Current Microbiology最新文献

The early innate host immune response is crucial in the susceptibility to tuberculosis (TB). This study aimed to investigate the potential role of Toll-interacting protein (TOLLIP), a negative regulator of the human innate immune response, and interleukin-10 (IL-10), an anti-inflammatory cytokine, in susceptibility to TB. The peripheral blood mononuclear cells of 30 active pulmonary TB patients and 30 healthy volunteers were included. TOLLIP mRNA expression levels, single nucleotide polymorphisms (SNPs) of the TOLLIP gene, such as rs5743899A/G and rs3750920C/T, and IL-10 -1082G/A SNP were detected using real-time PCR, PCR-restriction fragment length polymorphism (PCR-RFLP) and amplification refractory mutation system-PCR (ARMS-PCR), respectively. TOLLIP mRNA expression levels were significantly higher in TB patients than in healthy controls (expression fold difference = 2.72, the delta-delta Ct method, also known as the 2-∆∆Ct method). The heterozygous (GA) genotype of the IL-10 -1080G/A polymorphism was significantly predominant among the patient group (p = 0.02, Hardy-Weinberg equilibrium). However, the Kruskal‒Wallis analysis found no significant relationship between TOLLIP mRNA expression levels and SNPs. TOLLIP mRNA and IL-10 -1082G/A SNP were assessed as potential biomarkers to predict TB susceptibility. For more significant results, they should be examined with other negative regulators of innate immunity and other immune factors associated with susceptibility to TB. Our study is the first to investigate the association of TOLLIP polymorphisms and expression levels with TB susceptibility in Turkey.

Similar to other herbivores, healthy giraffes (Giraffa camelopardalis) rely on a variety of symbiotic microorganisms in their digestive systems to break down cellulose and hemicellulose. In this study, we investigate the impact that external stimuli might have on the faecal prokaryote composition of healthy, free-roaming giraffes. Faecal samples were collected from six male and seven female giraffe individuals, over a 2-year period, during the wet and dry seasons, from six locations within the Free State Province, South Africa. Giraffe populations were exposed to one of two feeding practices which included provision of supplemental feed or only naturally available vegetation. Seventeen (17) different prokaryotic phyla, consisting of 8370 amplicon sequence variants (ASVs), were identified from the 13 healthy, adult, free-roaming giraffes included in the study. Overall, the bacterial phyla with the largest relative abundance included Fusobacteria (22%), followed by Lentisphaera (17%) and Cyanobacteria (16%), which included 21 dominant prokaryotic ASVs. The relative abundance of Ruminococcaceae UCG 014 and Treponema 2 were found to be significantly (P < 0.05) higher and Escherichia / Shigella, Romboutsia and Ruminococcus 1 significantly lower for giraffes receiving supplemental feed compared to natural available vegetation. This is the first study to investigate the composition of the faecal prokaryotic communities of healthy, free-roaming giraffes. The analysis of faecal prokaryotes contributes to the development of non-invasive methods for assessing the nutritional status and identifying health issues in giraffe populations. Ultimately, such advances are beneficial towards the larger-scale conservation, determining nutritional needs and management of other sensitive wildlife species, as well.

A Gram negative bacterium, designated H3^T, was isolated from a forest soil sample collected in Zhangjiajie National Forest Park, Hunan Province, PR China. Cells of strain H3^T were yellow-pigmented, strictly aerobic, motile by means of a single polar flagellum. Growth occurred at 15-37 °C (optimum, 25-30 °C), pH 6.0-8.0 (optimum, 7.0) and 0-1.0% (w/v) NaCl (optimum 0%). Phylogenetic analysis based on 16S rRNA gene sequences and genome showed that strain H3^T was affiliated to the genus Uliginosibacterium within the family Rhodocyclaceae of the class Betaproteobacteria and shared the highest sequence similarities with U. sediminicola M1-21 ^T (96.3%). The DNA G + C content of the genomic DNA was 61.4%. The major fatty acids of strain H3^T were C_16:0, summed feature 3 (16:1 ω7c/16:1 ω6c) and C_12:0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipid, an unidentified aminolipid, three unidentified lipids, an unidentified glycolipid, and two uncharacterized phospholipids. The major respiratory quinone was ubiquinone-8. The dDDH and ANI values between strain H3^T and the type strains of the genus Uliginosibacterium were 19.2-20.7% and 71.4-76.0%, respectively. Based on the evidences in this study, strain H3^T represents a novel species of the genus Uliginosibacterium, for which the name Uliginosibacterium silvisoli sp. nov. is proposed. The type strain is H3^T (= MCCC 1K09133^T = KCTC 8564 ^T = JSACC 33374 ^T).

The Chishui River is the prime production area for Jiang-flavor Baijiu in China, with 85% of the country's production capacity. To understand the spatial and temporal characteristics of fungal communities in the water column of the Maotai reach of the Chishui River and the relationship between fungal communities and environmental factors as well as the brewing of Jiang-flavor Baijiu, we analyzed the fungal species richness and diversity, structural changes, community composition, and correlation with environmental factors in different seasons and river reaches of the Chishui River Maotai reach. It was found that species richness and diversity followed the following seasonal pattern: summer > autumn > winter ≈ spring. Fungal species richness and diversity were significantly higher in polluted tributary river water than in main stream. The composition and structure of the fungal community varied in all seasons and in different river reaches. Ascomycota (76.5%), Basidiomycota (13.53%), and Chytridiomycota (9.37%) are the relatively dominant phyla, and a number of genera such as Trichosporon, Aspergillus, and Thermomyces have been reported to be associated with the brewing of Jiang-flavor Baijiu. In addition, total nitrogen (TN), chemical oxygen demand (COD), water temperature (WT), dissolved oxygen (DO), sulfate (SO₄^2-), and manganese (Mn) affected the fungal community structure of the Chishui River water body to different degrees (p < 0.05), and they were significantly correlated with Millerozyma and Candida, the genera related to Jiang-flavor Baijiu brewing, respectively. Our findings provide scientific basis and reference for further understanding the water ecological environment of Chishui River and its relationship with the brewing of Jiang-flavor Baijiu.

Maintenance of genomic integrity is a fundamental characteristic of viruses, however, RNA-dependent RNA Polymerase (RdRp) lacks exonuclease activity for proofreading. To facilitate genomic proofreading in viruses, an independent exonuclease domain assists RdRp to maintain fidelity during replication. In contrast to high fidelity in DNA viruses, RNA viruses have to evolve into new variants through comparatively delicate mutagenesis activity for genetic diversity. Coronavirideae, a family of single positive-stranded RNA (+ ssRNA) viruses, meticulously sustain a balance between genetic diversity and large-size RNA genome. In coronaviruses, the proofreading activity is accomplished by an exonuclease (ExoN) domain located at the N-terminal of non-structural protein 14 (nsp14). ExoN is responsible for the new variants and antiviral resistance towards nucleotide analogs. Here, we provide an evolutionary characterization of ExoN by using a well-defined phylogenetic pipeline and structural analysis based on host and habitat. We carried out a phylogenetic analysis on ExoN, methyltransferase domain, nsp14, and whole genomes of ExoN-containing viruses. Furthermore, a three-dimensional structural comparison of the ExoN domain from various sources is also carried out to understand structural preservation. Our study has unveiled the evolutionary trajectories and structural conservation of the ExoN domain within the Coronaviridae family, highlighting its distinct evolutionary path independent of other domains. Structural analyses revealed minimal variance in RMSD values, underscoring the conserved nature of ExoN despite diverse ecological settings.

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.