Microorganisms最新文献

Artificial cyanobacterial crusts (ACCs) are a potentially effective biological strategy for combating desertification. However, while functional microorganisms influence ACCs formation efficiency, research on their role is limited, and their underlying promotion mechanisms remain unclear. Here, we investigated the effects of three functional synthetic microbial communities (SynComs), each dominated by microorganisms specialized in exopolysaccharide (EPS) production (3 strains), siderophore production (3 strains), or nitrogen fixation (4 strains), on ACCs formation following inoculation with Microcoleus vaginatus. This study was carried out in a controlled laboratory setting with a 12 h light/dark cycle and a light intensity of 2400-2700 lux. Following a 24-day cultivation period, EPS-producing or nitrogen-fixing SynComs significantly increased the chlorophyll-a content by 16.0-16.3%. Except for the nitrogen-fixing bacteria treatment, other SynComs enhanced the soil organic matter content of ACCs by 9.1% to 27.3%. The content of EPS was significantly improved by all three SynComs by 14.1~19.2%. Urease activity rose by 6.7% when siderophore-producing bacteria were added. The impacts of SynComs on ammonium nitrogen (NH₄⁺-N) showed different temporal dynamics: nitrogen-fixing SynComs significantly increased NH₄⁺-N early (≤10 days), while EPS-producing and siderophore-producing SynComs enhanced accumulation later (17-24 days). SynComs inoculation markedly accelerated cyanobacterial and general microbial colonization and growth. In comparison to day 0, the 16S rRNA gene copy number of ACCs increased by 24.1% and 43.0%, respectively, in the EPS-producing and nitrogen-fixing SynComs. Additionally, correlation analysis showed that SynComs transformed the weak correlations in the control into a strong positive correlation between NH₄⁺-N and both Chl-a and microbial biomass. Our findings demonstrate SynComs, particularly the EPS-producing or nitrogen-fixing SynComs, enhance ACCs formation through elucidated mechanisms, providing a theoretical basis for optimizing ACCs-based desertification control strategies.

Carbon dioxide (CO₂) is a cost-effective, abundant, and renewable carbon source, but its utilization technologies face several issues. The reductive glycine pathway (RGP) is recognized as one of the most efficient one-carbon (C1) assimilation routes in nature, with its core component-the glycine cleavage system (GCS: GcvP, GcvH, GcvT, and GcvL)-playing an essential role in C1 metabolism. To develop efficient CO₂ conversion and utilization pathways, we identified NhFtfL and AmFchA-MtdA with high catalytic efficiency through gene mining and constructed a four-plasmid co-expression system in E. coli BL21(DE3) using Gibson Assembly. This system integrated GcvP-GcvH, GcvT-GcvL, NhFtfL-AmFchA-MtdA, and RsPPK2, thereby reconstituting the complete RGP while enhancing ATP supply. The engineered strain functioned as an efficient whole-cell biocatalyst, achieving a glycine space-time productivity of 0.125 mmol/L/h via one-pot conversion of formate. Furthermore, we expanded the application scope by developing a whole-cell electrocatalysis system that directly synthesized glycine from CO₂ and NH₄Cl, achieving a glycine space-time productivity of 0.135 mmol/L/h. This study demonstrates the potential of the engineered RGP system for upgrading C1 resources and supports the transition toward carbon neutrality.

Aspergillus fumigatus is the primary pathogen causing aspergillosis. Recent molecular population genetic studies have demonstrated that A. fumigatus exhibits high local genetic diversity, with evidence for limited differentiation among geographic populations. However, research on the impacts of geomorphological factors on shaping the population genetic diversity patterns of this species remains scarce. In this study, large-scale sampling and in-depth population genetic analysis were performed on soil-derived A. fumigatus from Guizhou Province, a representative karst landscape in southern China. This area is dominated by plateaus and mountains (accounting for 92.5% of the total area) and represents a classic example of conical karst landscapes. A total of 206 A. fumigatus strains were isolated from 9 sampling sites across Guizhou. Genetic diversity, genetic differentiation, and population structure of these strains were analyzed based on short tandem repeats (STRs) at 9 loci. The results revealed that A. fumigatus in the karst region of Guizhou harbors abundant novel alleles and genotypes, with high genetic diversity. Gene flow among geographical populations was infrequent, and significant genetic differentiation was detected between 30 of the 36 pairs of geographical populations where mountain ranges played a very important role, with the overall regional genetic differentiation reaching PhiPT = 0.061 (p = 0.001). Furthermore, the Guizhou populations showed significant differences from those reported in other regions worldwide. Surprisingly, only one of the 206 (0.49%) A. fumigatus isolates from this region exhibited resistance to the two medical triazoles commonly used for treating aspergillosis, and this resistance frequency was far lower than those reported in previous studies from other regions. We discuss the implications of our results for evolution and environmental antifungal resistance management in this important human fungal pathogen.

Between 2015 and 2022, we evaluated a novel broad-range (BR) 16S PCR rDNA PCR/Sanger sequencing assay to improve diagnosis of invasive infections in culture-negative specimens. Using dual-priming oligonucleotides (DPO), this assay analyzed ribosomal DNA from sterile fluids or tissues. A total of 762 specimens were analyzed from 661 patients: 61% had negative cultures and BR 16S PCR tests; 35% had negative cultures but positive BR 16S PCR tests; and only 4% had negative cultures with indeterminate BR 16S PCR results. After resolution of indeterminate BR 16S PCR results (i.e., 29 negative, 1 false-positive, and 1 positive) the assay showed a sensitivity of 98.26% (95% CI = 96.00-99.43%), specificity of 99.79% (95% CI: 99.82-99.99%), positive predictive value of 99.65% (95% CI: 97.56-99.95%), negative predictive value of 98.94% (95% CI: 97.51-99.55%), and accuracy of 99.21% (95% CI: 98.28-99.71%) for a disease prevalence of 38.10% (95% CI: 34.62-41.66%). Gram stain purulence predicted the BR 16S PCR result better (69.4%) than organisms (24.6%), but the latter had a higher PPV (78.5%). Increased peripheral WBC (86.1%) or CRP (71.8%) predicted positive BR 16S PCR results. Our DPO BR 16S PCR assay improved pathogen detection over culture and minimized contamination. Broad range 16S rDNA PCR/sequencing (BR 16S PCR) is an important diagnostic technique in cases with invasive infection due to fastidious or uncultivatable pathogens. However, appropriate case selection, the quality of clinical specimen, and the specific assay primers affect its performance. Our novel BR 16S PCR assay uses unique dual-priming oligonucleotides (DPO) primers and fast protocols for rapid, optimal detection of bacterial pathogens, while minimizing contamination. Fast BR 16S PCR assay reports occurred within 24-48 h. BR 16S PCR and culture analyzed a diverse range of clinical specimens from patients with invasive infections. BR 16S PCR demonstrated a high performance for accurately detecting pathogens, ruling out infections, and minimizing contamination. BR 16S PCR detection of a pathogen allowed the appropriate clinical management of one-third of patients in this cohort. BR 16S PCR is an essential tool for the clinical management of patients with invasive infection when primary cultures are negative or contaminated.

The rise of multidrug-resistant tuberculosis (TB) necessitates alternative therapeutic sources. This study investigated the polyphenolic content and the antioxidant, antimycobacterial, and anti-virulence activities of selected medicinal plants traditionally used to treat TB and related symptoms. Total phenolics, tannins, and flavonoids were quantified using colorimetric assays. Antioxidant capacity was assessed via DPPH and ferric-reducing power assays. Antimycobacterial activity against Mycobacterium smegmatis was evaluated using broth microdilution, growth kinetics, cell constituent leakage, and respiratory chain dehydrogenase inhibition assays. Anti-virulence effects were examined using crystal violet biofilm and swarming motility assays. Tarchonanthus camphoratus showed the highest polyphenolic levels and, together with Combretum hereroense, strong antioxidant activity. Extracts of Senecio macroglossus, Nerium oleander, and Tetradenia riparia displayed potent antimycobacterial activity (MIC = 0.16 mg/mL), characterized by delayed exponential growth, membrane damage, and metabolic inhibition. Tabernaemontana elegans exhibited the weakest activity (MIC > 2.5 mg/mL). Most extracts also significantly impaired motility (12-100%) and early-stage biofilm formation. Polyphenolic-rich plant extracts demonstrated promising antimycobacterial and anti-virulence properties against M. smegmatis, highlighting their potential as leads for developing novel anti-TB agents.

Natural killer (NK) cells are central to antiviral immunity through a balance of activating and inhibitory receptors, including killer immunoglobulin-like receptors (KIRs). We have previously observed that an increased frequency of the inhibitory receptor KIR2DL2 and its ligand HLA-C1 is associated with heightened susceptibility to human herpesvirus (HHV) infection, supporting a role for KIR-mediated NK cell regulation in host-virus interactions. We investigated whether the co-infection of SARS-CoV-2 and human herpesvirus 6 (HHV-6) might be connected to the expression of KIR2DL2/HLA-C1. We analyzed 110 SARS-CoV-2-positive subjects and 109 SARS-CoV-2-negative subjects for the KIR2DL2 and HLA-C1 genotype and for HHV-6A/B reactivation in plasma samples. SARS-CoV-2-positive subjects showed a significantly higher frequency of the KIR2DL2/HLA-C1 haplotype and increased reactivation of HHV-6A. Among deceased and comorbid patients, the co-occurrence of the KIR2DL2/HLA-C1 haplotype and HHV-6A DNAemia was more frequent, particularly in those with cardiovascular disorders. These findings suggest that the KIR2DL2/HLA-C1 haplotype might promote NK cell inhibition, facilitating HHV-6A persistence and contributing to immune dysregulation during SARS-CoV-2 infection. The combined presence of KIR2DL2/HLA-C1 and HHV-6A may, therefore, represent a molecular signature of COVID-19 outcomes.

The nasal microbiome represents a complex and dynamic microbial ecosystem that contributes to mucosal defense, epithelial homeostasis, immune regulation, and olfactory function. Increasing evidence indicates that this microbial community actively interacts with host physiology, while alterations in its composition are associated with chronic inflammation, oxidative stress, and olfactory impairment. Such changes have been reported in conditions including chronic rhinosinusitis, allergic rhinitis, and post-viral anosmia. Beyond local effects, chronic nasal inflammation has been hypothesized to influence neuroinflammatory processes and protein aggregation pathways involving α-synuclein and tau, potentially linking nasal microbial imbalance to neurodegenerative mechanisms. However, current evidence remains largely indirect and does not support a causal relationship. This narrative review summarizes current clinical and immunological evidence on the role of the nasal microbiome in olfactory function and dysfunction, highlighting limitations of existing studies and outlining future research directions.

Identifying pathogens causing periprosthetic joint infection (PJI) is a challenge for clinicians. We aimed to evaluate the application of metagenomic next-generation sequencing (mNGS) to identify pathogens in PJI. A prospective analysis was conducted of patients diagnosed PJI between 2022 and 2024 at twelve hospitals in Taiwan. Both conventional bacterial culture (CMT) and mNGS of joint fluid and debrided tissue were performed. Demographic characteristics, laboratory results and clinical outcomes were collected. The diagnostic performance of these two methods was analyzed. A total of 42 patients with a mean age of 67.9 years were enrolled in analysis. The knee was the most common joint involved (69.1%). A high proportion of patients (78.6%) received prior antibiotics within the two weeks at sample collection. mNGS identified pathogens in 28 out of 42 patients (66.7%), whereas CMT yielded positive results in 12 out of 42 patients (28.6%) (McNemar's test, p = 0.01). Staphylococcus species was the most common genus detected (n = 11), followed by Cutibacterium (n = 4). Other detected genera included Escherichia, Mycobacterium, Enterobacter, Klebsiella (n = 2 each), Acinetobacter, and Corynebacterium (n = 1 each). Our results support the idea that mNGS could serve as a valuable diagnostic tool for PJI in addition to traditional culture methods.

Vietnam faces a hyperendemic burden of hepatitis B virus (HBV) infection, but the prevalence of occult HBV infection (OBI) and its underlying molecular mechanisms in healthy populations remain poorly understood. This study aimed to characterize the serological and molecular HBV profile of a healthy Vietnamese adult cohort in Southern Vietnam. We assessed the prevalence of occult HBV infection (OBI) and HBsAg-positivity (serving as a proxy for probable chronic infection). In this cross-sectional study, 397 healthy adults from Southern Vietnam underwent serological screening for HBsAg, anti-HBs, and anti-HBc. All participants were screened for HBV DNA using a high-sensitivity PCR assay (LOD ≥ 5 IU/mL). For all viremic cases, the full Pre-S/S region was sequenced to determine genotype and characterize escape mutations. We uncovered a high prevalence of both HBsAg-positivity (17.6%) and OBI (9.3% HBsAg-negative, HBV DNA-positive). Serological analysis revealed a massive, age-dependent reservoir of past exposure (63.7% anti-HBc) characterized by a high and increasing prevalence of the anti-HBc only profile (31.5%), a key serological marker for OBI. This trend contrasted sharply with a steep age-related decline in protective anti-HBs. The viral landscape was dominated by genotypes B (73.8%) and C (26.2%), with sub-genotypes B4 and C1 being the most prevalent. Critically, individuals with OBI carried a significantly higher burden of S gene escape mutations compared to those with HBsAg-positivity (p < 0.001). Canonical escape variants, including sG145R (21.6%), sK141R/T/E/Q (24.3%), and sT116N/A/I/S (18.9%), were exclusively or highly enriched in the OBI group. A LASSO-logistic model based on this mutational profile successfully predicted occult infection with high accuracy (AUC = 0.83). A substantial hidden reservoir of occult HBV infection exists within the healthy adult population of Vietnam, driven by a high burden of S gene escape mutations. These findings highlight the significant limitations of conventional HBsAg-only screening. They also underscore the need for comprehensive molecular surveillance to address the true scope of HBV viremia, hopefully enabling a reduction in hidden transmission of clinically significant viral variants.

Prior to the introduction of antiretroviral therapy (ART), people with HIV (PWH) had high risk of fungemia. No systematic review has assessed the prevalence of fungemia in PWH after the introduction of combination ART in 1996. The primary objective of this systematic review was to determine the prevalence of fungemia in adult PWH after 1996. Furthermore, we aimed to compare the prevalence of fungemia in different ART time periods to determine geographic differences and fungal pathogen distribution. A systematic literature search was performed on 7 March 2025 across six databases and the study quality was assessed using the Newcastle-Ottawa scale. Prevalence estimates were extracted, and a meta-analysis was performed using a random effects model. Twelve studies comprising 27,729 PWH were included. The overall pooled prevalence in PWH was 3.3% (95% CI: 1.53; 4.96%, I² = 98.9%). The most common pathogen to cause fungemia was Talaromyces marneffei with a prevalence of 4.8%, although this pathogen was limited to studies from Asia. The highest prevalence of fungemia in PWH was 6.8% in Asia. The prevalence of fungemia was 5.8% between July 1996-September 2015 and 1.0% between September 2015-January 2025, but the difference was not statistically significant (p = 0.273). However, all findings were limited by very low certainty of evidence and should be interpreted with caution. In conclusion, our findings suggest that fungemia persists among PWH despite ART, especially in Asia. Given the limited available evidence, it was not possible to determine whether the prevalence of fungemia changed following the change in ART treatment guidelines in September 2015. The protocol is registered in PROSPERO (CRD420251005081).