Frontiers in Microbiology最新文献

Respiratory tract infections (RTIs) are among the most prevalent diseases in human society and pose a major global health threat, affecting millions annually. A wide range of pathogens, primarily viruses and bacteria, cause RTIs. These infections often present with similar symptoms, which limits effective clinical treatment. Extensive research has addressed RTIs, with ongoing discussion regarding their current status and advancements in detection technologies. Novel laboratory methods that offer rapid, sensitive, and specific results now supplement traditional diagnostic approaches. In this review, we summarize the infection characteristics and detection methods of common respiratory pathogens, evaluate the effectiveness and limitations of current detection methods, and aim to promote advancements in laboratory diagnosis and explore the potential of emerging technologies in this field.

Microplastic pollution fosters the development of distinct microbial biofilm communities, termed the plastisphere, that vary across environmental contexts. Here, we used 16S rRNA gene sequencing combined with machine learning (ML) approaches to explore plastisphere microbial diversity and the interactions between potential plastic-degrading bacteria (PDBs) and non-plastic-degrading bacteria (NDBs) across ocean, surface water, and wastewater habitats. Our findings reveal that wastewater plastispheres harbor the most diverse and compositionally even microbial communities, likely driven by complex nutrient loads, pollutant inputs, and high microbial seeding potential. Genus-level analysis of potential PDBs indicated habitat-specific taxa, including Pseudomonas, Acinetobacter, and Aquabacterium in wastewater, Flavobacterium and Alteromonas in ocean, and Psychrobacter and Novosphingobium in surface waters. Network analyses using Pearson's correlation and Random Forest modeling uncovered consistent co-occurrence patterns between potential PDBs and diverse NDB taxa such as Clostridium_sensu_stricto_5, Lachnospiraceae_UCG-001, and Cloacibacterium, suggesting potential facilitative interactions, including redox modulation, nutrient exchange, and biofilm support. ML tools proved effective in identifying key taxa and potential ecological interactions, but their application remains limited by taxonomic resolution, lack of functional validation, and insufficient integration of environmental metadata. These findings underscore the ecological complexity of plastisphere communities and the need for community-level approaches in plastic biodegradation research.

Spring viremia of carp (SVC), caused by spring viremia of carp virus (SVCV), is a highly contagious disease that poses a serious threat to cyprinid aquaculture and international trade, and it is listed as a notifiable disease by the World Organization for Animal Health (WOAH). Effective surveillance and control of SVCV rely on accurate and highly sensitive molecular diagnostic methods. However, several previously published RT-qPCR assays contain mismatches between primer/probe sequences and viral genomes, which may lead to false-negative results and reduced diagnostic reliability. In this study, a whole-genome comparison of 24 representative SVCV strains covering all four genotypes (SVCVa-d) was conducted, and a new primer-probe set (Cefas AR) targeting a highly conserved region of the L gene was designed. Reaction conditions were optimized, and the assay was rigorously validated in accordance with the WOAH Manual of Diagnostic Tests for Aquatic Animals. The developed RT-qPCR assay exhibited excellent analytical performance, with a limit of detection of 1.28 copies/μL, diagnostic sensitivities of 100% for cell-culture isolates and 96.6% for tissue samples, and a diagnostic specificity of 100%. In addition, the assay demonstrated strong reproducibility and consistency across nine independent laboratories. In conclusion, the WOAH-validated RT-qPCR assay developed in this study provides a highly sensitive, specific, and reliable tool for rapid screening, routine surveillance, and confirmatory diagnosis of SVCV, supporting sustainable aquaculture development and international aquatic animal health management.

Background: The normal intestinal microbiota undergoes rapid and notable changes in patients in the intensive care unit (ICU) because of factors such as host physiological stress, changes in gastrointestinal function, and antibiotic exposure. Different specimen types are used for intestinal microbial analysis because of sampling difficulties. Therefore, this study conducted a meta-analysis to investigate changes in the intestinal microbiota of patients admitted to the ICU and whether using different specimen types affects microbiota analysis.

Methods: A systematic review was conducted encompassing studies published in electronic databases up to May 1, 2024. We included 11 studies that compared the abundance and diversity of the gut microbiota between ICU patients and healthy cohorts (HC). A standardized mean difference (SMD) meta-analysis using random effects models was performed to quantify microbial differences, including an assessment of various sampling methods.

Results: After ICU admission, the intestinal microbiota of patients differed significantly from that of the normal population, showing lower diversity and richness. A significant difference in beta diversity was also observed. Specifically, the relative abundances of Proteobacteria and Fusobacteria were elevated in ICU patients, while Firmicutes abundance was diminished. Crucially, the comparison of stool versus rectal swab specimens demonstrated no significant difference in the measured alpha diversity of the gut microbiota.

Conclusion: The early intestinal microbiota of patients in the ICU differed from that of healthy individuals. A comprehensive understanding of the early changes in the intestinal microbiota of patients in the ICU can help formulate prevention and treatment strategies. Furthermore, using feces and swab samples for analysis did not significantly affect the diversity of the intestinal microecology. Therefore, rectal swabs may be an attractive method for sampling the gut microbiota and metabolome.

Systematic review registration: PROSPERO Registration number is CRD42022385146 (Available from: https://www.crd.york.ac.uk/PROSPERO/view/CRD42022385146).

Introduction: This study clarifies the taxonomic identity of Bacillus paralicheniformis MHN12 and maps the genetic foundations of its beneficial traits. It also provides functional insights into the salinity-stress response and paves the way for the development of MHN12 as a potential bioinoculant to enhance crop stress resilience and productivity.

Methods: The endophytic strain MHN12, isolated from Vigna radiata, was initially identified as Bacillus licheniformis based on its 16S rRNA sequence. To ascertain its identity and ensure accurate taxonomic classification, a comparative genomic analysis based on genome relatedness indexes and secondary metabolite biosynthetic gene clusters was conducted, involving MHN12 and 22 other B. paralicheniformis strains.

Results and discussion: There were high similarities among the strains and antiSMASH revealed the presence of biosynthetic gene clusters specifically fengycin and bacitracin in MHN12 encoded by the genomes of B. paralicheniformis but absent in B. licheniformis. The whole genome analysis of B. paralicheniformis MHN12, focusing on identifying genes contributing to its potential to promote plant growth and abiotic stress tolerance was also performed. Genes linked to chemotaxis, motility, polysaccharide synthesis, plant growth promoting traits, antimicrobial and stress mitigation compounds were annotated. This highlights MHN12's potential to efficiently colonize plants, stimulate their growth, and protect them from environmental stresses and pathogens. In vitro assays also supported the genomic data, demonstrating MHN12's ability to synthesize enzymatic antioxidants and exopolysaccharides (EPS) while retaining plant growth promoting traits under salinity stress. Gas chromatography (GC)-based analysis revealed modulation of plasma membrane lipids aiding MHN12 to combat salt stress.

Staphylococcus aureus is a leading cause of skin and wound infections worldwide, with methicillin-resistant strains (MRSA) posing a persistent clinical challenge due to antibiotic tolerance and biofilm formation. Lactoferrin, an iron-binding glycoprotein abundant in mammals' secretions and neutrophil granules, has emerged as a promising multifunctional agent that could help manage staphylococcal skin and wound infections, as it combines direct antimicrobial activity with immunomodulatory and tissue-repair effects. This mini-review aims to synthesize current evidence on the role of lactoferrin in the prevention and treatment of staphylococcal skin and wound infections, focusing on its antimicrobial mechanisms, modulation of host responses, and therapeutic applications. In vitro studies demonstrate that lactoferrin inhibits S. aureus growth through iron sequestration and membrane disruption, and it can also disrupt biofilm formation and persistence. Additionally, experiments showed that lactoferrin modulates inflammation, reduces oxidative stress, and promotes fibroblast migration and collagen deposition, facilitating wound closure. Lactoferrin incorporated into hydrogels, films, or nanocarriers enhanced antibacterial activity and synergized with antibiotics or bacteriophages in preclinical models. Nonetheless, variability in dosing, formulation, and study design limits cross-study comparisons, and potential bacterial resistance mechanisms remain underexplored. Therefore, further controlled and standardized studies are needed in order to optimize clinical translation and integration into modern wound care.

Hospital wastewater (HWW) is a complex matrix of pharmaceutical residues, antibiotic resistance genes (ARGs), pathogens, and emerging contaminants that threaten public health and ecosystems. Conventional wastewater treatment plants (WWTPs) often fail to eliminate persistent compounds like carbamazepine and sulfamethoxazole, contributing to antimicrobial resistance and environmental toxicity. This review explores advanced treatment strategies with a focus on bioremediation and phytoremediation. Microbial approaches using bacteria, fungi, algae such as Labrys portucalensis, Trametes versicolor, and Chlorella vulgaris demonstrate degradation of pharmaceuticals and ARGs. Similarly, phytoremediation with species like Typha angustifolia and Vetiveria zizanioides supports on-site through rhizospheric uptake. Integrated systems combining membrane bioreactors (MBRs), advanced oxidation processes (AOPs), constructed wetlands (CWs), and microbial consortia offer enhanced removal efficiency and ARG reduction. While hybrid systems show strong potential, they face challenges such as high costs, difficulties in large-scale application, and limited regulation. Overall, this review highlights how integrating biological and technological methods provides a practical and sustainable path forward for treating hospital wastewater (HWW) and reducing its environmental and health impacts. A multidisciplinary, globally coordinated approach is essential for sustainable HWW management.

Microbial fermentation is an established technology that is becoming increasingly used to produce key food components. Among the various microorganisms used, yeasts play crucial roles due to their efficiency in synthesizing a wide range of industrially important compounds. The growing demand for sustainable, locally sourced, and animal-free food ingredients has increased the focus on yeast biomass and its derivatives. These yeast-based products, such as food emulsifiers, are a promising next-generation of food components, offering advantages like a low risk of allergenicity. Yeast biomass-based fractions have been effectively used as emulsifiers in various food products including in dairy, meat, bakery, meat alternatives, mayonnaises and salad dressing, with effective properties demonstrated in a range of oil-in-water, water-in-oil, and Pickering emulsion models. Both whole cell biomass and yeast cell fractions such as the yeast cell wall, mannoproteins, glucans, exopolysaccharides and other yeast-derived compounds have been demonstrated to function as effective emulsifiers. An increasingly large number of yeasts, beyond just Saccharomyces cerevisiae, have been studied as potential sources of these emulsifiers with the extraction and purification methods employed depending on the specific emulsifier targeted, the required purity, and the intended application. Efficient, cost-effective, and sustainable processes are key to enabling industrial-scale production of these emulsifiers, as such this article reviews the potential yeast-derived food emulsifiers, lists the various yeast species investigated to date, examines the extraction and purification methods, and highlights the potential food applications of these yeast-derived emulsifiers.

Antimicrobial resistance (AMR) is a critical global health threat. This phenomenon involves the diffusion of bacteria and genes among humans, animals and the environment. In particular, the presence of third generation cephalosporin (3GC)-resistant Enterobacteriaceae in natural environments is of high concern as they are classified as critical-priority pathogens of public health importance. In this work we studied the relation among plastic pollution in freshwater ecosystems, the spread of multidrug-resistant (MDR) bacteria and diffusion of antibiotic resistance genes (ARGs). Caged plastic fragments were deliberately introduced in a river of central Italy. Plastic samples were collected and analyzed in parallel with river water samples. Out of 267 cefotaxime (CTX) resistant isolates obtained, 65 CTX-resistant Enterobacteriaceae were selected for further analysis. Most of the isolates (75% of plastic-derived and 84% of water-derived isolates) were MDR with seven being carbapenem-resistant enterobacteria (CRE). Five of them synthesize KPC (Klebsiella pneumoniae carbapenemases) enzymes, and two strains were positive for metallo-β-lactamases (NDM). Among the KPC producers, three isolates were identified as K. pneumoniae sequence type ST1519. Their isolation in a natural ecosystem is alarming because they can potentially re-enter human populations through environmental pathways. Shotgun metagenomic analysis provided a comprehensive snapshot of the microbial communities associated to the plastisphere, revealing dominance of families such as Comamonadaceae, Sphaerotilaceae, and Flavobacteriaceae, which play key roles in environmental biofilm formation and stability. The resistome analysis highlighted the presence of ARGs conferring resistance to clinically important antibiotics, such as beta-lactams, vancomycin, and tetracyclines, alongside mobile genetic elements (MGEs) such as integrons, which facilitate the horizontal transfer of resistance genes. This study provides crucial experimental evidence that riverine plastic debris acts as a genetic reservoir and could act as an efficient vehicle for the accumulation and transfer of clinically relevant resistance determinants.

Background: Clostridioides difficile infection (CDI) is a leading cause of healthcare-associated diarrhea. Although gut microbiota dysbiosis is central to CDI, the specific commensal species that confer protection are not well defined.

Methods: We performed 16S rRNA sequencing on fecal samples from a clinical cohort of 30 CDI patients, 30 non-CDI diarrhea patients, 27 asymptomatic C. difficile carriers, and 30 healthy controls. To functionally validate the clinical finding, an in vitro anaerobic co-culture system was established between the Odoribacter splanchnicus type strain and C. difficile. Toxin protein levels in the supernatant were quantified by ELISA at multiple time points (24, 48, and 72 h). Sporulation was assessed via ethanol resistance assays, and the expression of toxin genes (tcdA/tcdB) was measured by quantitative PCR (qPCR).

Results: Clinical analysis revealed a significant negative correlation between the abundance of Odoribacter splanchnicus and CDI severity. In vitro, a high initial ratio of O. splanchnicus significantly suppressed C. difficile toxin production during the stationary phase, without inhibiting bacterial growth. This reduction in vitro levels was accompanied by a concurrent increase in sporulation and was preceded by a downregulation of tcdB gene expression.

Conclusion: This work positions O. splanchnicus as a highly promising candidate for the development of next-generation, defined microbial therapeutics and provides a mechanistic foundation for future anti-virulence approaches to combat CDI.