Archives of Microbiology最新文献

The occurrence of microcystins in freshwater bodies is a global concern as they pose possible health effects on aquatic life, humans, wildlife and livestock. In a continued drive to find technologies for their safe removal from water, biodegradation has been identified as one of the effective, low cost and safe technologies. Using classic batch culture experiments, this work identified a bacterial consortium obtained from abattoir effluents, that could metabolize microcystin-LR (MC-LR) as the sole source of carbon. After 21 days of incubation the MC-LR concentrations (3 mg L^− 1) were reduced by 57% due to biological activities. The composition of the bacterial consortium was determined from 16 S rRNA gene sequencing and 20 dominant genera were identified. Among the 20 dominant genera identified, five (Stenotrophomonas, Aeromonas, Alcaligenes, Morganella and Citrobacter) are known MC-LR degraders. The remaining genera have not previously been reported to degrade MC-LR. These taxa may represent novel MC-LR-degrading bacteria, or alternatively, they may play supportive roles in the consortium without directly participating in MC-LR degradation. Hence their exact role needs to be established. Compared to the indigenous abattoir effluent bacterial communities, the MC-LR degrading consortium exhibited improved metabolic potentials as measured by their ability to metabolize a set of 31 different carbon substrates. Overall, these results confirm the ubiquitous distribution of microcystin degraders and further highlight industrial effluents as potential sinks for biotechnological tools for environmental bioremediation. Nonetheless, further work to optimize the degradation reaction, identify the role and pathogenicity of each individual bacterium as well as identify the genes involved remain crucial to cement possible future applications of this bacterial assemblage.

Morganella morganii exemplifies a typical case of an open pangenome, where genes move intra- and interspecies via horizontal gene transfer. Through pangenome analysis, the study maps three agriculture isolates; M. morganii with strong plant growth promoting (PGP) activity, along with 78 publicly available genomes from clinical, food, wastewater, and animal sources. The analysis showed 20,860 gene clusters with only 9.99% core genes and a discriminating distribution of 75.20% cloud genes across different niches. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed 33, 36, and 38 genes related to nutrient solubilization in M. morganii isolates HM01, HM02, and HM03, respectively. Chemotaxis genes, crucial for stress response, were most abundant in HM03 (30), followed by HM01 (17) and HM02 (27). Additionally, numerous biosynthetic gene clusters encoding antibacterial and antifungal metabolites were identified. Clinical and wastewater isolates harboured a higher number of mobile genetic element (MGE) linked antimicrobial resistance (AMR) genes that confer resistance to 15 antibiotic classes. These AMR genes were predominantly plasmid-borne and found to transfer in M. morganii from clinical pathogens such as E. coli and A. baumannii. This study indicates that habitat pressure creates the scenario for selection of functional traits which enables the ecosystem specific survival of M. morganii. Together, the present investigation provides important insight into the genomic diversity and remarkable PGP potential of M. morganii strains for sustainable agriculture. The pangenome analysis proposes that detailed investigation is needed to confirm their efficacy as PGP bacteria and to distinguish them from pathogenic strains.

Canine distemper is a highly contagious disease of domestic dogs and various species of wild animals, and is associated with high mortality. It is caused by canine morbillivirus (formerly known as CDV or canine distemper virus), a member of the Morbillivirus genus under Paramyxoviridae family. The disease is endemic in many parts of the world, including India. For effective control of the disease, reliable diagnostic tools are of utmost importance. The circulating CDV strains in India belong to a novel “India1/Asia-5” lineage, highlighting the need for the development of new diagnostic tools. The nucleocapsid (N) protein is the major structural protein and one of the most immunogenic proteins of the virus; thus, it has been the preferred diagnostic target. Therefore, the present study was aimed at expressing the nucleocapsid protein of CDV using the baculovirus expression system in insect cells and its successful purification using affinity column chromatography. Expression and specificity of the recombinant N protein were confirmed using SDS-PAGE and Western blot analysis, revealing a band of approximately 58 kDa. The purified protein also reacted with CDV polyclonal serum, suggesting that the N protein was expressed in an immunoreactive form. Among the panel of monoclonal antibodies generated against CDV, only CDV-2F8 exhibited specific reactivity with the recombinant N protein, indicating the preservation of at least one linear epitope. The diagnostic suitability of the expressed protein was further confirmed by using it as a coating antigen in an indirect ELISA, which clearly distinguished between CDV-positive and negative dog serum samples. The recombinant N protein developed in the present study can facilitate large-scale field application of recombinant protein-based diagnostics for CDV, as it eliminates the need for live virus antigen in routine serodiagnostic assays.

Microorganisms remain a prolific source of bioactive compounds, yet discovery efforts are often hindered by traditional methods and the repeated isolation of known molecules. In the post-genomics era, advances in genome mining and multi-omics technologies have revealed the hidden potential of biosynthetic gene clusters. A major challenge, however, lies in reliably linking these gene clusters to their metabolites and in the activation of silent pathways. This review summarizes recent breakthroughs addressing these challenges, focusing on the most recent case studies (up to 2025), and covering three interconnected themes. First, it reviews the current strengths and limitations of microbial genomics and artificial intelligence in natural product discovery, emphasizing different genome-guided discovery strategies and the emerging applications of artificial intelligence. Second, it highlights strategies for activating silent gene clusters, covering both untargeted and targeted approaches. Third, it discusses the expansion of chemical diversity through bioprospecting in underexplored ecological niches, the integration of sustainable, ethically informed practices, and the development of novel cultivation platforms. By synthesizing these advances, this review provides a forward-looking perspective, proposing how the integration of current tools in one framework can establish a predictive and potentially highly efficient method for linking biosynthetic gene clusters to their metabolites. Such integrative approaches may accelerate the discovery of microbial natural products and contribute sustainable solutions to global health challenges, including antimicrobial resistance. In conclusion, this review represents an up-to-date roadmap for researchers in microbial natural product research from a biological perspective, identifies existing strengths and knowledge gaps, and highlights promising, proof-of-concept strategies that can drive future advances in the field.

This study investigated the antifungal mechanisms of geraniol against Candida albicans. Geraniol significantly inhibited growth and biofilm formation, with a minimum inhibitory concentration (MIC) of 0.5 µL/mL. At concentrations of 0.3, 0.45, and 0.6 µL/mL, geraniol substantially reduced biofilm biomass (P < 0.05). Microscopic analyses revealed apoptosis induction, membrane shrinkage, and structural damage. Mechanistically, geraniol disrupted cell membrane permeability, inhibited ergosterol synthesis, and downregulated the expression of key virulence genes (SAP5, SAP6, SAP7). These multifaceted mechanisms highlight geraniol as a promising antifungal candidate with potential clinical relevance in combating antifungal resistance. Future studies should include vivo validation to explore its therapeutic application.

Postbiotics, defined as microbial metabolites, confer health and nutritional benefits. Postbiotics, which are a step beyond probiotics, have emerged as a promising alternative to live microbial cells. While offering stability and safety, postbiotics improve efficacy and avoid the risks associated with live microorganisms. Key metabolite substances such as bacteriocin, peptides, and exopolysaccharides exhibit biological activities, thereby improving food preservation and functional enhancement. This comprehensive review aims to provide know-how for postbiotics’ technological, functional, and health-promoting applications across various food systems. Advanced transport mechanisms for delivering postbiotics, such as encapsulation, nanoemulsions, and microfluidic microspheres, have created effective postbiotic delivery systems (PDS). Despite significant progress, mechanistic understanding, production standardization, and regulatory frameworks are still not well understood. Therefore, in-depth research into transport mechanisms and global compliance standards will ensure safe and reproducible applications of postbiotics. Future innovations that integrate agro-industrial by-product bioconversion, advances in omics technologies, and AI-assisted modeling will further support the circular bioeconomy, optimization, and functional prediction from a sustainability perspective.

Biofilm formation and antimicrobial resistance (AMR) are critical global health concerns, necessitating the discovery of novel therapeutic compounds. Enterococcus gallinarum, an opportunistic pathogen intrinsically resistant to vancomycin, is responsible for severe infections, often leading to endocarditis, bloodstream dissemination, immune dysregulation, and tissue damage. The limited efficacy of existing treatments underscores the urgent need for alternative therapeutic strategies. Recently, we reported the efficacy of 4,5,7-trihydroxyflavanone (THF) as an exhibited potential antimicrobial agent. In this study, the antibiofilm activity of THF against E. gallinarum was examined. In addition, the role of THF in preventing infection and mortality in zebrafish was also analysed using histopathological studies. The host-drug interaction was investigated through a network pharmacology approach for bacterial endocarditis. The top hub genes found in this analysis were docked with THF using the Glide XP protocol, and simulations were performed by GROMACS version 2020. The results suggest the potential of THF in inhibiting bacterial adhesion to extracellular matrix (ECM) and the disruption of mature biofilms. The histopathological results showed significantly recovered tissues after THF treatment. Furthermore, the network pharmacology studies of bacterial endocarditis disease revealed the identification of top hub genes MMP-2 and MMP-9, which have the function of binding to ECM and causing inflammation. The molecular docking and dynamics simulations performed between MMP-2 & MMP-9 showed a strong binding score of -4.652 kcal/mol & -7.597 kcal/mol between THF and MMP-2 & MMP-9, suggesting the anti-inflammatory potential of THF as well. This significant influence on host-pathogen interactions, particularly in modulating immune responses and inflammation, makes it a promising drug candidate for bacterial infections and necessitates its consideration for future research and studies.

Graphical abstract

Biofilms are organized microbial communities that are surrounded by a matrix of extracellular polymeric substance (EPS), which raises significant challenges to environmental, and medical applications. Their intricate architecture and adaptive behavior enable them to resist conventional antimicrobial therapies, primarily due to restricted drug diffusion, altered metabolic activity, and the emergence of resistance mechanisms. To address these challenges, synthetic drug-based strategies have emerged, focusing on the disruption of key stages in biofilm development, such as bacterial adhesion, quorum sensing (QS), EPS production, and biofilm maturation. Quorum sensing inhibitors, including synthetic furanones, peptide-based inhibitors, and nanoparticles, have shown promising results in interfering with biofilm signaling pathways and preventing biofilm maturation. EPS matrix, such as chelating agents and enzymatic treatments, weaken the biofilm matrix, rendering the microbial cells more susceptible to antimicrobial agents. Nanotechnology-driven approaches, utilizing metal nanoparticles, functionalized nanoparticles, and nanocarrier-based drug delivery systems, enhance. These strategies enhance antimicrobial penetration and efficacy while reducing off-target effects; however, clinical translation is limited by cytotoxicity, pharmacokinetic constraints, and microbial adaptation. Future work should prioritize multi-targeted therapies, personalized biofilm disruption, and advanced drug delivery systems to combat biofilm-related infections and industrial biofouling.

Graphical abstract

Lupinifolin possesses the capability to combat specific pathogenic bacteria. Nonetheless, Gram-negative bacteria exhibit minimal inhibition by lupinifolin. This study evaluated the synergistic antibacterial and antibiofilm activities of combinations of lupinifolin and antibiotics against pathogenic bacteria using a checkerboard assay and time-kill analysis. Crystal violet staining and confocal laser scanning microscopy (CLSM) were utilized to evaluate antibiofilm properties. After treatment, gene expression changes in isolates were evaluated using quantitative real-time PCR. Lupinifolin and streptomycin synergistically inhibited MRSA and VRE with a FIC index of 0.5, whereas lupinifolin and vancomycin similarly inhibited S. aureus ATCC25923. Partially synergistic interaction against E. faecalis ATCC29212 between lupinifolin and tetracycline, vancomycin, and chloramphenicol with an FIC index of 0.625, 0.5625, and 0.625, respectively. Partially synergistic interaction against E. faecium HTY0256 between lupinifolin and tetracycline with an FIC index of 0.625. The interaction between lupinifolin and streptomycin against Gram-negative bacteria, such as E. coli ATCC25922, showed a synergistic effect. The time-kill assay of the combinations showed an inhibitory effect of more than 3 log and 2 log (CFU/ml) at 4 h incubation. CLSM revealed that the combinations reduced biofilm formation. The combination of lupinifolin and streptomycin altered biofilm-forming genes in E. faecalis ATCC29212 and VRE isolates; gelE and bepA were down-regulated. In contrast, MRSA isolates had sarA and ebpS up-regulated. In addition, our findings suggested that lupinifolin destroys cell membranes, as demonstrated by the expression of secA. Our investigation enabled the prospective integration of lupinifolin with antibiotics, enhancing their efficacy and application against antimicrobial-resistant pathogens.

Rapid industrialisation, urbanisation, and agricultural chemical fertilizer expansion have raised concerns over the accumulation and biomagnification of recalcitrant and emerging contaminants. Often, these compounds are resistant to degradation, and their conversion may lead to generation of even more toxic derivatives, which ultimately makes their remediation a crucial environment concern. Conventional treatment techniques are often considered expensive, inefficient and harmful to the environment; therefore the necessity to shift towards sustainable alternatives is required. Microalgae have emerged as a promising tool for bioremediation, offering cost-effective and eco-friendly solutions. Using microalgae as sustainable approach will not only remove toxic pollutants but also enable the generation of biomass that has numerous applications. Microalgae degrade the pollutants by using biosorption, bioaccumulation, biotransformation, biodegradation, and photodegradation and use their byproducts for their own growth. This review mainly addresses and critically examines the potential of microalgae-based bioremediation processes for eliminating persistent and newly discovered toxic contaminants. For example, Microspora amoena, Cladophora. glomerata, Enteromorpha intestinalis removes heavy metal chromium by the biosorption process with a removal capacity of 66.6%. Like that, microalgae have various species that have remarkable potential of removing pharmaceuticals, dyes, hydrocarbons, pesticides and plastic waste by using mechanisms like biosorption, bioaccumulation, biodegradation, biotransformation and photodegradation. They also have various applications in wastewater treatment and new developments in the phycoremediation process. This review paper also emphasizes on emerging technologies, mechanisms and potential sustainable environment solutions for the future. It may also serve as a feasible door for future research focusing on microalgae and their applications.

Graphical abstract