Current Microbiology最新文献

Human Papillomavirus (HPV) is a major contributor to various human cancers, particularly cervical cancer. Despite its significant impact, the codon usage bias in high-risk HPV types has not been extensively studied. Understanding this bias, however, could provide valuable insights into the virus itself and inform the optimization of vaccine design. This study explores codon usage bias within the genomes of 17 high-risk HPV types (HPV-16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, and 82) through comparative analysis. While overall codon usage preference across these genotypes is not highly significant, a notable trend emerges in the preference for codons ending in A or U, with 24 out of 26 favored codons (Relative Synonymous Codon Usage > 1) ending in A or U. Moreover, no common optimal codons are shared among the 17 genomes. The study also identifies the underrepresentation of CpG and ApA dinucleotides, alongside the overrepresentation of CpA and UpG, which likely contribute to codon usage preferences that may influence viral replication and immune evasion strategies. Integrated analysis further suggests that natural selection is the primary force driving codon usage bias in these high-risk HPV genomes. Additionally, these HPVs exhibit a limited set of favored codons shared with humans, potentially minimizing competition for translation resources. This study offers new insights into codon usage bias in high-risk HPVs and underscores the importance of this understanding for optimizing vaccine design.

False smut caused by Ustilaginoidea virens is an emerging disease of rice in India. The disease is causing economic loss to farmers through the reduction of yield and quality of rice. To devise a suitable approach to manage the disease effectively, an understanding of the genetic diversity and population structure of the pathogen is essential. Hence, a total of 34 isolates of U. virens obtained from different locations in India were characterized using 25 genomes-specific SSR markers showing higher polymorphic information content (PIC) that produced 203 alleles with a mean of 8.12 per marker. The genetic diversity varied from 0.00 to 0.885 with an average of 0.673. Based on the phylogenetic tree, the 34 isolates of U. virens were grouped into two major clusters (Cluster I and Cluster II). Cluster I included isolates from Andhra Pradesh, Bihar, Kerala, Manipur, Mizoram, Punjab, and West Bengal, while Cluster II included isolates from Assam, Manipur, Meghalaya, and Odisha. The isolates from the same/nearby locations were partially assembled into the same cluster. The analysis of molecular variance (AMOVA) showed the highest variation of 86% found among the individuals while the least variation of 14% was observed between the populations. The population structures of 34 isolates of U. virens evaluated using STRUCTURE and Principal coordinates analysis (PCoA) separated the 34 isolates into two distinct subpopulations. The high genetic variation in the isolates indicated their substantial potential to evolve and mutate, potentially causing damage to rice crops in future.

Infections by Mycobacterium spp. are responsible for thousands of deaths every year worldwide. Microbial resistance, toxic effects, and adverse consequences of conventional therapies bring forth the need to search for new therapeutic agents. The aim of this study was to determine the antimicrobial action of the molecule Rottlerin against Mycobacterium spp. The broth microdilution assay showed that Rottlerin inhibited the mycobacterial growth at concentrations ≤ 50 µg/mL (≤ 96.81 µM), and the lowest bactericidal concentration was observed against M. tuberculosis (25 µg/mL-48.40 µM). The cytotoxicity of Rottlerin was conducted in a epithelial cell culture and evaluated through 2,3-Bis-(2-Methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) colorimetric assay, revealing an IC₅₀ equivalent to 81.89 ± 4.64 µM. The antioxidant action determined by the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay demonstrated that Rottlerin reduced at least 50% of free radicals at 109.2 µM. To gain insights into the antimycobacterial activity of Rottlerin, we performed molecular docking simulations with therapeutic targets of M. tuberculosis and observed that Rottlerin binds into the inhibitory site of the anti-infective target diterpene synthase (Rv3378c). Our findings indicate that Rottlerin presents antimicrobial effects with antioxidant action and prominent therapeutic targets, showing its biotechnological potential for the development of new agent against Mycobacterium spp. infection.

Carrot psyllid Trioza apicalis is a serious pest of cultivated carrot and also a vector of the plant pathogen 'Candidatus Liberibacter solanacearum' (Lso). To find out whether T. apicalis harbours other species of bacteria that might affect the Lso infection rate, the bacterial communities and metagenome in T. apicalis were studied. Lso haplotype C was detected in a third of the psyllids sampled, at different relative amounts. Surprisingly, T. apicalis was found to harbour only one secondary endosymbiont, a previously unknown species of gamma proteobacterium endosymbiont (Gpe), beside the primary endosymbiont 'Candidatus Carsonella ruddii' (CCr). The relative abundancies of these two endosymbionts were approximately equal. The genomes of CCr, Gpe and Lso were assembled from a T. apicalis metagenome sample. Based on the 16S rRNA gene, the closest relative of Gpe of T. apicalis could be a secondary endosymbiont of Trioza magnoliae. The 253.171 kb Gpe genome contains all the tRNA and rRNA genes and most of the protein-coding genes required for DNA replication, transcription and translation, but it lacks most of the genes for amino acid biosynthesis. Gpe has no genes encoding cell wall peptidoglycan synthesis, suggesting it has no cell wall, and could thus live as an intracellular endosymbiont. Like the CCr of other psyllids, CCr of T. apicalis retains a broad amino acid biosynthetic capacity, whilst lacking many genes required for DNA replication and repair and for transcription and translation. These findings suggest that these two endosymbionts of T. apicalis are complementary in their biosynthetic capabilities.

The bacterial community in soil is often affected by agricultural practices, but how they affect protists and fungi is less documented. Soil from treatments that combined different N fertilizer application rates, tillage and crop residue management was sampled from a field trial started by the International Maize and Wheat Improvement Center (CIMMYT) at the 'Campo Experimental Norman E. Borlaug' (CENEB) in the Yaqui Valley in the northwest of Mexico in the early 1990s, and the fungal and protist community determined. Tillage, residue burning, and N fertilizer application had no significant effect on the fungal and protists alpha diversity expressed as Hill numbers and no significant effect on the fungal and protist community structure considering all species. The relative abundance of plant pathogens and undefined saprotrophs as determined with FUNGuildR increased significantly with tillage, while that of dung-plant and dung-soil saprotroph, and plant pathogens by burning (P < 0.05). It was found that the protists and fungal community structures were not altered by different agricultural practices, but some fungal guilds were, i.e., plant pathogens and saprotrophs, which might affect soil organic matter decomposition, nutrient cycling and crop growth.

Molecular mechanisms of C₁₉-steroid core degradation have been intensively studied mostly in mycolic acid rich actinobacteria, mainly in the representatives of Mycobacterium, Mycolicibacterium and Rhodococcus genera, whilst much less data evidencing functionality of the 9(10)-seco pathway in other actinobacteria was reported. In this study, degradation of androstenedione (AD), androstadienedione (ADD), testosterone (T), Δ¹-dehydrotestosterone (DT) and 9α-hydroxyandrostenedione (9α-OH-AD) by the biotechnologically relevant actinobacterium of Nocardioides simplex VKM Ac-2033D was investigated. Key intermediates of 9α-OH-AD degradation were isolated and identified as 3-hydroxy-9,10-seco-androsta-1,3,5(10)-triene-9,17-dione (3-HSA) and 3,17β-dihydroxy-9,10-seco-androsta-1,3,5(10)-trien-9-one (3,17-DHSA). The structures of the compounds were confirmed by MS, ¹H- and ¹³C-NMR. Differential gene expression on medium with glycerol and yeast extract with and without AD addition was estimated. The expression of two sets of the genes related to the 9(10)-seco pathway was increased in the presence of AD. One set comprised the genes from the KstR2-regulons in the clusters A and C, while another set included the genes without the binding sites for KstR/KstR2 (Cluster D). These genes putatively encoded 3-oxosteroid-Δ¹-dehydrogenase and 3-oxosteroid 9α-hydroxylase, as well as a group of enzymes dealing with the ring B opening (HsaA3, HsaB3, HsaC3 and HsaD3). Process of degradation of exogenous C₁₉-steroids in N. simplex proceeds via the 9(10)-seco pathway and can be controlled not only by KstR2 regulator, but also by other transcriptional factors. The results contribute to the knowledge on steroid core degradation in actinobacteria and are of significance at the development of methods for production of valuable indane compounds.

A Gram-stain positive, long-rod-shaped, motile, and aerobic bacterial strain, designated 16A2E^T, was isolated from mangrove sediment sample. The 16S rRNA gene sequence similarity analysis indicated that strain 16A2E^T exhibited high similarity to Ornithinibacillus contaminans CCUG 53201^T (98.2%), Ornithinibacillus bavariensis WSBC 24001^T (98.1%), and Ornithinibacillus scapharcae TW25^T (97.7%). Strain 16A2E^T grew within a temperature range of 20-50 °C (optimum 40 °C), a pH range of 6.0-9.0 (optimum pH 8.0), and in the presence of 0-10% (w/v) NaCl (optimum 1%). The genome size of strain 16A2E^T is 3.60 Mbp, with a G + C content of 36.7%. The overall genome related index (OGRI) analyses revealed low average nucleotide identity (ANI < 75.9%), average amino acid identity (AAI < 77.5%), and digital DNA-DNA hybridization (dDDH < 19.8%) with other species in the genus Ornithinibacillus. Chemotaxonomic analyses revealed that the major polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phospholipids, and an aminophospholipid. The predominant fatty acids were iso-C_15:0, anteiso-C_15:0, and anteiso-C_17:0. The sole respiratory quinone was menaquinone-7 (MK-7), and the peptidoglycan amino acid type was determined to be A4β. Based on phenotypic and genotypic analyses, strain 16A2E^T (= GDMCC 1.4379^T = JCM 36753^T) represents a novel species within the genus Ornithinibacillus, for which the name Ornithinibacillus xuwenensis sp. nov. is proposed.

Potassium (K) in plants participates in a variety of physiological processes and is kept at a higher concentration than its soluble form in soil. Potassium solubilizing bacteria (KSB) release K from minerals. Arbuscular mycorrhizal (AM) fungi facilitate bacterial movement along their extraradical hyphae and improve plant K status. However, the interaction of KSB and AM fungi is rarely reported. This study aimed to isolate KSB and evaluate their interaction with AM fungi in promoting plant K uptake and growth. Soil was sampled from the rhizosphere of Robinia pseudoacacia in the southern area of the Loess Plateau, where soil available K is lower than plant demand. KSB from soil was isolated using a select medium in which K-feldspar is the only K source. KSB that showed an obvious dissolving circle and relatively high K solubilizing efficiency (over 20%) were isolated and identified. A pot experiment was conducted in a randomized design to evaluate the effect of KSB and AM fungi and their interaction. Four out of 12 isolated strains that showed high potassium solubilizing efficiency were from the genus Pseudomonas. Inoculation of KSB promoted the growth and K content of R. pseudoacacia. KSB showed a variety of (increase, decrease, and not-obvious) influences on the colonization status of R. irregularis. Co-inoculation of R. irregularis and KSB promoted plant growth, K content of the plant, and the available K in the growth substrate. This study provided a basis for the utilization of KSB and AM fungi as biofertilizers in the Loess Plateau.

Aspergillus flavus contamination has long been a major problem in the food and agriculture industries, while peppermint essential oil (PEO) is increasingly recognized as an effective alternative for controlling fungal spoilage. However, its biocontrol effect and action mode on A. flavus have rarely been reported. Here, the inhibition rates of PEO on A. flavus were determined by the plate fumigation and mycelial dry weight method. The minimum inhibitory concentration (MIC) was identified as 0.343 μL/mL. In the biocontrol tests, the moldy rates of maize kernels, wheat grains, and peanut kernels in the PEO treatment group were significantly reduced by 65%, 72%, and 63.33%, respectively. The biocontrol efficacy of PEO on maize kernels, wheat grains, and peanut kernels reached 80.67%, 82%, and 67.67%, respectively. Furthermore, antifungal action mode analysis showed that PEO changed the mycelial morphology, damaged the integrity of cell wall and membrane. Moreover, it reduced the ergosterol content, elevated the malondialdehyde content, increased the relative conductivity, and led to the intracellular leakage of nucleic acids and proteins, thereby enhancing the cell membrane permeability. In addition, PEO decreased the antioxidant-related catalase (CAT) and superoxide dismutase (SOD) activities, significantly increased the hydrogen peroxide (H₂O₂) content, and induced the accumulation of reactive oxygen species (ROS) in the mycelia. In conclusion, this study confirms that PEO, as an effective natural antimicrobial agent, has good application prospects in controlling the spoilage of A. flavus during grain storage and preventing food mold.

Listeria monocytogenes is the causative agent of the globally prevalent foodborne illness listeriosis. Infection is caused by the ingestion of food contaminated with L. monocytogenes, which invades host cells via the bacterial cell surface protein internalin A (InlA). Fewer outbreaks of listeriosis have been reported in Japan than in other countries, suggesting that circulating L. monocytogenes strains in Japan have an increased prevalence of InlA mutations or mutations in other virulence factors, thereby impairing cell invasion. Herein, we investigated the molecular characteristics of inlA and other key virulence factors in L. monocytogenes isolated from retail meats sold in Japan. We isolated L. monocytogenes from retail meats in Sapporo, Japan and investigated the presence of five virulence-related genes (actA, hlyA, iap, plcA, and prfA). We also determined the sequences of the inlA gene, which encodes InlA. Ninety-three L. monocytogenes strains (31.0%) were isolated from 300 meat samples. The major serogroup of the strains was serogroup IIc (49.5%), followed by serogroup IIa (41.9%). Overall, 98.9% of the 93 strains possessed the five examined virulence-related genes. However, 51.6% of these strains exhibited premature stop codons in inlA. We showed that approximately half of the L. monocytogenes strains contaminating retail meats in Sapporo, Japan express mutated InlA, suggesting that their ability to invade host cells may be impaired. This may be one reason why fewer listeriosis outbreaks occur in Japan than in other countries, and provides new insight into geographical differences in the incidence of a common infectious disease.