Frontiers in Microbiology最新文献

Laguna Lake, the largest freshwater lake in the Philippines, has been reported to harbor antibiotic-resistant bacteria, posing health risks to the millions who depend on it. However, limited knowledge of antibiotic resistance genes (ARGs) in the lake highlights the need for a comprehensive assessment of its resistome. In line with this, we characterized ARGs in the West Bay of Laguna Lake using shotgun metagenomic sequencing based on six metagenomes collected from three stations across two sampling months at a single depth. ARGs were quantified from short reads, and assembled contigs containing these genes-antibiotic-resistant contigs (ARCs)-were analyzed to assess mobility through associations with plasmids and mobile genetic elements (MGEs). β-lactam resistance genes (0.023-0.048 copies per cell) were the most prevalent, corroborating previous reports. Meanwhile, the detection of bacitracin (0.013-0.028 cpc) and polymyxin (0.009-0.011 cpc) resistance genes raises new concerns, as resistance to these antibiotic classes has not been previously reported in the lake. Furthermore, 44.8 and 30.4% of ARCs were associated with plasmids and MGEs, respectively. ARCs carrying genes for resistance to β-lactams, chloramphenicol, and tetracyclines were frequently identified as mobile, indicating a high potential for horizontal gene transfer and suggesting possible antibiotic contamination in the lake. Overall, this study provides the first metagenomic insight into the resistome of Laguna Lake using short-read sequencing and highlights its role as an environmental reservoir of mobile ARGs. The findings underscore the need for expanded ARG surveillance to improve antimicrobial resistance risk prediction.

Introduction: To investigate the horizontal transmission of oral-gut microbiota in autism spectrum disorder (ASD) families and its potential implications for ASD pathogenesis.

Methods: The research employed a paired cohort design using family cohorts (23 ASD children/17 parents vs. 18 Non-ASD children/16 parents), conducting integrated microbiome and metabolomic analyses of oral and fecal samples.

Results: The findings revealed that ASD families exhibited significantly increased oral microbial species diversity alongside substantial alterations in gut microbiota composition, particularly demonstrating a lower Firmicutes/Bacteroidetes ratio (3.60/2.97) compared to Non-ASD families (5.59/5.35). Specific microbial changes included notable enrichment of Prevotella_9 in ASD gut microbiota. Metabolomic profiling identified significant disruptions in multiple metabolic pathways, including impaired L-rhamnose degradation and glutathione metabolism. The study observed coordinated oral-gut axis alterations through synchronized changes in Caulobacter and Serratia abundances, suggesting a distinct dysbiotic pattern along this microbial continuum. Additional metabolic findings demonstrated reduced levels of fecal glutamine and Ala-Gly in ASD children, with glycylproline exhibiting high predictive value for family typing (AUC = 0.91). Integrative analysis further revealed significant correlations between Holdemanella and various lipid metabolites.

Discussion: It indicates that ASD families display characteristic oral-gut microbiota interactions accompanied by metabolic abnormalities, potentially reflecting familial microbial transmission patterns that may contribute to ASD pathophysiology.

The mitogen-activated protein kinase (MAPK) pathway is a vital cellular signaling cascade that viruses exploit. When activated by viruses, this pathway also initiates the host's inflammatory response. This pathway has a crucial role in viral respiratory infections, serving as a key intersection where viral replication and host inflammation are coordinated. Some viruses activate this pathway to enhance their own replication while also triggering inflammatory responses in the host. Understanding this intersection is essential because therapeutic agents could target the same pathway to inhibit both viral replication and inflammation. This perspective considers targeting the MAPK pathway as a potential way to treat viral respiratory infections by suppressing viral replication and reducing inflammation.

This study evaluated the antimicrobial activity of pure juniper essential oil and its nanoemulsion formulations (2, 4, and 6%) against five foodborne and fish spoilage bacterial species, including Staphylococcus aureus, Salmonella Paratyphi A, Vibrio vulnificus, Photobacterium damselae and Proteus mirabilis. The GC-MS profile of pure juniper essential oil (EO) revealed thirty components, including α-pinene, which accounted for 90.05% of the total volatiles. The antimicrobial activity was studied by measuring the inhibition zone diameters by the agar well diffusion method and determining the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values by micro dilution method. A clear dose-response relationship was observed in nanoemulsion formulations; as EO concentration increased, inhibition zones enhanced and MIC/MBC values decreased. S. aureus showed inhibition even at 2%JNEO (~15 mm), reaching a maximum of 22.1 mm at 6%JNEO. Among Gram-negative pathogens, Vibrio vulnificus showed the highest susceptibility, particularly to pure juniper essential oil, as reflected by low MIC and MBC values. P. damselae and S. paratyphi A exhibited intermediate susceptibility (MIC 1.56-12.5 mg/mL; MBC 12.5-25 mg/mL), while P. mirabilis showed high resistance (MIC 12.5 mg/mL; MBC > 100 mg/mL) and only limited inhibition. Among the tested bacteria, Staphylococcus aureus and Vibrio vulnificus showed the highest susceptibility, with inhibition zones and MIC/MBC values decreasing in a concentration-dependent manner. This antimicrobial activity may be associated with the high α-pinene content of juniper essential oil. These results highlight the potential of juniper essential oil nanoemulsions as effective natural preservatives to control fish spoilage and foodborne bacteria in the seafood industry.

Introduction: Owing to its remarkable capacity to modify the aroma profile of wine, Lactiplantibacillus plantarum (L. plantarum) derived from wine has emerged as a potential starter for malolactic fermentation. However, the inadequate acid resistance of this bacterium severely restricts its application. In some bacterial species, GlnR is considered a universal transcriptional regulator in response to acid stress.

Methods: In this study, we determined the function of GlnR in the acid resistance of L. plantarum for the first time. RT-qPCR and yeast one-hybrid assays revealed a direct regulatory correlation between GlnR and genes associated with the glutamate metabolic pathway. Metabolomics analysis via liquid chromatography-mass spectrometry and fermentation studies confirmed that GlnR affected γ-aminobutyric acid (GABA) production.

Results: The growth and survival rate of the knockout strain XJ25-ΔglnR were significantly lower than those of the wild-type strain XJ25. GlnR can directly bind to the promotor regions of the genes glnA, gadB, and glms1, thereby upregulating gadB transcription while downregulating glnA and glms1 transcription, directing the increased metabolic flux toward GABA synthesis.

Discussion: We present evidence that GlnR plays a vital role in the glutamate metabolic pathway and is a positive transcriptional regulator that can control the acid resistance of L. plantarum XJ25. Although GlnR interacts with glnA, gadB, and glms1, additional studies are warranted to determine how this interaction affects its acid resistance.

Objective: JR20, a novel sesamin-derived arylnaphthalene lignan, has demonstrated potent antifungal activity. This study further investigates its antibacterial potential against MRSA (methicillin-resistant Staphylococcus aureus).

Methods: The highlights of this research include the use of SYTO9 and PI fluorescence double staining, along with three-dimensional confocal microscopy to reveal the thickness and viability of biofilms under JR0's influence. Additionally, scanning and transmission electron microscopy were employed to observe the morphological changes of MRSA under JR0's impact. By combining the observed reduction in ATP content within MRSA, a preliminary mechanism was hypothesized. In vivo anti-infection experiments were further conducted to evaluate the compound's biological activity in liver and spleen tissues of mice.

Results: JR20 exhibited potent anti-MRSA activity (IC₅₀ = 20.88 μg/mL). Mechanistic investigations revealed multi-level effects: confocal microscopy demonstrated altered biofilm thickness and viability; SEM/TEM confirmed distinct morphological changes in bacterial cells; And ATP content reduction indicated metabolic disruption. In vivo experiments validated these antibacterial effects and further revealed anti-inflammatory properties, underscoring JR0's therapeutic potential against MRSA infections.

Conclusion: This study confirms JR0's potent anti-MRSA activity, clarifies its effects on biofilms and MRSA morphology, and proposes a preliminary mechanism by reduced ATP. JR20 demonstrates significant potential for combating drug-resistant bacteria and advancing antibiofilm drug discovery.

Artificial intelligence now shapes the design of biological matter. Protein language models (pLMs), trained on millions of natural sequences, can predict, generate, and optimize functional proteins with minimal human input. When embedded in experimental pipelines, these systems enable closed-loop biological design at unprecedented speed. The same convergence that accelerates vaccine and therapeutic discovery, however, also creates new dual-use risks. We first map recent progress in using pLMs for fitness optimization across proteins, then critically assess how these approaches have been applied to viral evolution and how they intersect with laboratory workflows, including active learning and automation. Building on this analysis, we outline a capability-oriented framework for integrated AI-biology systems, identify evaluation challenges specific to biological outputs, and propose research directions for training- and inference-time safeguards.

This review highlights the potential of endophytic microorganisms and their secondary metabolites as innovative biopesticides for sustainable disease management in agriculture. Agriculture faces substantial challenges from phytopathogens, resulting in significant economic losses worldwide, which are typically addressed with synthetic pesticides that pose environmental and health hazards. Endophytic microorganisms residing within plant tissues without inducing disease provide a natural defence alternative by synthesising a variety of beneficial secondary metabolites, including alkaloids, terpenoids, phenolics, and peptides. These chemicals serve as ecological mediators, directly inhibiting pathogens, promoting plant systemic resistance, and improving nutrient absorption and stress resilience. The review elucidates the biosynthesis routes of these metabolites, their ecological functions, and the symbiotic chemical interactions between endophytes and host plants that enhance plant growth and defence. Bacterial endophytes, including Bacillus and Pseudomonas, generate lipopeptides that compromise pathogen membranes and to improve plant immunity, whereas fungal endophytes, such as Trichoderma and Penicillium, produce antifungal and insecticidal agents. The manuscript additionally examines the molecular mechanisms that govern these relationships, encompassing phytohormonal signalling and quorum sensing. While the potential of endophytic microorganisms as biopesticides is promising, significant gaps remain in our understanding of their long-term ecosystem effects, molecular mechanisms, and scalable manufacturing techniques. This review highlights the importance of comprehensive research to fully harness the biotechnological potential of endophytes. Integrating their secondary metabolites into crop protection strategies could reduce our reliance on chemical pesticides, promoting environmental sustainability and food security. Understanding the long-term ecosystem effects of endophytic microorganisms is crucial for bolstering resilient agricultural systems globally.

Outbreaks of mosquito-borne viruses are increasing in temperate regions, with West Nile and Usutu viruses now established in wide regions across Europe, and both detected in the UK. Current surveillance strategies focus on targeted approaches which are well suited for monitoring established threats but limited in their ability to detect recently described or neglected viruses. High throughput sequencing (HTS) provides an unbiased alternative, allowing simultaneous identification of well-recognised and overlooked arboviruses, alongside insect-specific viruses (ISVs) that may modulate vector competence of the insects transmitting these pathogens. This study presents the first comprehensive virome survey of Culex mosquitoes in the UK, analysing populations collected from 93 sites across England and Wales through HTS and a systematic virus discovery pipeline. Across these sites, 41 distinct viral taxa were identified, including 11 novel species. Most viruses were rare or confined to a few sites, with only three detected in more than one third of sites, suggesting the absence of a broad conserved virome across populations. Within this diversity, three arbovirus-related lineages were detected: Hedwig virus (Peribunyaviridae), Umatilla virus (Sedoreoviridae), and Atherstone virus (Peribunyaviridae), the former two representing the first detections in the UK. These putative arboviruses were embedded in viral communities that showed minimal structuring by coarse land type but a modest decline in richness with latitude across rural sites, consistent with diversity gradients observed in other microbial systems. Together, these findings provide the first national-scale baseline of Culex mosquito-associated viral diversity in the UK, and demonstrate the value of metagenomic approaches in arbovirus preparedness.

This study was part of an in vivo investigation of methane (CH₄) abatement feed on local Menz breed sheep in Ethiopia, conducted over 90 days period using a randomized complete block design. Sheep were subjected to four dietary treatments: Control, Acacia (Acacia nilotica), BSG (Brewer's Spent Grain), and Ziziphus (Ziziphus spina-christi). The aim of the study was to investigate the rumen microbial community composition, diversity, and their relationships with CH₄ intensity. Rumen fluid was collected on days 0 (SD_0), 45 (SD_45), and 90 (SD_90), using an esophageal tube. The dynamics of the bacterial and archaeal domains were assessed by 16S rRNA gene sequencing. The sequencing results showed that 92.9% of ASVs were Bacteria, and 0.05% Archaea. At the genus level, Rikenellaceae RC9 gut group (18%), Prevotella (17%), and Candidatus Saccharimonas (8.9%) were the most abundant Bacteria, while Methanobrevibacter (88%) dominated the Archaeal genera across all treatment groups. Treatment feed significantly altered microbial profiles, notably reducing Methanobrevibacter abundance in CH₄ abatement diets and increasing the presence of Methanosphaera. Shannon diversity increased in the abatement diet and decreased when the sheep were fed BSG. CH₄ intensity was most strongly associated with the archaeal genus Methanomicrobium, but did not associate strongly with any other Bacteria or Archaea, although Methanobrevibacter and Methanosphaera were correlated negatively (r = -0.97). CH₄ intensity also did not covary with volatile fatty acids (VFAs), of which Acacia yielded the highest acetate (772 mmol/mol) and BSG the highest propionate (172 mmol/mol) concentration. The volatile fatty acids (VFAs) showed a strong correlation: a positive correlation between acetate and butyrate (r = 0.80) and a strong negative correlation between acetate and propionate (r = -0.92). These findings highlight the complex relationship between diet, rumen microbiota, and fermentation products, with implications for CH₄ mitigation strategies in sheep.