RESUMEN
A Gram-negative, aerobic, non-motile, ovoid bacterium, designated strain MF3-039T, was isolated from tidal mudflat sediment sampled in Gunsan, Republic of Korea. The strain formed yellow-pigmented colonies on marine agar and was positive for catalase and oxidase. It grew at temperatures ranging from 10 to 37 °C (optimum, 25 °C), pH levels from 6.0 to 9.0 (optimum, 7.0), and 0 to 7.0% (w/v) NaCl (optimum, 2.0%). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain MF3-039T clustered within the genus Altererythrobacter (family Erythrobacteraceae), with closest sequence similarity to Altererythrobacter insulae KCTC 63421T (97.9%), Altererythrobacter ishigakiensis ATCC BAA-2084T (97.9%), Altererythrobacter rubellus NBRC 112769T (97.2%), and Tsuneonella suprasediminis KCTC 62388T (97.1%). The draft genome was 2.9 Mbp with a G + C content of 60%. Genomic comparisons indicated average nucleotide identity and digital DNA-DNA hybridisation values below 95% and 70%, respectively, with related Altererythrobacter species. Chemotaxonomic analysis revealed ubiquinone-10 as the primary respiratory quinone, C17:1 ω6c and summed feature 8 (comprising C18:1 ω7c/C18:1 ω6c), and summed feature 3 (C16:1 ω7c/C16:1 ω6c) as predominant fatty acids, and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, a sphingoglycolipid, an unidentified glycolipid, and an unidentified lipid as major polar lipids. The combination of phenotypic, chemotaxonomic, genomic, and phylogenetic features clearly distinguishes strain MF3-039T from existing genera within the family Erythrobacteraceae. On the basis of these polyphasic analyses, strain MF3-039T represents a novel genus and species, for which the name Litorerythrobacter xanthomarinus gen. nov., sp. nov. is proposed. The type strain is MF3-039T (= KEMB 23948T = KCTC 8705T = TBRC 19385T).
Asunto(s)
Alphaproteobacteria , Sedimentos Geológicos , Agua de Mar , Filogenia , Sedimentos Geológicos/microbiología , ARN Ribosómico 16S/genética , Composición de Base , Ácidos Grasos/análisis , ADN Bacteriano/genética , ADN Bacteriano/química , República de Corea , Técnicas de Tipificación Bacteriana , Fenotipo , Fosfolípidos/análisis , Agua de Mar/microbiología , Alphaproteobacteria/clasificación , Alphaproteobacteria/genética , Alphaproteobacteria/aislamiento & purificación , Hibridación de Ácido Nucleico , Análisis de Secuencia de ADNRESUMEN
An actinomycete, designated strain H11422T, was isolated from sediment collected from Mahu Lake, Sichuan Province, P.R. China, and characterized by a polyphasic taxonomic approach. Strain H11422T, based on the 16 S rRNA gene sequence analysis, exhibited the highest similarities to Pseudonocardia acidicola K10HN5T (98.5%), Pseudonocardia bannensis YIM63101T (97.9%), Pseudonocardia nigra ATK03T (97.8%) and Pseudonocardia saturnea IMSNU 20,052T (97.7%). Phylogenetic analysis based on the 16 S rRNA gene sequence placed strain H11422T into the genus Pseudonocardia, where it formed a subclade with Pseudonocardia acidicola K10HN5T. Genomic comparison with the closest type strain revealed average nucleotide identity (ANI) value of 84.8%, average amino acid identity (AAI) value of 81.6%, and digital DNA-DNA hybridization (dDDH) value of 28.9%, all significantly below the accepted species delineation thresholds. The whole-cell hydrolysates of strain H11422T were composed of meso-diaminopimelic acid (meso-DAP) as the diagnostic diamino acid, and arabinose, galactose, glucose and ribose as the major sugars. Mycolic acids were not present. The only menaquinone was determined to be MK-8(H4). The phospholipid profile included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, three unidentified phospholipids, two unidentified aminophospholipids and two unidentified lipids. The predominant fatty acid was iso-C16:0. Based on this comprehensive taxonomic evidence, strain H11422T represents a novel species within the genus Pseudonocardia, for which the name Pseudonocardia mahuensis sp. nov. is proposed. The type strain is H11422T (= JCM 34850T = CICC 25117T).
Asunto(s)
Actinomycetales , Sedimentos Geológicos , Lagos , China , Lagos/microbiología , Filogenia , Sedimentos Geológicos/microbiología , ARN Ribosómico 16S/genética , Ácidos Grasos/análisis , Ácidos Grasos/química , ADN Bacteriano/genética , Técnicas de Tipificación Bacteriana , Actinomycetales/clasificación , Actinomycetales/genética , Actinomycetales/aislamiento & purificación , Composición de Base , Hibridación de Ácido Nucleico , Análisis de Secuencia de ADN , Fosfolípidos/análisis , Vitamina K 2/análisisRESUMEN
The generation and maintenance of biodiversity are strongly influenced by adaptations to symbiotic interactions. In antagonistic host-parasite systems, such as phytophagous insects on plants, the prevalence of host-associated differentiation (HAD) may be underestimated as a key driver in parasite diversification. Even less well understood is how HAD may cascade up the food chain to influence diversification in higher trophic levels. Gall-inducing insects, which exhibit strong plant host specialisation, create microhabitats that support diverse associated communities that include predators, parasitoids and inquilines. In this study, we investigate whether HAD in gall-inducing Aciurina flies extends to their associates, resulting in a pattern of cascading HAD. We analysed genomic and ecological data across parasitoid species from three functional guilds, testing for host-driven divergence. Our results reveal that cascading HAD in Aciurina galling systems occurs in endoparasitoids, with no evidence for it in generalist ectoparasitoids and inquilines, underscoring that different types of interactions have different impacts on diversification. Additionally, evidence for host-specific cryptic species within the dominant endoparasitoid allowed us to formally describe Eurytoma trixa, Eurytoma ericameria and Eurytoma luminaria as new species. These findings provide strong evidence of multiple cascading HAD events within a galling insect community and highlight the compounding influence of gall inducers, as ecosystem engineers, on biodiversity.
Asunto(s)
Dípteros , Cadena Alimentaria , Interacciones Huésped-Parásitos , Insectos , Tumores de Planta , Animales , Interacciones Huésped-Parásitos/genética , Tumores de Planta/parasitología , Biodiversidad , Simbiosis , Insectos/genética , Dípteros/genética , FilogeniaRESUMEN
Porcine reproductive and respiratory syndrome virus (PRRSV) remains a major threat to global swine production. In this study, a novel strain (PRRSV-AH1) was isolated during a respiratory disease outbreak at a commercial swine operation in Anhui Province, China. Viral replication in MARC-145 cells was confirmed by observing cytopathic effects (CPEs) and conducting immunofluorescence assays (IFAs). Whole-genome sequencing revealed a 15,020 bp genome exhibiting 90.0% identity with the NADC30 reference strain, including lineage 1-characteristic nonstructural polyprotein (Nsp)2 deletions. A distinctive L10S substitution in GP2 aligned with conserved residues of PRRSV-1. Recombination analysis identified PRRSV-AH1 as a novel chimera with a NADC30-like backbone incorporating CH-1a-like (lineage 8), JXA1-like (lineage 8), and QYYZ-like (lineage 3) sequences-representing the first reported instance of this specific recombination pattern. Experimental infection of piglets induced characteristic PRRSV pathology, including sustained pyrexia, reduced weight gain, prolonged viremia, and neutralizing antibody seroconversion. Comparative pathogenicity analysis revealed that the PRRSV-AH1 strain elicited febrile responses and peak body temperatures intermediate between classic NADC30-like strains and JXA1 strains. Notably, PRRSV-AH1 demonstrated a PRRSV-N-specific IgG induction capacity comparable to that of highly pathogenic variants. These findings establish PRRSV-AH1 as a multilineage recombinant (NADC30-like, CH-1a, QYYZ, and JXA1 Lineages) resulting from multiple genetic exchanges, underscoring the increasing complexity of PRRSV diversity in China. Accelerated mutation and recombination across lineages complicate disease control efforts, emphasizing the need for enhanced surveillance, mechanistic recombination studies, and the development of novel vaccines to mitigate future outbreaks.
Asunto(s)
Síndrome Respiratorio y de la Reproducción Porcina , Virus del Síndrome Respiratorio y Reproductivo Porcino , Animales , Virus del Síndrome Respiratorio y Reproductivo Porcino/genética , Virus del Síndrome Respiratorio y Reproductivo Porcino/clasificación , Virus del Síndrome Respiratorio y Reproductivo Porcino/aislamiento & purificación , Virus del Síndrome Respiratorio y Reproductivo Porcino/patogenicidad , Síndrome Respiratorio y de la Reproducción Porcina/virología , Síndrome Respiratorio y de la Reproducción Porcina/epidemiología , Porcinos , China/epidemiología , Recombinación Genética , Filogenia , Genoma ViralRESUMEN
Ovine herpesvirus 1 (OvHV-1) was first identified over 50 years ago in sheep with ovine pulmonary adenocarcinoma (OPA). An aetiological role in OPA was later ruled out and OvHV-1 was found to be a common infection in sheep in several countries. Here, we report the sequence and annotation of the complete OvHV-1 genome. The virus has a similar genomic architecture to members of the Macavirus genus of the subfamily Gammaherpesvirinae and is most closely related to bovine gammaherpesvirus 6 (BoGHV6). The OvHV-1 genome comprises a 144,637 bp unique region predicted to encode at least 74 proteins bounded by multiple copies of a 699 bp GC-rich repetitive terminal repeat. Predicted genes include 61 ORFs conserved among all gammaherpesviruses, and 12 genes present only in macavirus genomes, including a homologue of ovine IL-10, previously reported only in ovine gammaherpesvirus 2, and an ornithine decarboxylase, previously described only in BoGHV6. A further gene appears unique to OvHV-1 among macaviruses, encoding a viral-FLIP (FLICE-like inhibitory protein), similar to those found in some other gammaherpesviruses. Notably, several macavirus genes previously predicted in BoGHV6 are defective in OvHV-1. The availability of the genome sequence of OvHV-1 will facilitate studies on its relationship to other macaviruses and its role, if any, in disease.
Asunto(s)
Gammaherpesvirinae , Genoma Viral , Animales , Ovinos , Gammaherpesvirinae/genética , Gammaherpesvirinae/clasificación , Gammaherpesvirinae/aislamiento & purificación , Sistemas de Lectura Abierta , Anotación de Secuencia Molecular , Filogenia , Proteínas Virales/genética , Enfermedades de las Ovejas/virología , Infecciones por Herpesviridae/veterinaria , Infecciones por Herpesviridae/virología , Análisis de Secuencia de ADN , ADN Viral/genética , ADN Viral/químicaRESUMEN
Infectious Bursal Disease (IBD), or Gumboro disease, is an acute, highly contagious viral infection that primarily affects young chickens, causing immunosuppression and mortality. This study aimed to characterize the genetic and pathological features of recent IBD outbreaks in Kashmir, India. A total of 32 suspected outbreaks were investigated from 2021 to 2023 across three districts: Srinagar, Ganderbal, and Budgam. Bursal tissues were collected for both histopathology and molecular detection. RT-PCR targeting the hypervariable region (HVR) of the VP2 gene confirmed IBDV infection in 29 samples (90.63%), yielding a 912 bp amplicon. Four representative strains (GDK1-GDK4) were sequenced, showing 99.89% nucleotide identity. Phylogenetic analysis grouped these isolates under Genotype A3, closely related to the Indian vvIBDV strain MF142522 and distinctly separate from commonly used vaccine strains (Genotype A1), suggesting possible vaccine mismatch. Clinically, affected birds exhibited depression, anorexia, diarrhea, and ruffled feathers. Gross lesions included hemorrhages in the thigh and breast muscles, and severe bursal enlargement with hemorrhagic folds. Histopathological findings revealed hemorrhages at interfollicular junctions, lymphoid depletion, heterophilic infiltration, interfollicular fibroplasia, and cystic degeneration of follicles. Besides the bursa, lesions were also noted in the kidneys, thymus, and caecal tonsils. These findings confirmed the involvement of vvIBDV strains in the outbreaks. The study highlights the genetic divergence of circulating field strains from vaccine strains and emphasizes the need for continuous molecular surveillance and vaccine reevaluation to control the disease effectively in this region. The distinct ecological and poultry trade dynamics of Kashmir may contribute to the emergence and persistence of such virulent strains.
Asunto(s)
Infecciones por Birnaviridae , Pollos , Virus de la Enfermedad Infecciosa de la Bolsa , Enfermedades de las Aves de Corral , Animales , Virus de la Enfermedad Infecciosa de la Bolsa/genética , Virus de la Enfermedad Infecciosa de la Bolsa/patogenicidad , India/epidemiología , Infecciones por Birnaviridae/veterinaria , Infecciones por Birnaviridae/virología , Infecciones por Birnaviridae/epidemiología , Infecciones por Birnaviridae/patología , Enfermedades de las Aves de Corral/virología , Enfermedades de las Aves de Corral/epidemiología , Enfermedades de las Aves de Corral/patología , Filogenia , Brotes de Enfermedades/veterinaria , Virulencia , GenotipoRESUMEN
A strain designated YIM 98842T, belonging to the genus Virgibacillus was isolated and characterized from a hypersaline sediment of Aiding Lake in Xinjiang Province, North-west China. The strain was Gram-positive, halophilic, rod-shaped, aerobic and motile, could grow at 10-50 â, 0-20% (w/v) NaCl concentrations, pH 6.5-9.5, with optimal growth at 37 â, 5-10% (w/v) NaCl and pH 7.5. The lipidomic profile showed diphosphatidylglycerol, phosphatidylglycerol and one undetermined phospholipid as the major polar lipids. The whole cell analysis indicated MK-7 as the predominant menaquinone, meso-diaminopimelic acid with ribose and glucose-NH3 as the typical whole-cell sugars, anteiso-C15:0, iso-C16:0, iso-C15:0, iso-C14:0 as the main fatty acids. The genomic DNA G + C content was 40.4 mol%. A phylogenetic analysis based on the 16S rRNA gene of the strain YIM 98842T with publicly available reference data revealed that the YIM 98842T belongs to the genus Virgibacillus, with the highest similarity to Virgibacillus kimchii (98.25%) and Virgibacillus salarius SA-Vb1T (97.04%). The evidence of the phenotypic, chemotaxonomic, and phylogenetic analysis indicated that strain YIM 98842T represents a novel species of the genus Virgibacillus, for which the name Virgibacillus aidingensis sp. nov. is proposed. The type strain is YIM 98842T (= CGMCC 1.17259T = NBRC 114104T).
Asunto(s)
Sedimentos Geológicos , Virgibacillus , China , Sedimentos Geológicos/microbiología , Filogenia , ARN Ribosómico 16S/genética , Virgibacillus/clasificación , Virgibacillus/genética , Virgibacillus/aislamiento & purificación , Virgibacillus/fisiología , Composición de Base , Ácidos Grasos/análisis , ADN Bacteriano/genética , Técnicas de Tipificación Bacteriana , Cloruro de Sodio/metabolismo , Lagos/microbiología , Salinidad , Fosfolípidos/análisisRESUMEN
Twenty-three novel psychrophilic bacteria, represented by the type strains LB2P44T, LB2P6T, LB1P62T, LB3P6T, LS1P3T, XS2P39T, XS1P32T, ZB4P13T, ZS1P14T and GT2P42T, were isolated from ice, cryoconite and meltwater of five Tibetan Plateau glaciers. All strains were Gram-stain-negative, aerobic, rod-shaped and psychrophilic, with optimal growth at 14-20 °C and pH 7.0. 16S rRNA gene sequence similarities to validly named Flavobacterium species ranged from 98.12% to 99.56%. Phylogenomic analysis of 81 concatenated core genes positioned the 23 strains (comprising the ten novel species) within a robust monophyletic clade - the 'Cryospheric Lineage' - together with 31 other psychrophilic type strains predominantly from glaciers, permafrost and polar regions. Average nucleotide identity (ANI) values of ≤94.4% and digital DNA-DNA hybridization (dDDH) values of ≤57.3% against closest relatives were below species thresholds (95-96% ANI, 70% dDDH). Major fatty acids were iso-C15:0 (8.1-16.8%), iso-C15:0 3-OH (3-hydroxy, 5.2-16.0%) and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c, 10.1-27.6%), with elevated branched-chain and unsaturated components typical of cold adaptation. Polyphasic taxonomic evidence supports the description of ten novel species within the genus Flavobacterium: Flavobacterium amylolyticum sp. nov. (LB2P44T=CGMCC 1.11256T=NBRC 114815T), Flavobacterium glucosi sp. nov. (LB2P6T=CGMCC 1.11263T=NBRC 114816T), Flavobacterium esculini sp. nov. (LB1P62T=CGMCC 1.11346T=NBRC 114817T), Flavobacterium labens sp. nov. (LB3P6T=CGMCC 1.11428T=NBRC 114818T), Flavobacterium pasteuri sp. nov. (LS1P3T=CGMCC 1.11474T=NBRC 114821T), Flavobacterium rhamnosi sp. nov. (XS2P39T=CGMCC 1.23204T=NBRC 115054T), Flavobacterium frigidum sp. nov. (XS1P32T=CGMCC 1.23370T=NBRC 115055T), Flavobacterium glycogeni sp. nov. (ZB4P13T=CGMCC 1.24050T=NBRC 115056T), Flavobacterium kochi sp. nov. (ZS1P14T=CGMCC 1.24093T=NBRC 114828T) and Flavobacterium cryophilum sp. nov. (GT2P42T=CGMCC 1.24821T=NBRC 114831T).
Asunto(s)
Flavobacterium , Cubierta de Hielo , Filogenia , Flavobacterium/clasificación , Flavobacterium/genética , Flavobacterium/aislamiento & purificación , Tibet , Cubierta de Hielo/microbiología , ARN Ribosómico 16S/genética , ADN Bacteriano/genética , Técnicas de Tipificación Bacteriana , Análisis de Secuencia de ADN , Composición de Base , Ácidos Grasos/análisis , Frío , Hibridación de Ácido NucleicoRESUMEN
A novel Agromyces strain, designated as M3QZ16-3T, was isolated from the rhizosphere soil of Excoecaria agallocha, collected from the Maowei Sea Mangrove Nature Reserve in the Guangxi Zhuang Autonomous Region, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M3QZ16-3T was closely related to species of the genus Agromyces and shared the highest similarity of 99.26% with Agromyces kandeliae Q22T. The average nucleotide identity and digital DNA-DNA hybridization values between strain M3QZ16-3T and the type strain of A. kandeliae Q22T were 88.2% and 34.4%, respectively. The polar lipids of strain M3QZ16-3T comprised diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid, one unidentified polar lipid and two unidentified lipids. The major cellular fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C15:0 and iso-C16:0, and the predominant menaquinones (MK; vitamin K2) were MK-12 (78.3%) and MK-11 (14.3%). Cell-wall amino acids were 2,4-diaminobutyric acid, glutamic acid, glycine and alanine. The genome size of strain M3QZ16-3T was 3.8 Mb, with a DNA G+C content value of 71.7 mol%. Based on the above descriptions, we propose strain M3QZ16-3T to represent a novel species of the genus Agromyces, for which the name Agromyces excoecariae sp. nov. is proposed. The type strain is M3QZ16-3T (=MCCC 1K07179T=JCM 34940T).
Asunto(s)
Euphorbiaceae , Filogenia , Rizosfera , Microbiología del Suelo , ARN Ribosómico 16S/genética , Ácidos Grasos/análisis , Ácidos Grasos/química , Composición de Base , China , Hibridación de Ácido Nucleico , ADN Bacteriano/genética , Técnicas de Tipificación Bacteriana , Análisis de Secuencia de ADN , Vitamina K 2/análisis , Fosfolípidos/análisis , Euphorbiaceae/microbiologíaRESUMEN
Cyclic dinucleotides (CDNs), such as cyclic di-AMP (c-di-AMP) and cyclic di-GMP (c-di-GMP), are key second messengers that regulate fundamental bacterial processes, including cell wall synthesis, biofilm formation, antibiotic resistance, stress response, and virulence. These pathways are particularly relevant in major pathogens like Mycobacterium tuberculosis. Increasing evidence highlights the pathogenic potential of non-tuberculous mycobacteria (NTM), originally environmental species that are emerging as significant human pathogens. Understanding the evolution of CDN signaling may therefore provide critical insights into this transition. Our comparative genomic analysis revealed that the c-di-AMP synthase disA is present as a single copy in nearly all mycobacterial genomes, except within the genus Mycolicibacter.The corresponding phosphodiesterases, pde and ataC, are variably distributed, with pathogenic mycobacteria showing a preference for pde over ataC. In contrast to the relatively conserved c-di-AMP system, the c-di-GMP pathway comprising diguanylate cyclases (DGCs) and phosphodiesterases (PDEs), exhibits remarkable variation in gene presence/absence and domain architecture across the Mycobacteriaceae family. This diversity suggests multiple independent gene gain and loss events throughout evolution, often accompanied by the acquisition of accessory domains. Evolutionary analyses reveal a clear dichotomy between the two CDN signaling systems. The c-di-AMP pathway, governed by disA, which is under strong purifying selection similar to core housekeeping genes, and pde, which shows low genetic variability, underscores its conserved and essential role in maintaining core cellular physiology. In contrast, the c-di-GMP system is markedly more heterogeneous, consistent with its function in environmental sensing and adaptation. Together, these findings highlight a sharp evolutionary split in CDN signaling within the Mycobacteriaceae family, c-di-AMP serves as an indispensable regulator of core physiological processes, whereas c-di-GMP confers flexibility for niche-specific adaptation and survival.
Asunto(s)
GMP Cíclico , Fosfatos de Dinucleósidos , Evolución Molecular , Mycobacterium , Transducción de Señal , GMP Cíclico/metabolismo , GMP Cíclico/análogos & derivados , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Hidrolasas Diéster Fosfóricas/genética , Hidrolasas Diéster Fosfóricas/metabolismo , Filogenia , Liasas de Fósforo-Oxígeno/genética , Liasas de Fósforo-Oxígeno/metabolismo , Mycobacterium/genética , Mycobacterium/metabolismo , Genoma Bacteriano , Fosfatos de Dinucleósidos/metabolismo , Mycobacterium tuberculosis/genética , Proteínas de Escherichia coliRESUMEN
C-phycocyanin (C-PC) is a high-value blue phycobiliprotein extensively utilized as a natural colorant and multifunctional bioactive compound. This study employed a polyphasic framework to characterize eleven native cyanobacterial isolates (NTBN series) from temple ponds in Tamil Nadu, India, with the aim of quantifying extractable C-PC and correlating pigment yield with molecular traits of the C-PC ß-subunit. All isolates were cultivated under identical, non-optimized conditions (BG-11 medium, 25 ± 2 °C, 16:8 h light: dark, ~ 50 µmol photons m⻲ s⻹, 21 days, n = 3). Crude pigments were extracted and quantified spectrophotometrically, while cpcB sequences were subjected to homology modeling and physicochemical profiling (GRAVY, aliphatic index, instability index). Among the isolates, NTBN-07 and NTBN-15 exhibited the highest extractable C-PC content. Strains with lower GRAVY values (greater hydrophilicity) and moderate aliphatic indices consistently showed higher pigment productivity, as supported by multivariate analyses (heatmap and PCA). Homology models revealed conserved chromophore-binding residues with subtle tertiary conformational variations potentially influencing pigment stability and extractability. Although several native isolates yielded more C-PC than the laboratory reference Synechocystis sp. PCC 6803 under uniform, non-optimized conditions, their yields remained lower than those reported for optimized Arthrospira cultures. Study limitations include the use of crude extracts and reliance on in silico predictions pending protein-level validation. Overall, this work identifies temple-pond cyanobacteria as promising native bioresources for predictive strain selection, downstream process optimization, and sustainable pigment biotechnology.
Asunto(s)
Cianobacterias , Ficocianina , Estanques , Ficocianina/química , Ficocianina/genética , Ficocianina/metabolismo , Cianobacterias/genética , Cianobacterias/aislamiento & purificación , Cianobacterias/química , Cianobacterias/metabolismo , Cianobacterias/clasificación , India , Estanques/microbiología , Proteínas Bacterianas/genética , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Filogenia , Pigmentos Biológicos/metabolismo , Pigmentos Biológicos/química , Modelos MolecularesRESUMEN
Acute gastroenteritis (AGE) is a significant cause of morbidity and mortality among children under five years where viral agents are major contributors to AGE. Limited data exist on molecular epidemiology of viral gastroenteritis in northeastern India. The present study aimed to determine the prevalence and molecular diversity of major viral agents causing AGE in children under five years in Assam, India. A hospital-based prospective study was conducted from January 2022 to December 2023. Stool samples (n = 110) from children with AGE were screened for rotavirus A (RVA), adenovirus (HAdV), norovirus (NoV), astrovirus (HAstV) and sapovirus (SaV) using multiplex real-time Polymerase Chain Reaction, followed by genotyping and sequencing of selected isolates. Phylogenetic analysis was conducted to identify specific circulating strains. Enteric viruses were detected in 44.5 % (49/110) of samples. HAdV (16.36 %) was the most prevalent, followed by RVA (11.81 %), NoV GII (7.27 %), SaV (0.9 %) and HAstV (0.9 %). Mixed infections occurred in 14.55 %, mainly HAdV-NoV GII. Phylogenetic analysis identified HAdV species F (serotypes 40 and 41), NoV genotypes GII.4 and GII.2, RVA genotype G3P[8] and HAstV-1. HAdV-41 was the predominant adenovirus type, closely related to global strains. No correlation was found between mixed infections and disease severity. The predominance of HAdV-41 and exclusive detection of RVA G3P[8] reflect evolving viral epidemiology in the post-rotavirus vaccine era. Continuous molecular surveillance and strengthened WASH (water, sanitation and hygiene) interventions are essential to guide vaccine strategies and reduce the burden of viral gastroenteritis in young children in northeast India.
Asunto(s)
Gastroenteritis , Virosis , Virus , Humanos , Gastroenteritis/virología , Gastroenteritis/epidemiología , India/epidemiología , Preescolar , Lactante , Estudios Prospectivos , Filogenia , Heces/virología , Masculino , Femenino , Genotipo , Prevalencia , Epidemiología Molecular , Enfermedad Aguda/epidemiología , Virus/genética , Virus/clasificación , Virus/aislamiento & purificación , Rotavirus/genética , Rotavirus/aislamiento & purificación , Norovirus/genética , Norovirus/aislamiento & purificación , Virosis/epidemiología , Virosis/virologíaRESUMEN
Bacterial blight (causal agent Pseudomonas syringae complex, Psc) is an endemic and economically important disease of northern highbush blueberry production in Canada and the Pacific Northwest of the USA. To date, there is no comprehensive survey of the disease in the region and detailed characterization of associated pathogens from Pacific western Canada. Therefore, we did comprehensive disease survey and characterization of associated pseudomonads population using pathogen morphology, biochemical tests, and molecular characterization. We isolated 380 strains of pseudomonads from symptomatic plants from 32 research and commercial fields in 10 diverse geographic locations in British Columbia. We used P. syringae specific (Psy) primers and identified 197 Psy-PCR positive isolates out of 380. We further sequenced Psy-PCR positive isolates of pseudomonads using four housekeeping genes and identified four phylogenomic species: P. syringae (40%), Pseudomonas avellanae (29%), Pseudomonas viridiflava (20%), and phylogenomic species A (7%). P. avellanae and P. viridiflava are new phylogenomic species of Psc causing bacterial blight in highbush blueberry. We found some patterns among geographical locations and highbush blueberry varieties in the frequency distribution of isolates of these phylogenomic species. Genetic fingerprinting with rep-PCR assays identified a very high genetic diversity of pseudomonads populations among geographical locations, varieties, and phylogenomic species. Biochemical characterization (LOPAT- levan, oxidase, pectolytic activity, arginine dihydrolase, and tobacco hypersensitivity) revealed that the vast majority of isolates were Pseudomonas Group Ia. Findings of this study provide insight into the population biology of pseudomonads infecting highbush blueberry, provide information for disease diagnosis, and exploit disease management options, including identifying sources of disease resistance. KEY POINTS: ⢠High prevalence of bacterial blight caused by P. syringae complex (Psc) in highbush blueberry in Pacific western Canada ⢠We report two new phylogenomic species of Psc, P. viridiflava and P. avellanae, that cause bacterial blight and canker disease in highbush blueberry ⢠The genetic diversity of the population of Psc was very high.
Asunto(s)
Arándanos Azules (Planta) , Variación Genética , Enfermedades de las Plantas , Pseudomonas syringae , Pseudomonas , Arándanos Azules (Planta)/microbiología , Enfermedades de las Plantas/microbiología , Filogenia , Colombia Británica , Pseudomonas/genética , Pseudomonas/clasificación , Pseudomonas/aislamiento & purificación , Pseudomonas syringae/genética , Pseudomonas syringae/aislamiento & purificación , Pseudomonas syringae/clasificación , ADN Bacteriano/genéticaRESUMEN
Magnetotactic bacteria (MTB) are a diverse group of microorganisms that synthesize intracellular magnetic nanocrystals termed magnetosomes. In this study, a novel marine magnetotactic coccus, designated strain HHB-1, was magnetically enriched from intertidal sediments in Houhai Bay, southern China. Optical microscopy, electron microscopy and elemental analysis revealed that HHB-1 cells are relatively large coccoid-ovoid bacteria (3.9 ± 0.3 µm × 2.8 ± 0.2 µm) containing multiple chains of prismatic magnetite magnetosomes and prominent intracellular Ca/Mg-rich polyphosphate (Ca-Mg-polyP) granules. Whole-genome sequencing and phylogenomic analyses revealed that HHB-1 represents a novel and deeply branching lineage within the order Magnetococcales, exhibiting low average amino acid identity (57.3%-58.7%) with previously reported strains. The magnetosome gene cluster (MGC) of HHB-1 comprises a nearly complete set of mam (magnetosome membrane) genes with conserved gene order and structure, representing the first genomic and MGC characterization of a novel magnetococcus possessing multi-chain magnetosomes. These findings expand our understanding of the diversity, biomineralization strategies and evolutionary history of MTB in marine environments.
Asunto(s)
Sedimentos Geológicos , Magnetosomas , Filogenia , Magnetosomas/genética , Magnetosomas/metabolismo , Magnetosomas/ultraestructura , Sedimentos Geológicos/microbiología , China , Familia de Multigenes , Secuenciación Completa del Genoma , Genoma BacterianoRESUMEN
A novel polysaccharide-degrading bacterial strain, designated ASW11-125T, was isolated from intertidal sediments in Aoshan Bay, Qingdao, China. The strain was strictly aerobic, Gram-stain-negative, catalase-positive but oxidase-negative, short rod-shaped, and exhibited gliding motility without flagella. Growth occurred at 4-35°C (optimum 28°C), pH 6.0-8.0 (optimum pH 7.0), and in 0.5-16.0% NaCl (optimum 2.5-3.0%). The predominant polar lipid was phosphatidylethanolamine. Major fatty acids were iso-C15:0 and iso-C17:0 3-OH, and the primary respiratory quinone was menaquinone-6 (MK-6). Based on the phylogenetic analyses of 16S rRNA gene sequences and 1542 single copy orthologous clusters, strain ASW11-125T affiliated with the genus Christiangramia and was closely related to Christiangramia portivictoriae MCCC 1A00585T (98.8%), Christiangramia aquimixticola KCTC 42706T (98.8%) and Christiangramia marina KCTC 12366T (98.6%). Comparative genomic analysis revealed that the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain ASW11-125T and its closely related species were 74.6-91.5% and 18.6-44.3%, respectively, which were below the cutoff values for proposing a novel species. Based on a polyphasic characterization integrating phenotypic, phylogenetic, and chemotaxonomic evidence, strain ASW11-125T represents a novel species of the genus Christiangramia, for which the name Christiangramia qingdaonensis sp. nov. is proposed. The draft genome of strain ASW11-125T is 3.2 Mb in size with a G + C content of 38.3%. Notably, genomic analysis revealed an abundance of genes encoding putative carbohydrate-active enzymes (CAZymes), particularly those associated with starch, laminarin, and fructan utilization, suggesting its potential role in the marine carbon cycle. The type strain is ASW11-125T (= KCTC 102340T = MCCC 1K09555T).
Asunto(s)
Bacteroidetes , Sedimentos Geológicos , Polisacáridos , Sedimentos Geológicos/microbiología , Filogenia , ARN Ribosómico 16S/genética , Ácidos Grasos/análisis , Composición de Base , ADN Bacteriano/genética , ADN Bacteriano/química , China , Bacteroidetes/clasificación , Bacteroidetes/aislamiento & purificación , Bacteroidetes/genética , Bacteroidetes/metabolismo , Polisacáridos/metabolismo , Técnicas de Tipificación Bacteriana , Hibridación de Ácido Nucleico , Genoma BacterianoRESUMEN
Solute carriers (SLCs) mediate cell- and organelle-specific import and export of nutrients and metabolites required for every biochemical process that occurs in a cell. Functional studies have ascribed activities to many human genes annotated as SLCs, but more than 100 SLCs remain orphans. Here, we applied a set of computational tools to characterize the orphan carriers SLC35F4 and SLC35F5. Phylogenetic analysis grouped SLC35F4 sister to SLC35F3, a suspected thiamine transporter, in a clade with SLC35F5, and distinct from an SLC35F6/2/1 clade. Transcriptome datasets revealed a restricted function for SLC35F4 in the cerebellum, in contrast to the more widespread distribution of SLC35F5. Gene ontology identified the Golgi apparatus as the likely residence of both transporters. Conceptual docking of 71 candidate substrates predicted high affinities of SLC35F4 (10-40 nM) and SLC35F5 (0.1-0.4 nM) for flavin adenine dinucleotide (FAD), straddling that of the known FAD transporter SLC25A32 (2-4 nM), while returning much lower affinities (by 30-fold or more) for all other tested substrates. Docking to SLC35F3 returned low affinity for both FAD and thiamine as candidate substrates. Thus, SLC35F4 and SLC35F5 but not closely related SLC35F3 likely import FAD into the Golgi apparatus, where the cofactor serves as the oxidant for disulfide-bond formation during tissue-specific, post-translational modification of secretory proteins. These findings provide strong direction for the definitive experiments yet needed to confirm the carriers' subcellular localization, transport activities, and contributions to protein maturation and trafficking.
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Aparato de Golgi , Proteínas de Transporte de Membrana , Humanos , Aparato de Golgi/metabolismo , Proteínas de Transporte de Membrana/metabolismo , Proteínas de Transporte de Membrana/genética , Proteínas de Transporte de Membrana/química , Filogenia , Ontología de Genes , Modelos Moleculares , Simulación del Acoplamiento Molecular , Transporte BiológicoRESUMEN
A short rod-shaped, Gram-negative, strictly aerobic, non-motile bacterium, designated as NW5T, was isolated from a eutrophic pond in Jimo District, Qingdao, Shandong Province, China. The strain exhibited growth between 20-42 °C (optimal at 30 °C), pH 6.0-10.0 (optimal at pH 8.0), and 0-2.0% (w/v) NaCl (optimal at 0% NaCl). Based on 16S rRNA gene sequence analysis, strain NW5T showed the highest similarity with 'Pseudomonas oryzae' CGMCC 1.12417T (98.2%), followed by Pseudomonas oryzagri CGMCC 1.12618T (97.8%), and Pseudomonas guguanensis JCM 18416T (97.7%). Phylogenetic analysis based on 16S rRNA gene sequence and whole-genome sequence indicated that strain NW5T belongs to the genus Pseudomonas. The genome size of strain NW5T is approximately 2.6 Mb with a DNA G+C content of 65.3%, which is one of the smallest genomes reported to date among all Pseudomonas type strains. The average nucleotide identity and digital DNA-DNA hybridization values between strain NW5T and the closely related type strains were in the range of 75.8-87.2% and 21.4-26.6%, respectively, which were below the species delineation thresholds. The major fatty acids (≥5.0%) were C10:0 3-OH, C12:0, C16:0, summed feature 3 and summed feature 8. The predominant isoprenoid quinone was ubiquinone-8 (Q-8) and small amounts of Q-7 and Q-9 were also detected, which is quite different from the ubiquinone profile of Pseudomonas. Strain NW5T harbored a relatively large number of genes in the metabolic pathway for multi-xenobiotics degradation. In addition, strain NW5T was highly resistant to zinc (100 mM), consistent with the genotype. Based on the phenotypic, phylogenetic, chemotaxonomic, and physiological analyses, strain NW5T is considered to represent a novel species of the genus Pseudomonas, for which the name Pseudomonas eutrophicaquae sp. nov. is proposed. The type strain is NW5T (=GDMCC 1.3065T =MCCC 1K07223T =JCM 35388T).
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Pseudomonas , Ubiquinona , Pseudomonas/clasificación , Pseudomonas/aislamiento & purificación , Pseudomonas/genética , Pseudomonas/metabolismo , Pseudomonas/fisiología , Filogenia , China , ARN Ribosómico 16S/genética , Ubiquinona/análogos & derivados , Ubiquinona/análisis , Ubiquinona/metabolismo , Composición de Base , ADN Bacteriano/genética , ADN Bacteriano/química , Ácidos Grasos/análisis , Genoma Bacteriano , Técnicas de Tipificación Bacteriana , Análisis de Secuencia de ADN , Hibridación de Ácido Nucleico , EcosistemaRESUMEN
Intestinal parasites continue to pose a significant public health burden in low- and middle-income countries and are increasingly recognized in developed regions. Traditional diagnostic methods, primarily based on microscopy, remain widely used despite limitations in sensitivity and taxonomic resolution. In this exploratory study, we applied a next-generation sequencing (NGS)-based metataxonomic approach, integrated with classical phylogenetic methods, to characterize intestinal parasites in rural Colombian populations. We compare its performance with conventional microscopy, focusing on both protist and geohelminth detection. Metataxonomics outperformed microscopy in detecting Strongyloides stercoralis and enabled precise species and subtype level assignment for Blastocystis and Entamoeba spp., revealing frequent mixed infections. Microscopy detected Trichuris trichiura, Giardia, Cyclospora, and Chilomastix more effectively, highlighting limitations of current primers and DNA extraction methods. Cystoisospora was only identified by NGS. These results demonstrate the utility of NGS-based metataxonomics for broad parasite detection while emphasizing areas for methodological improvement and providing a foundation for future, larger-scale studies.
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Helmintos , Secuenciación de Nucleótidos de Alto Rendimiento , Parasitosis Intestinales , Parásitos , Animales , Humanos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Parasitosis Intestinales/diagnóstico , Parasitosis Intestinales/parasitología , Helmintos/genética , Helmintos/aislamiento & purificación , Helmintos/clasificación , Heces/parasitología , Filogenia , Parásitos/genética , Parásitos/aislamiento & purificación , Colombia , Entamoeba/genética , Entamoeba/aislamiento & purificación , MicroscopíaRESUMEN
Whole-genome duplication (WGD) has been proposed as a catalyst for evolutionary innovation in seed plants and angiosperms, yet their occurrence remains contentious. By integrating gene dosage balance principles with phylogenomic reconciliation and probabilistic modeling, we revisit the debated ancestral seed and angiosperm WGDs. Leveraging dosage-sensitive orthologous gene groups (OGs) as evolutionary markers across representative plants for gene tree/species tree reconciliation, we demonstrate that gene retention patterns in Amborella and Aristolochia-early-diverging plants lacking post-angiosperm origin WGDs-reveal a single gene duplication peak predating the seed plant diversification, with no signal of ancestral angiosperm WGD. Correlation analyses of observed and expected OG copy numbers, given proposed WGD(s), further refute an angiosperm WGD. Probabilistic retention modeling analysis corroborates these findings and shows that retention rates of dosage-sensitive genes from the putative angiosperm WGD are extremely low. Besides, our study establishes that genes inferred to have higher dosage sensitivity based on their sequential retention following WGD events may have increased utility in resolving ancestral polyploidy.
Asunto(s)
Dosificación de Gen , Duplicación de Gen , Genes de Plantas , Genoma de Planta , Magnoliopsida , Semillas , Magnoliopsida/genética , Semillas/genética , Filogenia , Evolución MolecularRESUMEN
This study evaluated the bioremediation potential of two psychrotolerant strains, Pusillimonas sp. ANT_WB101 and Dietzia sp. ANT_WB102, isolated from an uncontaminated water pond. Comparative analysis indicated affinities with P. gingsengisoli/soli and D. kunjamensis/maris. Both strains demonstrated substantial crude oil degradation efficiency, achieving ≥ 79% under aerobic conditions and ≥ 34% under anaerobic conditions. Genomic analysis identified crucial genes involved in crude oil degradation, including alkane monooxygenase, cytochrome P450, and polyphenol monooxygenase. These strains displayed adaptability to a wide range of environmental factors, such as pH (4-11), salinity (up to 6%-9%), temperature (4°C-37°C), resistance to freeze-thaw cycles, and tolerance to high crude oil concentration. Biosafety evaluations indicated the sensitivity of the strains to various antibiotics, ensuring their suitability and safety for environmental applications. At low temperature, these strains increased microbial activity in environmental samples (1.34 times in biological oxygen demand compared to the control) and showed effective biodegradation (~39%). In conclusion, the study highlights the potential of ANT_WB101 and ANT_WB102 for treating contaminated sites and indicates the possible challenges of using microorganisms not initially adapted to site-specific conditions in bioremediation efforts.