Archives of Microbiology最新文献

Chlorogenic acid (CA), a principal bioactive constituent prevalent in numerous Chinese herbal medicines, exhibits well-documented antibacterial efficacy. However, CA is rapidly metabolized in the intestine and liver, and the specific mechanisms of its metabolites against Pseudomonas aeruginosa (P. aeruginosa) biofilms remain unclear. This study demonstrated that shikimic acid, a key metabolite of CA, effectively inhibits biofilm formation in clinical P. aeruginosa strains without impeding bacterial growth. This antibiofilm activity was linked to the significant suppression of extracellular polymeric substance (EPS) and alginate production, as well as the impairment of bacterial motility. By integrating transcriptome analysis with RT-PCR validation, it is postulated that the antibiofilm action of shikimic acid may be attributed to its regulatory effects on the constituents of the EPS within the biofilm, especially extracellular polysaccharides. Moreover, shikimic acid predominantly downregulated genes associated with alginate synthesis, among which algD exhibited the most significant expression alteration. In order to ascertain the role of algD in the antibiofilm action of shikimic acid, an algD knockout strain, PA2209ΔalgD, was constructed. The results demonstrated that shikimic acid did not exerted notable inhibitory effects on biofilm formation or alginate production in the algD knockout strains, suggesting that the algD gene is essential for the antibiofilm effect of shikimic acid. These findings elucidate a novel mechanism by which a CA-derived metabolite disrupts biofilm integrity by targeting the algD-dependent alginate biosynthesis pathway, positioning shikimic acid as a potential lead for developing non-bactericidal anti-biofilm agents.

Complete ammonia oxidizers (comammox bacteria) can independently perform two-step nitrification and are crucial for nitrogen cycling. However, their niche differentiation across different types of aquatic environments remains poorly understood. Here, we investigated the niche differentiation of comammox bacteria in sediments from three typical water bodies (river, lake, and pond) in the middle reaches of the Yangtze River. The results showed that the amoA gene abundance of comammox Clade B was significantly greater in stagnant water bodies (pond: 2.89 × 10⁸ copies g^− 1) than in flowing water bodies (river: 5.58 × 10⁷ copies g^− 1, P < 0.05; lake: 8.69 × 10⁷ copies g^− 1, P < 0.01). Compared to non-rhizosphere sediments, rhizosphere sediments in the three water bodies showed higher mean amoA abundances of Clade A and Clade B. In addition, the mean total nitrification rate followed an order of the pond (1.744 ± 0.3045 mg N kg^− 1d^− 1) < the lake (2.033 ± 0.5871 mg N kg^− 1d^− 1) < the river (3.308 ± 0.7078 mg N kg^− 1d^− 1), displaying an increasing trend with water fluidity, which was also reflected in comammox bacterial diversity. In the three water bodies, Clade A was identified as the predominant group within the comammox community, while Clade A.1 was the dominant functional clade in nitrification. Furthermore, the C/N ratio was identified as a key driver shaping niche differentiation among comammox clades in sediments. These results indicate that water flow shapes the niche differentiation of comammox bacteria in the middle reaches of the Yangtze River and provide new perspectives for aquatic ecological restoration.

Heavy metal contamination of water and soil poses grave issues for the environment as well as human health owing to its high toxicity, persistence in the environment, and probable bioaccumulation. Conventional methods, including chemical leaching, membrane filtration, etc., are advantageous but produce secondary pollutants. However, microbial bioremediation appears to be one of the most promising eco-friendly techniques that involves bacteria, fungi and algae. In addition to that, indigenous microbes are more adaptive to polluted environments, thereby ensuring enhanced bioremediation efficacy. Basic microbial mechanisms of biosorption, bioaccumulation, extracellular precipitation, and biotransformation that stabilize and detoxify heavy metals have also been outlined. This study also hypothesizes the integration of genetic engineering and nanotechnology in heavy metal bioremediation for large-scale applications. Finally, the review addresses the existing challenges and limitations, such as bioavailability of metals and complex pollutant interactions and emphasizes the need for further research for scale expansion and to conquer environmental constraints.

Polyunsaturated fatty acids (PUFAs) are essential lipids that play a key role in human health with various industrial and pharmaceutical applications. The main conventional source is marine fish; however, owing to sustainability and dietary preferences, microbial sources such as marine microalgae, yeast, fungi, and psychrophilic organisms have drawn interest as alternatives. This review considers the diverse microbial and natural sources of PUFAs and their biosynthesis pathways. In addition to their role in immune regulation and metabolic health, PUFAs are biologically significant, as they can reduce risk of chronic diseases, such as breast cancer, cardiovascular disorders, and neurodegenerative conditions. The expanding global and Indian PUFA markets are driven by demand for plant and algae-based ω-3 alternatives, vegetarian dietary preferences, and rising consumer awareness. The findings suggest that microbial PUFA sources have become increasingly important and researchers should optimize their sustainable production and application strategies. By providing a comprehensive perspective, this review intends to present the microbial importance and scope for PUFA production.

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Overuse and misuse of antibiotics used for treating bacterial infections has resulted in ineffectiveness of the drugs and hence increase in the cases of antimicrobial resistance. This has precipitated to the need for research and development of novel strategies to target pathogenic microbes. ESKAPE pathogens include high priority pathogens such as Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae (sometimes K. aerogenes), Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species (e.g., E. cloacae) which are responsible for causing healthcare associated infections whereas non ESKAPE pathogens such as Escherichia coli and Mycobacterium tuberculosis contribute to community acquired infections. Hence, targeting enzymes involved in amino acid and protein biosynthesis pathways is one such strategy for growth inhibition of these pathogens. Amino acids and their products are essential for various functions such as bacterial survivability, pathogenicity, cell wall integrity, essential mineral acquisition from surrounding or inside pathogen and activation of transporters. This review details the amino acid and protein biosynthetic pathways in pathogenic bacteria along with efficacy and translational potential of various natural and synthetic antimicrobial molecules discovered and synthesized against enzymes of these pathways for combating bacterial growth. This review also highlights promising antibacterial molecules such as quercetin, pyrazinoic acid, mupirocin and enrofloxacin etc. which are at various phases of clinical trials and hold promise for treatment of bacterial infections. Lastly, the review also lists risks such as cytotoxicity, redundancy and metabolic bypass associated with these inhibitors and also proposes future strategies such as trojan horse and combination therapy to deal with the above issues.

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Plant growth-promoting bacteria may act by enhancing soil fertility, nutrient cycling, and pathogen suppression. We analyzed the genomes and metabolomes of six strains, Chromobacterium violaceum CNPSo 1954, Pantoea agglomerans CNPSo 2602, Bacillus velezensis CNPSo 2657, Bacillus altitudinis CNPSo 2658, Bacillus safensis CNPSo 2725, and the novel species Pseudomonas sp. CNPSo 2799. Genomic bioprospection revealed diverse biosynthetic gene clusters (BGCs) involved in secondary metabolites production, accounting for 4.26% of the total genome in strain CNPSo 2602 and 18.03% in strain CNPSo 2657. An average of 79 carbohydrate-active enzymes (CAZymes) were identified per genome, with glycoside hydrolases and glycosyltransferases accounting for more than 50% of all identified enzymes. The strains exhibited distinct antibiotic resistance profiles, ranging from three (CNPSo 2658 and CNPSo 2725) to 12 (CNPSo 2602). All strains carried the genes for tryptophan-biosynthesis, and targeted metabolomic analysis confirmed the production of the phytohormones indole-3-acetic (IAA), indole-3-butyric (IBA), indole-3-pyruvic acids (IPA), and L-tryptophan (TRP), with strain-specific variation in metabolic profiles. These strains exhibited multiple growth-promoting and biocontrol traits, highlighting a potential as multifunctional next-generation bio-inputs for sustainable agricultural applications.

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The present study focused on the extraction and identification of endophytic fungi from Bambusa pallida and Dendrocalamus sikkimensis. A total of 126 fungal specimens were isolated and categorized into 19 distinct morphotypes spanning 12 genera with highest isolates belonging to the class Sordariomycetes. The study reveals that B. pallida exhibits higher colonization frequency of 68% where Colletotrichum gloeosporioides is the most dominant fungal isolates with dominance percentile of 45.59%. In D. sikkimensis, Nemania diffusa was found to be most dominant among the 58 fungal isolates with dominance percentile of 36.21% Notably, Chaetomium madrasense and Colletotrichum gloeosporioides emerged as prominent candidates, displaying significant antagonism against the target microorganisms, Bacillus subtilis and Staphylococcus aureus. ITS rDNA sequences confirmed the identity of the isolates. Of particular interest was C. madrasense, which exhibited a larger zone of inhibition compared to positive controls, underscoring its potential as a novel antibacterial agent. This research showcases the diverse array of endophytic fungi associated with bamboo, unearthing a relatively untapped reservoir of antimicrobial compounds. Given the mounting concerns about antibiotic resistance, these findings illuminate a promising avenue for future endeavors in drug discovery.

Pseudomonas aeruginosa forms resilient, antibiotic-tolerant biofilms, with quorum sensing (QS) as a central regulator of biofilm formation and virulence. In this study, we report Nocardia sp. EMB45, isolated from termite nest soil, as a novel source of antibiofilm metabolites. The crude extract inhibited P. aeruginosa PAO1 biofilm formation with a minimum biofilm inhibitory concentration (MBIC) of 6 mg/mL. Morphological analyses by FE-SEM and AFM revealed disrupted biofilm architecture, while confocal microscopy showed sparse and less dense biofilms composed predominantly of viable cells. Mechanistic studies demonstrated QS inhibition using the biosensor Chromobacterium violaceum CV026, suggesting interference with AHL-mediated signalling. The extract markedly reduced QS-regulated phenotypes, including exopolysaccharide production and virulence factors. qRT-PCR analysis demonstrated strong suppression of QS genes, with lasI, lasR, rhlI, and rhlR showing ~ 14- to 20-fold downregulation relative to untreated controls. GC–MS analysis identified 22 metabolites, among which compound C1 (1,2-oxathiane,6-dodecyl-,2,2-dioxide) and compound C4 (Pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro-3-(phenylmethyl)-) exhibited the highest binding affinities toward LasR and RhlR, respectively, in molecular docking and dynamics simulations. These findings highlight Nocardia sp. EMB45 is a promising and underexplored source of antibiofilm metabolites with potential applications in anti-virulence therapy against P. aeruginosa.

Food spoilage is a significant global issue, with approximately 31% of the food supply being wasted, resulting in economic and environmental problems worldwide. While synthetic preservatives effectively extend shelf life, they pose health risks due to possible carcinogenic properties and adverse effects, leading to a shift toward natural preservation methods. The modern food industry market is shifting from synthetic to natural preservatives, driven by rising consumer demand for clean-label products and concerns about the health risks associated with synthetic additives. These compounds offer multifunctional properties, including antimicrobial, antioxidant, and anti-enzymatic activities, which help inhibit spoilage microbes and maintain food safety and quality standards. This review thoroughly examines the development of food preservation strategies, with a focus on natural alternatives that ensure food safety while meeting consumer expectations for quality and safety. Analysis of the global marketplace reveals that natural food preservatives are experiencing significant growth, with variations in market concentration and adoption patterns across different regions. Plant, animal, and microbial preservatives demonstrate effectiveness comparable to that of synthetic preservatives while addressing safety concerns. This review aims to explore antimicrobial peptides, particularly bacteriocins, their classification, and antimicrobial mechanisms, including membrane disruption and metabolic interference, highlighting their potential applications in various food matrices. Current food challenges include stability, scalability, and regulatory harmonisation. This review highlights the transformative approach involving nanotechnology, hurdle technology, and biotechnological innovations, which could lead to the development of a potential natural preservative for creating sustainable, safe, and consumer-acceptable food preservation systems.

Triazoles have significant antibacterial and antifungal properties that protect against dangerous fungus, bacteria, pathogens, and even antibiotic-resistant microbes that lead to infectious disorders and food degradation. Although they are known to target a number of essential metabolic pathways in bacterial cells, very little is known about how they affect the integrity of the cell membrane. In the current investigation, we compared the antibacterial activity of various distinct substituted 1,2,4-triazole-3-one Schiff base derivatives and found that bis-1,2,4-triazole-3-one Schiff bases have higher antibacterial activity against both Gram-positive and Gram-negative bacteria than 1,2,4-triazole-3-one Schiff bases. We further show that these compounds enhance ionic cell membrane permeability more than the other substituted components, and that the cell membrane is the first barrier that these molecules encounter during their action. Ion leakage is particularly detectable within minutes as the bacteria cells are treated with the minimum inhibitory concentration amounts of the compounds. The antibacterial activity of bis-1,2,4-triazole-3-one Schiff bases is superior to that of other substituted derivatives, and ions detectable by the conductivity measurements leak out from the bacteria. The loss of cell membrane integrity is also demonstrated by the propidium iodide uptake experiments. Therefore, we suggest that the disruption of the cell membrane integrity and ion leakage plays a role in the higher activity of triazole compounds against both Gram-negative and -positive bacteria.

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