patients with hysterectomy specimens and 35/80 patients with paired curettage specimens were stratified as POLE mut, MSI-H, TP53 wt, or TP53 abn group by NGS panel. Histotype, tumor grade, IHC results, and other pathological details were taken from original pathological reports. The correlation analysis of 80 patients with hysterectomy specimens between NGS molecular classification and clinicopathological characters displayed that the POLE mut group was associated with EEC (87.5%) and TP53 abn subtype was correlated to a later stage (Stage II-IV, 47.6%), G3 (76.2%), serous histology (61.9%) and myometrial invasion ≥50% (47.6%). A favorable concordance (31/32, 96.9%) was shown in MSI analysis and MMR IHC results, and the agreement rate of p53 IHC and TP53 mutation was 81.5% (53/65). Compared with the p53 IHC abnormal group, the TP53 mutation group had a higher correlation with high-risk factors. A high level of concordance (31/35, 88.0%) of NGS molecular classification was achieved between curettage specimens and hysterectomy specimens while grade and histotype (including unclassified group) from curettage specimens and hysterectomy specimens showed only moderate levels of agreement, 54.3% (19/35) and 68.6% (24/35), respectively. NGS molecular classification achieved on curettage samples showed high concordance with the final hysterectomy specimens, demonstrating superior to the conventional pathological assessment of grade and histotype and potential utilization in clinical practice.

Molecular Characterization of Novel Mycoviruses in Seven Umbelopsis Strains.

The presence of viruses is less explored in Mucoromycota as compared to other fungal groups such as Ascomycota and Basidiomycota. Recently, more and more mycoviruses are identified from the early-diverging lineages of fungi. We have determined the genome of 11 novel dsRNA viruses in seven different Umbelopsis strains with next-generation sequencing (NGS). The identified viruses were named Umbelopsis ramanniana virus 5 (UrV5), 6a (UrV6a); 6b (UrV6b); 7 (UrV7); 8a (UrV8a); 8b (UrV8b); Umbelopsis gibberispora virus 1 (UgV1); 2 (UgV2) and Umbelopsis dimorpha virus 1a (UdV1a), 1b (UdV1b) and 2 (UdV2). All the newly identified viruses contain two open reading frames (ORFs), which putatively encode the coat protein (CP) and the RNA-dependent RNA polymerase (RdRp), respectively. Based on the phylogeny inferred from the RdRp sequences, eight viruses (UrV7, UrV8a, UrV8b, UgV1, UgV2, UdV1a, UdV1b and UdV2) belong to the genus Totivirus, while UrV5, UrV6a and UrV6b are placed into a yet unclassified but well-defined Totiviridae-related group. In UrV5, UgV1, UgV2, UrV8b, UdV1a, UdV2 and UdV1b, ORF2 is predicted to be translated as a fusion protein via a rare +1 (or -2) ribosomal frameshift, which is not characteristic to most members of the Totivirus genus. Virus particles 31 to 32 nm in diameter could be detected in the examined fungal strains by transmission electron microscopy. Through the identification and characterization of new viruses of Mucoromycota fungi, we can gain insight into the diversity of mycoviruses, as well as into their phylogeny and genome organization.

Efficient elimination of RNA mycoviruses in aspergillus species using RdRp-inhibitors ribavirin and 2'-C-methylribonucleoside derivatives.

RNA viruses in fungi (mycoviruses) are model systems for understanding the relationships between eukaryotic microorganisms and RNA viruses. To reveal the effects of mycoviruses on host fungi, it is essential to compare the phenotypes between isogenic fungal isolates with or without RNA virus infection. Since active entry machinery for RNA mycoviruses has never been identified, introducing mycoviruses to fungi is a difficult and time-consuming process. Therefore, most studies have tried to generate virus-free isolates from infected strains by eliminating the mycovirus. However, methods of elimination have not been evaluated in a quantitative and comparative manner. In this study, we established a method to remove mycoviruses from host cells using the antiviral drugs ribavirin, 2′-C-methylcytidine (2CMC), 2′-C-methyladenosine (2CMA), and 7d2CMA, and compared the efficiency of removal in virus-infected strains of Aspergillus fumigatus. The results indicated that treatment with the drugs removed RNA viruses of diverse proportions in the families Chrysoviridae, Mitoviridae, Partitiviridae, Polymycoviridae, and an unclassified RNA virus group. Viruses belonging to Narnaviridae were hardly eliminated by these antiviral treatments when they were the sole infectious agents. We found that 2CMC showed activity against a wider range of RNA mycoviruses compared to ribavirin, 2CMA, and 7d2CMA, although 7d2CMA also efficiently removed dsRNA viruses from the families Chrysoviridae, Partitiviridae, and Polymycoviridae. These results indicated that removal of mycoviruses depends on the specific viral species and antiviral drug. This is the first report demonstrating a preferential antiviral effect against mycoviruses, which will enhance research on microbial RNA viruses and support their elimination from economically important fungi such as edible mushrooms.

The global virome: How much diversity and how many independent origins?

Viruses are considered to be the most abundant biological entities on earth. They also display striking genetic diversity as emphatically demonstrated by the recent advances of metagenomics and metatranscriptomics. But what are the limits of this diversity, that is, how many virus species in the earth virome? By combining the available estimates of the number of prokaryote species with those of the virome size, we obtain back-of-the-envelope estimates of the total number of distinct virus species, which come out astronomically large, from about 107 to about 109 . The route of virus origins apparently involved non-viral replicators capturing and exapting various cellular proteins to become virus capsid subunits. How many times in the history of life has this happened? In other words, how many realms of viruses, the highest rank taxa that are supposed to be monophyletic, comprise the global virome? We argue that viruses emerged on a number (even if far from astronomical) independent occasions, so the number of realms will considerably increase from the current 6, by splitting some of the current realms, giving the realm status to some of the currently unclassified groups of viruses and discovery of new distinct groups.

New taxonomic framework for Arthrodermataceae: a comprehensive analysis based on their phylogenetic reconstruction, divergence time estimation, phylogenetic split network, and phylogeography.

The Arthrodermataceae, or dermatophytes, are a major family in the Onygenales and important from a public health safety perspective. Here, based on sequenced and downloaded from GenBank sequences, the evolutionary relationships of Arthrodermataceae were comprehensively studied via phylogenetic reconstruction, divergence time estimation, phylogenetic split network, and phylogeography analysis. These results showed the clades Ctenomyces, Epidermophyton, Guarromyces, Lophophyton, Microsporum, Paraphyton, and Trichophyton were all monophyletic groups, whereas Arthroderma and Nannizzia were polyphyletic. Among them, Arthroderma includes at least four different clades, Arthroderma I, III and IV are new clades in Arthrodermataceae. Nannizzia contains at least two different clades, Nannizzia I and Nannizzia II, but Nannizzia II was a new clade in Arthrodermataceae. The unclassified group, distributed in Japan and India, was incorrectly identified; it should be a new clade in Arthrodermataceae. The phylogenetic split network based on the ITS sequences provided strong support for the true relationships among the lineages in the reconstructed phylogenetic tree. A haplotype phylogenetic network based on the ITS sequences was used to visualize species evolution and geographic lineages relationships in all genera except Trichophyton. The new framework provided here for the phylogeny and taxonomy of Arthrodermataceae will facilitate the rapid identification of species in the family, which should useful for evaluating the results of preventive measures and interventions, as well as for conducting epidemiological studies.

Molecular characterization of a novel virga-like virus associated with wheat.

In this work, we report the detection of a novel single-strand RNA virus from wheat, tentatively named "Triticum aestivum-associated virga-like virus 1" (TaAVLV1). Further characterization revealed that the complete genome of TaAVLV1 is divided into two segments, RNA1 and RNA2, which are 3530 and 3466 nt in length, excluding their respective polyA tails, and each contains only one open reading frame (ORF). The ORF of RNA1 encodes an RNA-dependent RNA polymerase (RdRp), while the ORF of RNA2 encodes a putative protein with methyltransferase and helicase domains. Phylogenetic analysis showed that the RdRp of TaAVLV1 is closely related to those of members of the unclassified virga-like virus group in the family Virgaviridae. Thus, we have identified TaAVLV1 as a putative novel virga-like virus belonging to the family Virgaviridae.