Gene Sequence Analysis Research Articles

Metagenomic insights into the rapid recovery mechanisms of prokaryotic community and spread of antibiotic resistance genes after seawater disinfection

Disinfectants, such as bleaching powder, are widely employed in marine aquaculture worldwide to control the bacterial pathogens and eliminate antibiotic resistance genes (ARGs). Nevertheless, the rapid recovery of prokaryotic community compositions (PCCs) after disinfection may significantly influence the overall efficacy of disinfection. Presently, little is known about the rapid recovery mechanisms of PCCs and its impact on the removal of ARGs in seawater. In this study, 16S rRNA gene sequencing and metagenomic analysis were used to address the above concerns through simulating the disinfection process in aquaculture. The results showed that recovery of PCCs began within 16 h. The underlying mechanisms of the repaid recovery of PCCs were the synergistic interactions between microbes and the residues of disinfection-resistant bacteria (DRB). Disinfection resistance genes (DRGs) related to efflux pump serve as the primary molecular foundation providing DRB to resist disinfection. Among the 78 annotated ARGs, only 10 ARGs exhibited a significant decrease (P < 0.05) after 72 h, implying the ineffective removal of ARGs by bleaching powder. Furthermore, bacterial co-resistance to disinfectants and antibiotics was observed. Genome analysis of two highly resistant DRB from Pseuomonadaceae revealed that both DRB carried 16 DRGs, aiding the recovery of PCCs and the spread of ARGs. These findings provide novel insights in the mechanisms of the rapid recovery of PCCs and bacterial co-resistance to disinfectants and antibiotics, which can be crucial for the management of pathogens and antibiotic resistance in seawater.

Kosakonia calanthes sp. nov., a plant growth-promoting bacterium, isolated from Calanthe triplicata leaves in China.

A Gram-stain-negative, facultatively aerobic, rod-shaped and motile bacterium, designated as CCTCC AB 2023082T, was isolated from leaves of Calanthe triplicata in China. Optimal growth occurred at 4-45 ℃ and pH 4.0-10.0 and in the presence of 0-7% (w/v) NaCl. The major fatty acids of the strain CCTCC AB 2023082T were C16 : 0, sum of C16 : 1 ω7c/C16 : 1 ω6c, C17 : 0 cyclo and C18 : 1 ω7c. The polar lipids included unidentified lipids, phospholipids, phosphatidylethanolamine, phosphatidylglycerol and amino phospholipid. The DNA G+C content of strain CCTCC AB 2023082T was 54.2 mol%. 16S rRNA gene sequence analysis indicated that strain CCTCC AB 2023082T formed a distinct lineage within the genus Kosakonia and exhibited the highest similarity to Kosakonia quasisacchari, with a 97.9% 16S rRNA gene sequence similarity. Moreover, the preliminary analysis of the organism's genome suggested its potential as a biostimulant for augmenting plant growth. According to its genotypic, phenotypic, phylogenetic and chemotaxonomic characteristics, strain CCTCC AB 2023082T should be categorized as a novel species in the genus Kosakonia. The novel species was named Kosakonia calanthes sp. nov., and its type strain is CCTCC AB 2023082T (=JCM 36393T).

Intestinal bacterium Bacillus siamensis M54 from Allomyrina dichotoma is a potential biocontrol agent against maize stalk rot

Maize stalk rot, caused by Fusarium spp., is a significant disease that adversely impacts the yield and quality of corn. Biological control plays a crucial role in managing numerous crop diseases, including maize stalk rot. Biocontrol agents are predominantly derived from soil and plant tissues, with limited reports on isolating highly efficient biocontrol agents from insects. In this study, 144 bacterial strains were isolated from the intestinal tract of third instar larvae of Allomyrina dichotoma. Through dual culture tests, twelve strains exhibiting strong antagonism against two maize stalk rot pathogens, F. graminearum and F. verticillioides, were identified. Among them, the M54 strain exhibited the most potent antagonistic effect against the two pathogenic fungi and was identified as Bacillus siamensis through 16S rRNA gene sequence analysis. The complete genome for M54 was assembled using PacBio single-molecule real-time (SMRT) and Illumina sequencing technologies. Whole genome phylogenetic analysis further confirmed M54 was B. siamensis. Microscopic examination revealed that M54 had the ability to inhibit the fungal spore germination and hyphal formation. Furthermore, M54 exhibited effective colonization in the maize rhizosphere and enhanced maize growth. It showed that treatment with M54 significantly suppressed lesion expansion induced by F. graminearum on maize stalks in the seedling and adult plant assays. Genomic analysis using antiSMASH revealed 11 gene clusters for secondary metabolite synthesis. This study provides a novel approach for isolating biocontrol agents to manage plant diseases and highlights B. siamensis M54 as a potential efficient biocontrol agent for maize stalk rot.

Ischemic Postconditioning Regulates New Cell Death Mechanisms in Stroke: Disulfidptosis.

Stroke poses a critical health issue without effective neuroprotection. We explore ischemic postconditioning's (IPostC) potential to mitigate stroke-induced brain injury, focusing on its interaction with disulfidptosis, a novel cell death pathway marked by protein disulfide accumulation. We aim to clarify IPostC's protective mechanisms against stroke through gene sequencing and experimental analysis in mice. Through our initial investigation, we identified 27 disulfidptosis-related genes (DRGs) and uncovered their interactions. Additionally, differential gene analysis revealed 11 potential candidate genes that are linked to disulfidptosis, stroke, and IPostC. Our comprehensive study employed various analytical approaches, including machine learning, functional enrichment analysis, immune analysis, drug sensitivity analysis, and qPCR experiments, to gain insights into the molecular mechanisms underlying these processes. Our study identified and expanded the list of disulfidptosis-related genes (DRGs) critical to stroke, revealing key genes and their interactions. Through bioinformatics analyses, including PCA, UMAP, and differential gene expression, we were able to differentiate the effects of stroke from those of postconditioning, identifying Peroxiredoxin 1 (PRDX1) as a key gene of interest. GSEA highlighted PRDX1's involvement in protective pathways against ischemic damage, while its correlations with various proteins suggest a broad impact on stroke pathology. Constructing a ceRNA network and analyzing drug sensitivities, we explored PRDX1's regulatory mechanisms, proposing novel therapeutic avenues. Additionally, our immune infiltration analysis linked PRDX1 to key immune cells, underscoring its dual role in stroke progression and recovery. PRDX1 is identified as a key target in ischemic stroke based on colocalization analysis, which revealed that PRDX1 and ischemic stroke share the causal variant rs17522918. The causal relationship between PRDX1-related methylation sites (cg02631906 and cg08483560) and the risk of ischemic stroke further validates PRDX1 as a crucial target. These results suggest that the DRGs are interconnected with various cell death pathways and immune processes, potentially contributing to IPostC regulating cell death mechanisms in stroke.

Isolation, Antibacterial Activity and Molecular Identification of Avocado Rhizosphere Actinobacteria as Potential Biocontrol Agents of Xanthomonas sp.

Actinobacteria, especially the genus Streptomyces, have been shown to be potential biocontrol agents for phytopathogenic bacteria. Bacteria spot disease caused by Xanthomonas spp. may severely affect chili pepper (Capsicum annuum) crops with a subsequent decrease in productivity. Therefore, the objective of the study was to isolate rhizospheric actinobacteria from soil samples treated by physical methods and evaluate the inhibitory activity of the isolates over Xanthomonas. Initially, soil samples collected from avocado tree orchards were treated by dry heat air and microwave irradiation; thereafter, isolation was implemented. Then, antibacterial activity (AA) of isolates was evaluated by the double-layer agar method. Furthermore, the positive/negative effect on AA for selected isolates was evaluated on three culture media (potato-dextrose agar, PDA; yeast malt extract agar, YME; and oat agar, OA). Isolates were identified by 16S rRNA sequence analysis. A total of 198 isolates were obtained; 76 (series BVEZ) correspond to samples treated by dry heat and 122 strains (series BVEZMW) were isolated from samples irradiated with microwaves. A total of 19 dry heat and 25 microwave-irradiated isolates showed AA with inhibition zones (IZ, diameter in mm) ranging from 12.7 to 82.3 mm and from 11.4 to 55.4 mm, respectively. An increment for the AA was registered for isolates cultured on PDA and YME, with an IZ from 21.1 to 80.2 mm and 14.1 to 69.6 mm, respectively. A lower AA was detected when isolates were cultured on OA media (15.0 to 38.1 mm). Based on the 16S rRNA gene sequencing analysis, the actinobacteria belong to the Streptomyces (6) and Amycolatopsis (2) genera. Therefore, the study showed that microwave irradiation is a suitable method to increase the isolation of soil bacteria with AA against Xanthomonas sp. In addition, Streptomyces sp. BVEZ 50 was the isolate with the highest IZ (80.2 mm).

Whole Blood Transcriptome Analysis in Congenital Anemia Patients.

Congenital anemias include a broad range of disorders marked by inherent abnormalities in red blood cells. These abnormalities include enzymatic, membrane, and congenital defects in erythropoiesis, as well as hemoglobinopathies such as sickle cell disease and thalassemia. These conditions range in presentation from asymptomatic cases to those requiring frequent blood transfusions, exhibiting phenotypic heterogeneity and different degrees of severity. Despite understanding their different etiologies, all of them have a common pathophysiological origin with congenital defects of erythropoiesis. We can find different types, from congenital sideroblastic anemia (CSA), which is a bone marrow failure anemia, to hemoglobinopathies as sickle cell disease and thalassemia, with a higher prevalence and clinical impact. Recent efforts have focused on understanding erythropoiesis dysfunction in these anemias but, so far, deep gene sequencing analysis comparing all of them has not been performed. Our study used Quant 3' mRNA-Sequencing to compare transcriptomic profiles of four sickle cell disease patients, ten thalassemia patients, and one rare case of SLC25A38 CSA. Our results showed clear differentiated gene map expressions in all of them with respect to healthy controls. Our study reveals that genes related to metabolic processes, membrane genes, and erythropoiesis are upregulated with respect to healthy controls in all pathologies studied except in the SLC25A38 CSA patient, who shows a unique gene expression pattern compared to the rest of the congenital anemias studied. Our analysis is the first that compares gene expression patterns across different congenital anemias to provide a broad spectrum of genes that could have clinical relevance in these pathologies.

In-vitro antibacterial and antibiofilm activities and in-silico analysis of a potent cyclic peptide from a novel Streptomyces sp. strain RG-5 against antibiotic-resistant and biofilm-forming pathogenic bacteria.

The proliferation of multidrug-resistant and biofilm-forming pathogenic bacteria poses a serious threat to public health. The limited effectiveness of current antibiotics motivates the search for new antibacterial compounds. In this study, a novel strain, RG-5, was isolated from desert soil. This strain exhibited potent antibacterial and antibiofilm properties against multidrug-resistant and biofilm-forming pathogenic bacteria. Through phenotypical characterizations, 16S rRNA gene sequence and phylogenetic analysis, the strain was identified as Streptomyces pratensis with 99.8% similarity. The active compound, RG5-1, was extracted, purified by reverse phase silica column HPLC, identified by ESI-MS spectrometry, and confirmed by 1H and 13C NMR analysis as 2,5-Piperazinedione, 3,6-bis(2-methylpropyl), belonging to cyclic peptides. This compound showed interesting minimum inhibitory concentrations (MICs) of 04 to 15µg/mL and minimum biofilm inhibitory concentrations (MBICs 50%) of ½ MIC against the tested bacteria. Its molecular mechanism of action was elucidated through a molecular docking study against five drug-protein targets. The results demonstrated that the compound RG5-1 has a strong affinity and interaction patterns with glucosamine-6-phosphate synthase at - 6.0kcal/mol compared to reference inhibitor (- 5.4kcal/mol), medium with penicillin-binding protein 1a (- 6.1kcal/mol), and LasR regulator protein of quorum sensing (- 5.4kcal/mol), confirming its antibacterial and antibiofilm activities. The compound exhibited minimal toxicity and favorable physicochemical and pharmacological properties. This is the first report that describes its production from Streptomyces, its activities against biofilm-forming and multidrug-resistant bacteria, and its mechanism of action. These findings indicate that 2,5-piperazinedione, 3,6-bis(2-methylpropyl) has the potential to be a promising lead compound in the treatment of antibiotic-resistant and biofilm-forming pathogens.

Unique Fn3-like biosensor in σI/anti-σI factors for regulatory expression of major cellulosomal scaffoldins in Pseudobacteroides cellulosolvens.

Lignocellulolytic clostridia employ multiple pairs of alternative σ/anti-σ (SigI/RsgI) factors to regulate cellulosomal components for substrate-specific degradation of cellulosic biomass. The current model has proposed that RsgIs use a sensor domain to bind specific extracellular lignocellulosic components and activate cognate SigIs to initiate expression of corresponding cellulosomal enzyme genes, while expression of scaffoldins can be initiated by several different SigIs. Pseudobacteroides cellulosolvens contains the most complex known cellulosome system and the highest number of SigI-RsgI regulons yet discovered. However, the function of many RsgI sensor domains and their relationship with the various enzyme types are not fully understood. Here, we report that RsgI4 from P. cellulosolvens employs a C-terminal module that bears distant similarity to the fibronectin type III (Fn3) domain and serves as the sensor domain. Substrate-binding analysis revealed that the Fn3-like domain of RsgI4 represents a novel carbohydrate-binding module (CBM) that binds to a wide range of polysaccharide types. Structure determination further revealed that the Fn3-like domain belongs to the type B group of CBMs with a predicted concave face for substrate binding. Promoter sequence analysis of cellulosomal genes revealed that SigI4 is responsible for cellulosomal regulation of major scaffoldins rather than enzymes, consistent with the broad substrate specificity of the RsgI4 sensor domain. Notably, scaffoldins are invariably required as cellulosome components regardless of the substrate type. These findings suggest that the intricate cellulosome system of P. cellulosolvens comprises a more elaborate regulation mechanism than other bacteria and thus expands the paradigm of cellulosome regulation.

Evaluation of a Novel Streptomyces avermitilis Strain from Egyptian Soil for Biological Control of Tetranychus urticae in Greenhouse Cucumber Plantations

Background: Infestation in greenhouse cucumber with the two-spotted spider mite (Tetranychus urticae Koch) commonly causes severe damage to crop quality and quantity and increases crop production costs. Objective: This study was conducted to investigate the efficacy of high-abamectinproducing isolates of S. avermitilis against T. urticae-infested cucumber and to assess their impact on biochemical stress markers in these vegetables. Methods: In this study, 72 non-antagonistic Streptomyces were isolated from rhizospheric soil samples collected from eight different locations in Egypt and screened for their ability to produce the secondary metabolite, abamectin Results: The screening process identified two potent abamectin-producing isolates, EW8 and T2, which produced 42.7 and 29.6 μg/L abamectin, respectively, as confirmed by LC-MS/MS analysis. According to DNA sequence analysis of the 16S rRNA gene, these two isolates belong to the species S. avermitilis. The acaricidal activity of either culture suspensions of S. avermitilis strains WE8 and T2, or their extracts containing abamectin, against the mobile stages and egg hatchability of T. urticae was evaluated in the laboratory and the greenhouse. Data on the mortality among the examined female mites and the reduction in their number of eggs point out a potential acaricidal activity of the examined strains of S. avermitilis and their extracts containing abamectin against T. urticaes. Furthermore, the extracts containing abamectin from these two S. avermitilis strains induced oxidative stress in the infested cucumber plants by T. urticaes, as indicated by increased levels of malondialdehyde (MDA). However, the levels of MDA in T. urticae-infested cucumber plants varied depending on the strain and the specific abamectin crude extract used. Conclusion: S. avermitilis strains T2 or WE8, or their crude extract could be applied in greenhouse cucumber plantations to combat red mite infestation (Fig. 1).

Transcriptome Sequencing Analysis of Genes Associated with Different Developmental Periods of the Ovarian Follicle in the Duolang Sheep.

The ovaries are crucial reproductive organs in female mammals, directly influencing the reproductive efficiency and productivity of these animals. The Duolang sheep, native to Xinjiang, is known for its rapid growth and high fertility. However, the mechanisms underlying ovarian follicle development and regulation in sheep remain unclear. Employing transcriptome sequencing technology, this study methodically analyzed ovaries from sheep across various estrous cycles to uncover key genes and signaling pathways that play a role in the development of ovarian follicles. The results indicated that a total of 130, 183, and 175 differentially expressed genes were identified in the DTA/DTB, DTB/DTC, and DTA/DTC groups, respectively. Key genes like BAG3, GDF5, RHOB, RUNX2, LGALS3, and CDH1, along with pathways such as endoplasmic reticulum protein processing, the NOTCH signaling pathway, and the MAPK signaling pathway, were found to be involved. RT-qPCR confirmed the differential expression of BAG3, RHOB, and RUNX2. This research provides insights into the molecular mechanisms of ovarian follicle development and a basis for enhancing the reproductive performance of Duolang sheep.

Indole-3-acetic acid attenuates pulmonary fibrosis by modulating lung microbiota, inhibiting fibroblast activation, and alleviating alveolar epithelial cell senescence

AimPulmonary fibrosis (PF) is a relentlessly progressive disorder characterized by high mortality and limited effective therapeutic options. Indole-3-acetic acid (IAA), originally recognized as a plant hormone, is also identified as a tryptophan-derived metabolite catabolized from microbiota in mammals. IAA has exhibited antioxidative, anti-inflammatory, and anti-tumor effects in various disorders, yet its role in PF remains elusive. Main methodsBleomycin (BLM) was employed to induce PF in a mouse model. TGF-β1 was utilized in primary mouse lung fibroblasts (pMLFs) to establish a pro-fibrotic in vitro cellular model, and in A549 cells to create an in vitro cellular senescence model. The therapeutic effects of IAA on PF were evaluated using hematoxylin-eosin staining, immunofluorescence staining, western blotting, SA-β-gal assay, and network pharmacology analysis. Additionally, the effect of IAA on lung microbiota of PF was investigated using 16S rRNA gene sequencing analysis. Key findingswe observed a significant reduction in IAA levels in both PF patients and mouse models. Moreover, we demonstrated the therapeutic potential of IAA in alleviating PF in BLM-induced mouse models, showing a dose-dependent response. Mechanistically, we delineated three perspectives. Firstly, IAA promoted autophagic flux by inhibiting the PI3K/AKT/mTOR pathway, thereby suppressing lung fibroblast differentiation and extracellular matrix (ECM) deposition. Secondly, IAA attenuated alveolar epithelial cell senescence by modulating the PI3K/AKT and HIF-1 pathways. Lastly, IAA displayed the ability to mitigate PF by modulating the structure and composition of lung microbiota. SignificanceOur study demonstrates that IAA alleviates PF through multiple pathways, highlighting its potential as a therapeutic agent.

First detection of D181 genotype of infectious bronchitis in poultry flocks of Morocco

BackgroundThis paper reports the first pathological and molecular characterization of the novel variant of infectious bronchitis virus (IBV) D181 in poultry flocks in Morocco and Africa.MethodsThe study includes six poultry farms, involving three flocks of layers aged between 28 and 67 weeks and three broiler flocks aged 27, 39 and 42 days from different regions of Morocco. In all affected layer flocks, a severe drop in egg production with poor eggshell quality was reported. Necropsy of dead birds was carried out, and samples of trachea, lungs, oviduct, ovaries, and kidneys were fixed in 10% neutral buffered formalin for histopathologic examinations, while other portions were stored at -20 °C for molecular analysis. Real time RT-qPCR for IBV gene group was performed, and IBV variants were identified. Partial S1 gene sequences were amplified by conventional RT-PCR, sequenced, and aligned for phylogenetic and amino acid similarity analysis.ResultsNecropsy of dead birds revealed misshapen and hemorrhagic ovarian follicles with an edematous oviduct and severe reaction in the cecal tonsils. A caseous material accumulation in the sinus was noted in few birds. In contrast, the broiler flocks exhibited respiratory clinical signs such as difficulty in breathing, sneezing, tracheal rales, watery eyes and lethargy, associated with a decrease in feed consumption. Mortality in broiler ranged from 2 to 15%. Histopathological analysis of samples showed a lympho-plasmocytic inflammation in the oviduct, trachea, and lungs. Individual necrosis of epithelial cells, with sloughing of the bronchial epithelium and accumulation of desquamated cells with mucus in the airways, was observed in some birds. Partial S1 gene sequencing and phylogenetic analyses showed that the Moroccan strains were very closely related to D181 strains isolated in Dutch layers and breeders in 2018. Nucleotide sequence identities reached 90.9–95% with the Dutch isolates (strain CK/NL/D181/2018).ConclusionOur sequencing results demonstrate for the first time that the D181 IBV genotype is circulating in Moroccan poultry. These findings justify permanent monitoring of circulating strains in order to appropriately adjust vaccination strategies to align with the evolving field situation.

Paracoccus actinidiae sp.nov., a novel bacterium isolated from kiwi tree rhizosphere soil.

Strain M09T was isolated from the rhizoshere of kiwi fruit trees from an orchard located in Fangshan, Beijing, PR China (39° 49' 25.1″ N, 116° 4' 44.5″ E,). It is a short rod-shaped, Gram-stain-negative, facultatively anaerobic bacterium that tests positive for both oxidase and catalase. The strain exhibited growth within the temperature range of 15-45 °C (optimal growth at 30 °C) and the pH range of 4.0-10.0 (optimal growth at pH 7.0) and without NaCl. It also grew in a sodium chloride-free nutrient agar (NA) medium. The results of phylogenetic analysis of the 16S rRNA gene sequences indicated that M09T represents a member of the genus Paracoccus and shares high similarity with Paracoccus everestensis S8-55T (98.46%) and Paracoccus aerius 011410T (97.58%). The average nucleotide identity values between M09T and P. everestensis S8-55T, P. aerius 011410T, Paracoccus marinaquae X HP0099T and Paracoccus fontiphilus MVW-1T were 95.56, 84.51, 79.83 and 83.68%, respectively. The digital DNA-DNA hybridisation values between between M09T and P. everestensis S8-55T, P. aerius 011410T, P. marinaquae X HP0099T and P. fontiphilus MVW-1T were 56.40, 29.30, 21.60 and 28.60%, respectively. The major fatty acids identified were C10 : 0 3-OH (51.8%) and C18 : 1ω7c (35.5%). The major respiratory quinone was Q-10, with Q-8 present as a minor component. Polar lipids were mainly comprised of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylcholine (PC), and phosphatidylethanolamine (PE). Genome sequencing revealed that the strain has a DNA G+C content of 64.31 mol%. On the basis of this comprehensive taxonomic characterisation data, M09T represents a novel species within the genus Paracoccus and has been named Paracoccus actinidiae sp. nov. The type strain is designated as M09T (=GDMCC 1.4157T=KCTC 8143T).

Comparative Analysis of Intestinal Morphology and Gut Microbiota of Spinibarbus sinensis Under Different Aquaculture Systems.

Fish gut health is influenced by various factors, with the environment being a significant one. S. sinensis is a key aquaculture species in China, yet research on the impact of different aquaculture systems on its intestinal health remains limited. This study aims to explore the changes in intestinal morphology and gut microbiota of S. sinensis under two aquaculture systems. The juveniles of S. sinensis were divided into two groups and cultured in traditional ponds (CT) and an in-pond tank culture system (JY), with equal amounts of feed provided daily over a 72-day experimental period. The results showed no significant differences in growth performance metrics, including the specific growth rate, weight gain rate, hepatosomatic index, and viscerosomatic index between the two groups. In terms of intestinal morphology, the JY group villus width was significantly wider than the CT group, and the number of goblet cells in the CT group was significantly higher than that of the JY group (p < 0.05), which suggested that the fish in the JY group may have better intestinal nutrient absorption capacity, while the water quality in the CT group may be worse. The 16S rRNA gene sequencing analysis of the gut microbiota showed that the JY group had a significantly higher Shannon index compared to the CT group (p < 0.05), indicating greater species richness and evenness. Principal Coordinates Analysis (PCoA) revealed a distinct clustering of gut microbiota between the two groups. At the phylum level, the relative abundance of Fusobacteriota was significantly higher in the CT group, whereas Bacteroidota and Proteobacteria were significantly higher in the JY group (p < 0.05). Furthermore, KEGG pathway predictions indicated differences in the potential metabolic capabilities of the gut microbiota between the two groups (p < 0.05). Overall, this study is the first to conduct a comparative analysis of the growth performance, intestinal tissue morphology, and gut microbiota of S. sinensis under two different aquaculture systems, which has valuable implications for the further optimization of aquaculture practices.

First report on genetic characterization of egg drop syndrome 1976 virus in Egypt.

Since its first description in 1991 in Egypt, egg drop syndrome 1976 (EDS-76) virus has received a little attention as a potential cause for the drop in egg production as well as the reduction in egg quality. To date, no studies have been carried out to describe the genetic characteristics of the circulating field EDS-76 virus strains. Thus, the present study was attempted to estimate the emergence of EDS-76 virus in layer flocks and to determine the genetic diversity between the field strains and the vaccine strain 127. During 2022, a total of 5 apparently healthy backyard layer flocks were investigated for the presence of EDS-76 virus infection following complaints of sudden drop in egg production (25-30%), accompanied by high incidence of eggshell defects. EDS-76 virus DNA was detected in the oviduct samples of 4 (80%) flocks by polymerase chain reaction (PCR) assay targeting the hexon gene of the viral capsid. Attempts of viral isolation in duck embryo revealed no embryonic mortality, however, the allantoic fluids of inoculated eggs exhibited a sustained increase in the hemagglutinating (HA) activity throughout three consecutive passages. The obtained strain, designated BH-1, was characterized on the basis of partial hexon gene sequence analysis (GenBank accession number OR531368). The BH-1 strain displayed 99.6% nucleotide identity with the vaccine strain 127. However, amino acid alignments with the vaccine strain 127 revealed that the BH-1 strain carried 5 non-synonymous mutations. In addition, two of these mutations were incorporated into the hexon hypervariable regions (HVRs), which are strictly responsible for eliciting serotype-specific neutralizing antibodies. In conclusion, the present study represents a starting point for genetic characterization of EDS-76 virus in Egypt and highlights the importance for continuous monitoring and characterization of the circulating field EDS-76 virus strains, in order to determine the proper control strategy.

Pooled analysis of oral microbiome profiles defines robust signatures associated with periodontitis.

Oral microbial dysbiosis has been associated with periodontitis in studies using 16S rRNA gene sequencing analysis. However, this technology is not sufficient to consistently separate the bacterial species to species level, and reproducible oral microbiome signatures are scarce. Here, using ultra-deep metagenomic sequencing and machine learning tools, we defined a simple two-factor decision tree, based on Tannerella forsythia and Fretibacterium fastidiosum, that was highly associated with periodontitis. Altogether, we defined robust oral microbiome signatures relevant to the pathophysiology of periodontitis that can help define promising targets for microbiome therapeutic modulation when caring for patients with periodontitis.

Flavobacterium capsici sp. nov., isolated from the rhizospheric soils of bell pepper (Capsicum annuum L.).

Two separate bacterial strains, PMTSA4T and PMR2A8, were isolated from the rhizospheric soils of bell pepper plants grown in a plant nursery. These strains are Gram-negative, non-motile and rod-shaped and grow in aerobic conditions. They exhibit a positive reaction for catalase activity but negative results for oxidase activity. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the strains PMTSA4T and PMR2A8 are closely related to Flavobacterium piscinae ICH-30T (95.6%, respectively), Flavobacterium ahnfeltiae 10Alg 130T (95.5%) and Flavobacterium maris KMM 9535T (95.3%), aligning them within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) values and average nucleotide identities (ANIs) of the whole-genome sequences for the two strains and related Flavobacterium species were significantly below the established thresholds for prokaryotic species delineation (<70% for dDDH and <95% for ANI). The observed values were as follows: Flavobacterium aquatile LMG 4008T (dDDH: 19.8% and ANI: 75.5%), F. piscinae ICH-30T (dDDH: 18.6% and ANI: 73.3%) and F. stagni WWJ 16T (dDDH: 18.5% and ANI: 72.0%). The strains have genome sizes of 3 068 185 bp and 3 068 330 bp, with a G+C content of 32.5 mol%. In phenotypic characterization, the new strains grew at 10-35 °C and tolerated up to 4% NaCl at pH 5-9 (optimum pH 8). The predominant cellular fatty acids were observed to be iso-C15:0, iso-C17:0 3-OH and iso-C15:0 3-OH. Menaquinone-6 was the predominant quinone. Considering the results from phenotypic, chemotaxonomic, phylogenetic and genomic analyses, it is proposed that the strains PMTSA4T and PMR2A8 represent a novel species within the genus Flavobacterium.

Streptomyces yaizuensis sp. nov., a berninamycin C-producing actinomycete isolated from sponge.

While screening for antibiotics in a marine sample, we discovered a berninamycin C-producing actinomycete, designated YSPA8T, isolated from a sponge. A polyphasic approach was used to determine the taxonomic position of the strain. Strain YSPA8T formed sympodially branched aerial mycelia that ultimately segment into chains of spores. Comparative and phylogenetic analyses of the 16S rRNA gene sequence showed that strain YSPA8T were closely related to Streptomyces clavuligerus ATCC 27064T (99.66%), Streptomyces amakusaensis NRRL B-3351T (98.69%), Streptomyces inusitatus NBRC 13601T (98.48%), and 'Streptomyces jumonjinensis' JCM 4947 (98.41%). The phylogenetic tree using the 16S rRNA gene sequences, and both phylogenomic trees suggested that the closest relative of strain YSPA8T was S. clavuligerus ATCC 27064T. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between strain YSPA8T and S. clavuligerus ATCC 27064T were 84.1%, 28.9%, and 82.5%, respectively, which were below the thresholds of 95%, 70%, and 95% for a prokaryotic conspecific assignment. The G + C of the strain YSPA8T was 72.6%. Whole-cell hydrolysates of strain YSPA8T contained LL-diaminopimelic acid. The predominant menaquinones were MK-9(H6) (49%) and MK-9(H8) (48%), and the major fatty acids were C16:0 (26.8%), C16:1 ω7c/ω6c (17.2%), iso-C16:0 (16.0%), and iso-C15:0 (12.5%). The major phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, and other unidentified phospholipids. Based on the phenotypic, phylogenetic, genomic, and chemotaxonomic data, strain YSPA8T represents a novel species of the genus Streptomyces, and the proposed name for this species is Streptomyces yaizuensis sp. nov. The type strain is YSPA8T (=NBRC 115866T = TBRC 17196T).

Restoration of the spike architectonics in ancient barley excavated at the twelfth-century settlement of Usvyaty

Background. The data are presented on the architectonics of ancient barley spikes from the 12th century, excavated in 2019 at Usvyaty Settlement. Modern molecular genetics approaches were used to study domestication genes (Btr1, Btr2, and Vrs) in ancient and contemporary barleys (germplasm accessions preserved at VIR).Materials and methods. The carbonized kernels found by archaeologists during the excavations at Usvyaty were analyzed. Primers for domestication genes were designed, and PCR was performed on contemporary and ancient barley grains. Ancient kernels were studied in accordance with the rules established for organizing a paleogenetics laboratory, which excluded any contamination with contemporary DNA. Fragments of domestication genes from contemporary and ancient barley grain samples underwent Sanger sequencing. Results. Ancient DNA was isolated and enriched. The analysis of domestication gene sequences made it possible to reconstruct the ancient barley spike’s features. Conclusion. The ancient cereal crop architectonics was restored to ascertain a brittle two-row spike of ancient barley

Unveiling the hidden world: How arbuscular mycorrhizal fungi and its regulated core fungi modify the composition and metabolism of soybean rhizosphere microbiome

BackgroundThe symbiosis between arbuscular mycorrhizal fungi (AMF) and plants often stimulates plant growth, increases agricultural yield, reduces costs, thereby providing significant economic benefits. AMF can also benefit plants through affecting the rhizosphere microbial community, but the underlying mechanisms remain unclear. Using Rhizophagus intraradices as a model AMF species, we assessed how AMF influences the bacterial composition and functional diversity through 16 S rRNA gene sequencing and non-targeted metabolomics analysis in the rhizosphere of aluminum-sensitive soybean that were inoculated with pathogenic fungus Nigrospora oryzae and phosphorus-solubilizing fungus Talaromyces verruculosus in an acidic soil.ResultsThe inoculation of R. intraradices, N. oryzae and T. verruculosus didn’t have a significant influence on the levels of soil C, N, and P, or various plant characteristics such as seed weight, crude fat and protein content. However, their inoculation affected the structure, function and nutrient dynamics of the resident bacterial community. The co-inoculation of T. verruculosus and R. intraradices increased the relative abundance of Pseudomonas psychrotolerans, which was capable of N-fixing and was related to cry-for-help theory (plants signal for beneficial microbes when under stress), within the rhizosphere. R. intraradices increased the expression of metabolic pathways associated with the synthesis of unsaturated fatty acids, which was known to enhance plant resistance under adverse environmental conditions. The inoculation of N. oryzae stimulated the stress response inside the soil environment by enriching the polyene macrolide antifungal antibiotic-producing bacterial genus Streptomyces in the root endosphere and upregulating two antibacterial activity metabolic pathways associated with steroid biosynthesis pathways in the rhizosphere. Although inoculation of pathogenic fungus N. oryzae enriched Bradyrhizobium and increased soil urease activity, it had no significant effects on biomass and N content of soybean. Lastly, the host niches exhibited differences in the composition of the bacterial community, with most N-fixing bacteria accumulating in the endosphere and Rhizobium vallis only detected in the endosphere.ConclusionsOur findings demonstrate that intricate interactions between AMF, associated core fungi, and the soybean root-associated ecological niches co-mediate the regulation of soybean growth, the dynamics of rhizosphere soil nutrients, and the composition, function, and metabolisms of the root-associated microbiome in an acidic soil.