Frontiers in Microbiology最新文献

Background: Accurately diagnosing central nervous system (CNS) infections remains challenging. This study aimed to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) in diagnosing suspected CNS infections and its role in facilitating rapid and accurate pathogen identification.

Methods: This retrospective study enrolled cerebrospinal fluid specimens from 246 patients with suspected CNS infections and 20 controls with definitively ruled-out infections. Using clinical diagnoses established by an expert panel based on comprehensive criteria as the reference standard, we evaluated the diagnostic performance of mNGS relative to culture and conventional tests. Additionally, we analyzed the therapeutic guidance value of positive mNGS results and risk factors for false negatives.

Results: mNGS showed 73.2% (180/246) agreement with clinical diagnosis, superior to culture (54.1%, 133/246) and conventional methods (61.4%, 151/246). For general bacteria and fungi, mNGS showed 61.9% (26/42) concordance with culture. False negatives in mNGS predominantly involved viral missed detection. Age, presence of systemic infection, headache, and cerebrospinal fluid glucose levels were likely key determinants of mNGS performance. mNGS detection of Epstein-Barr virus, Streptococcus spp., Mycobacterium tuberculosis complex, herpes simplex virus type 1, and Staphylococcus spp. suggested high pathogenic potential, whereas Torque teno virus detection more likely indicated carriage or experimental contamination.

Conclusion: mNGS holds significant value for the diagnosis, therapeutic management, and prognostic assessment of suspected CNS infections.

Introduction: Environmental micropollutants and other anthropogenic xenobiotics are potential drivers behind compositional shifts and functional dysregulation of gut microbial communities. Mercury and many of its compounds are highly toxic and ubiquitous environmental pollutants that pose a risk for aquatic biota and humans. Here we compared the gut microbial communities of natural three-spined stickleback (Gasterosteus aculeatus Linnaeus, 1758) populations in Flanders, Belgium, with contrasting muscle mercury concentrations. We hypothesized that exposure to a high mercury load selects for gut flora species with the capacity to tolerate or adapt to this stressor and, thus, leads to a change in the composition of the gut microbiota.

Methods: The gut microbiota of 128 host individuals from four populations with low levels of accumulated mercury and four populations with high mercury levels were characterized using 16S rRNA amplicon sequencing. Gut microbial communities were compared across host muscle mercury content levels, host populations and sexes to consider the contribution of these factors in the observed differences in gut microbial diversity and composition.

Results: Microbial community composition varied significantly between males and females, as well as between host populations with high and low muscle mercury content. While the abundance of 22 amplicon sequence variants (ASVs) was associated with the host's muscle mercury content, we detected no specific indicator species for high mercury.

Conclusion: Overall, our results suggest that local factors specific to a host population, potentially including mercury accumulation and sex-specific factors, differentiate the microbial communities inhabiting the gastrointestinal tracts of the three-spined stickleback.

Introduction: Safflower (Carthamus tinctorius L.) is a prized medicinal species whose therapeutic value hinges on the abundance of bioactive metabolites. Accumulation of these metabolites are influenced by a range of environmental and edaphic factors, including soil physicochemical parameters, extracellular enzyme activities, composition and function of rhizosphere microbiome. However, how these factors individually and synergistically orchestrate the biosynthesis, transport, and ultimate storage of pharmaceutically active compounds within Safflower tissues remains unknown.

Methods: Here, high-throughput amplicon sequencing coupled with comprehensive physiological profiling was employed to investigate soil characteristics, enzyme activities, and rhizosphere microbial communities of safflower across 36 soil samples collected at two distinct altitudes and two growth stages.

Results: The effective component content was detected in 18 samples, and our results revealed that the safflower stigmas from the high- altitude site (YM) contained significantly elevated levels of hydroxysafflor yellow A (HSYA) compared to those from the lowland site (YF). Soils at the YM site exhibited markedly higher fertility, with available phosphorus, total nitrogen, and organic matter identified as key drivers of HSYA accumulation. Both sites showed high diversity and abundance in rhizosphere microbial communities, with Actinobacteria and Proteobacteria dominating the bacterial communities, and Ascomycota being the predominant fungal phylum.

Discussion: Taken together, our findings show that soil properties, microbial communities, and climatic conditions work interactively to influence the buildup of bioactive compounds in safflower. These insights suggest that precise management of soil nutrients and the rhizosphere microbiome can improve medicinal safflower quality.

Ganoderma leucocontextum is rich in bioactive compounds, including triterpenes and polysaccharides, and exhibits significant pharmacological effects. Its cultivation requires casing soil, crucial for achieving high productivity and superior quality. In this study, soil physicochemical properties and microbial communities were analyzed across four growth stages: casing (GCK), primordial (G1p), cap (G1c), and maturity (G1m) of G. leucocontextum. Results indicated that the soil pH significantly increased after cultivation, ranging from 6.78 to 7.11. The control soil contained the highest concentrations of total nitrogen (2.44 g/kg), available nitrogen (259.48 mg/kg) and organic matter (54.35 g/kg), significantly exceeding those in G. leucocontextum-cultivated soils. Soil available phosphorus and potassium gradually increased, peaking at maturity (42.01 mg/kg and 86.36 mg/kg, respectively). Microbial communities also shifted from bacterial to fungal dominance over time. Among bacteria, Acidobacteriota was the most prevalent phylum, averaging 28.46%, with a marked upward trend. Arthrobacter emerged as the most dominant genus, averaging 9.00%, with higher abundance at maturity. A Vicinamibacterales-order genus continuously increased in abundance, wheras Novocardioides, Sphingomonas, and an Intrasporangiaceae-family genus decreased during of G. leucocontextum growth. For fungi, Ascomycota was the most prevalent phylum, averaging 65.56%, followed by Basidiomycota at 21.60%, which dominated at maturity. Ganoderma was the most predominant genus, averaging 16.34%, and increased substantially with growth. The study revealed correlations between soil microbial communities and physicochemical properties, and demonstrated decreasing polysaccharide content but increasing triterpenoid acid content during growth. This research explores soil microbial community succession and physicochemical changes for G. leucocontextum cultivation, offering theoretical support for overcoming continuous cropping obstacles (CCOs) and insights for sustainable yield management.

Intercropping is widely promoted to sustain soil function, yet evidence for its application in rubber-based agroforestry, particularly with the shade-tolerant herb Amomum villosum, is limited. We evaluated whether A. villosum intercropping improves soil properties and reorganizes microbiomes across the vertical profile of mature rubber plantations. Soil samples were taken at 0-10, 10-20, and 20-30 cm depths in both intercropped and monoculture stands. Physical and chemical properties were quantified, and bacterial (16S rRNA V3-V4) and fungal (ITS2) communities were analyzed using high-throughput amplicon sequencing with depth-resolved data on diversity, composition, and functional inference (FAPROTAX, FUNGuild). Intercropping consistently improved soil structure and fertility, with the strongest effects at 0-10 cm. Total porosity (12%), organic matter (38.9%), alkali-hydrolyzable nitrogen (75.4%), and available phosphorus (131%) were markedly higher than in monoculture. Benefits extended to mid-depth with a 65.2% increase in alkali-hydrolyzable nitrogen. Microbial richness (bacteria and fungi) increased, and communities separated clearly by treatment and depth. Intercropped soils showed higher relative abundances of copiotrophic and particle-attached phyla (e.g., Proteobacteria, Planctomycetota), while Acidobacteriota and several Chloroflexi declined. Nitrospirota increased with depth. Fungal trophic structure shifted away from pathotrophs at 20-30 cm and toward symbiotrophs, particularly arbuscular mycorrhizal lineages, at subsurface layers. Functional predictions indicated greater potential for nitrogen transformations (e.g., nitrogen fixation, nitrification), greater C₁/hydrocarbon utilization, and a reduced bacterial plant-pathogen signal under intercropping. Collectively, A. villosum intercropping reorganizes the soil environment and microbiome in mutually reinforcing ways-improving physical structure, enlarging near-term nitrogen supply, and favoring beneficial fungal guilds. These depth-resolved effects help explain the agronomic appeal of rubber-A. villosum systems and support their wider deployment in rubber plantations.

The RNA cystovirus phi6 represents a unique evolutionary outlier, encoding a holin and endolysin similar to tailed phages, yet lacking an identified gene for outer membrane disruption. In this study, we investigated the phi6 lysis system using genetic complementation experiments and heterologous expression in Escherichia coli and Pseudomonas syringae. Our results demonstrate that the phi6 endolysin is functional in both bacterial systems, while the phi6 holin does not show activity in either bacterial system when expressed using moderate expression systems. Combinations of lambda lysis gene controls performed as expected in P. syringae. The phi6 holin requires overexpression or co-expression with other phi6 genes to exhibit lysis in E. coli. Overexpression of plasmids containing entire phi6 S-, M-, and L-segments cDNA in E. coli produced lysis profiles and cell morphology consistent with holin-endolysin expression, but outer membrane disruption was not observed. This suggests either phi6 has not evolved to carry an outer membrane disruptor or that the outer membrane disruptor is not active in our E. coli testbed. Our findings highlight the unusual nature of the phi6 lysis system.

Introduction: This study focused on three pecan (Carya illinoinensis) cultivars ('Pawnee', 'Mahan', and 'Jinhua'), systematically assessing variations in soil nitrogenase activity, characteristics traits of nifH-harboring microbial communities across these cultivars.

Methods: Using high-throughput sequencing technology, differences in the diversity, community composition, and network structure of nifH-harboring communities in the rhizosphere and bulk soils of pecan were examined across cultivars.

Results: Both cultivar type and soil compartment had significant effects on nitrogenase activity (p < 0.01). Among the three cultivars, 'Mahan' exhibited the highest soil nitrogenase activity in both its rhizosphere and bulk soils relative to the other two cultivars. Notably, rhizosphere soils across all cultivars displayed significantly stronger soil nitrogenase activity than their bulk soil counterparts. 'Mahan' harbored significantly higher microbial α-diversity (Sobs, Shannon, and Chao indices) than other cultivars (p < 0.05). β-diversity analysis revealed marked community divergence among cultivars, with the most pronounced differences observed in bulk soils. Specifically, the bulk soil of 'Jinhua' harbored a distinct microbial signature, marked by significant enrichment of Cyanobacteria and depletion of Alphaproteobacteria. Linear discriminant analysis effect size (LEfSe) further identified Rhizobiales and Burkholderiales as distinct biomarkers for the rhizosphere and bulk soils of 'Jinhua', respectively (LDA score > 4.0, p < 0.05). Microbial co-occurrence network analysis showed that the bulk soil of 'Jinhua' harbored the most complex microbial interaction network, characterized by the highest number of edges, and average connectivity. In co-occurrence networks, Azohydromonas, Bradyrhizobium, Azoarcus, Rhodomicrobium were found as the keystone taxa in maintaining network stability.

Discussion: This research elucidates the regulatory roles of pecan cultivars in shaping soil nitrogen fixation functions and microbial community assembly, providing valuable practical implications for precision microbiome management in pecan production.

The Ralstonia solanacearum species complex (RSSC) is a devastating soil-borne pathogen that causes bacterial wilt in solanaceous crops. However, the response of RSSC to monosaccharides-key components of root exudates released into the rhizosphere-remains unclear. We supplemented culture media with several typical monosaccharides derived from tobacco root exudates to mimic rhizosphere signals and examined their effect on the expression of bacterial virulence factors. Transcriptome analysis revealed that galactose markedly altered the physiological status of RSSC, inducing a state resembling that during plant infection. Among the monosaccharides tested, galactose specifically up-regulated the expression of type III secreted effectors. Notably, galactose also actively induced nitrogen metabolism, leading to the production of nitrous oxide and other reactive nitrogen species, which may, like reactive oxygen species, enhance pathogenicity. Furthermore, metabolites extracted from galactose-induced RSSC cultures triggered cell death when infiltrated into tobacco leaves.

Introduction: The appendix is thought to act as a regulatory immune organ and gut microbiota reservoir. Although appendectomy is linked to health risks, its impact on the gut microbiota remains understudied.

Methods: This study is conceived as a cross-sectional retrospective follow-up study. Three comparisons were performed on gut microbiota data using self-reported metadata retrieved from a European laboratory's extensive database. First, subjects with (wA) and without (noA) appendectomy during stool sampling were compared. Second, healthy individuals were selected based on specific criteria by comparing those with (HwA) and without (HnoA) appendectomies. Finally, healthy (HwA) and non-healthy (nHwA) subjects with a history of appendectomy were compared. Due to the study design, the timing and cause of the appendectomy were unknown. Data on confounding factors, such as age, BMI, and sex, were analyzed as covariates. Regarding the gut microbiota, alpha and beta diversity, relative abundance of phyla, genera, and metabolic pathways were compared.

Results: Significant differences were found in the gut microbiota composition and functionality between 2'615 adult subjects who had and 13'103 adults who had not undergone appendectomy (wA vs. noA), but also in confounding factors such as age, sex, and BMI. No significant differences were found in the gut microbiota between the 111 healthy adult subjects and 876 adults who had not undergone appendectomy (HwA vs. HnoA) at the time of stool sampling. Significant differences were found between 111 healthy and 2'504 non-healthy subjects who underwent appendectomy (HwA vs. nHwA). The gut microbiota composition of nHwA differed significantly in beta diversity; it was less diverse (Shannon entropy) and showed a decreased abundance of two genera, Eubacterium ruminantium and Lachnospiraceae FCS020. The HwA group was found to consume additional portions of vegetables and fruits and sleep longer, but these differences were not significant.

Conclusion: Our study found significant differences in the gut microbiota composition between healthy and non-healthy subjects who underwent appendectomy, but no difference in healthy subjects with or without appendectomy. Further studies are needed to elucidate whether these differences are due to different restorative capacities over time.