Letters in Applied Microbiology最新文献

Recombinase polymerase amplification (RPA) is a powerful isothermal nucleic acid amplification technique, yet its efficiency is critically dependent on the catalytic efficiency of the recombinase UvsX, a key enzyme mediating homologous DNA pairing and strand exchange. To address this limitation, in this study, we developed a specific, sensitive, and robust RPA detection method by optimizing the UvsX enzyme through protein engineering and refining the RPA reaction system. By conducting comparative structural and functional analysis of UvsX orthologs from 13 Myoviridae phages, we identified critical determinants of recombinase activity within the Loop 2 domain of T4 UvsX. Furthermore, we systematically optimized the stoichiometric ratios of core enzymes and crowding agents to establish a robust RPA system. This system was subsequently integrated with lateral flow strips for point-of-need detection of highly lethal Vibrio parahaemolyticus in shrimp. Our results demonstrated that the engineered UvsXv1 variant exhibited significantly improved strand displacement activity, leading to enhanced RPA amplification efficiency and stability.

Biofertilizers have gained attention as eco-friendly alternatives to mitigate the adverse effects of chemical fertilizers. This study focuses on recycling paddy straw waste using lignocellulolytic soil-borne bacteria isolated from paddy fields in Kırklareli and Samsun, Türkiye. This approach supports soil organic matter enrichment and reduces chemical fertilizer dependence, thus lowering greenhouse gas emissions. Microorganisms were isolated using selective media. Cellulolytic and ligninolytic activities were assessed via DNS and Azure-B methods, respectively. Among the isolates, Bacillus sp. S2 (Samsun) exhibited the highest enzymatic activities and grew on nitrogen-free Jensen's medium, suggesting potential nitrogen-fixing ability. Pseudomonas sp. K2 (Kırklareli) showed moderate but consistent lignocellulolytic activity. Following 30 days of incubation with powdered paddy straw, gas chromatography-mass spectrometry (GC-MS) analysis revealed that S2 produced the highest levels of 4-coumaric acid (2.371%), benzoic acid (3.019%), and formic acid (1.280%), along with xylitol (1.390%) and 1-triacontanol (1.298%)-compounds with agronomic relevance for plant growth, stress tolerance, and soil health. K2 uniquely produced arabitol, associated with osmoprotection. BLAST analysis showed that S2 shares 98% identity with Bacillus velezensis and B. amyloliquefaciens, while K2 showed 95% similarity to Ectopseudomonas chengduensis, E. alcaliphila, and P. sihuiensis. These traits support their potential use in sustainable agriculture and crop residue management.

Akkermansia muciniphila is a beneficial gut bacterium because of its improving metabolic effect. However, it is not fully understood how A. muciniphila interacts with host substances to inhabit the human gut. To examine the effect of deoxycholate (DCA) produced by the combination of host and gut bacteria, which enhances the growth of A. muciniphila, on the metabolic changes of A. muciniphila using transcriptome and proteome analyses. Transcriptome analysis showed that carbohydrate metabolism, including glycosyl hydrolase activity and glycosyl bond activity, was significantly upregulated. Notably, transcriptome and proteome analyses demonstrated that the γ-aminobutyric acid (GABA) production pathway, which is related to acid or osmotic stress responses, was upregulated in the presence of DCA. Our results demonstrated that carbohydrate metabolism and GABA production were altered in response to DCA. Therefore, DCA may be a key intestinal substance for the physiological regulation and persistence of A. muciniphila in the gut. This study provides valuable insights into understanding the interaction between host and gut bacterium to persist in the gut.

Arbuscular mycorrhizal fungi (AMF) are obligate biotrophs that form a symbiotic and mutualistic relationship with most terrestrial plants, playing an important role in plant growth, nutrient acquisition, and ecosystem stability. This review synthesizes current knowledge on AMF colonization in plants within New Zealand ecosystems, including the challenges and opportunities of molecular identification techniques used in characterizing AMF communities in natural and managed systems. The ecosystem services provided by AMF, such as improved growth parameters, enhanced nutrition, and disease control, are discussed in detail, highlighting their significance in sustainable agriculture and natural ecosystems. Additionally, the role of AMF in invasion ecology was examined, revealing their dual potential to either facilitate or hinder invasive plant species. Despite significant advances in understanding AMF biology, future research is needed to explore the underlying mechanisms of AMF-plant interactions and to address the challenges caused by changing environmental conditions. This review focused on the importance of AMF in promoting ecosystem resilience and suggests avenues for future research to harness their full potential in agricultural and ecological contexts.

The objective was to evaluate the capacity of Lactiplantibacillus plantarum LP5r to improve the microbiological and physicochemical quality of wastewater from a dairy company. Lactiplantibacillus plantarum LP5r was inoculated (8.8 log10 CFU g-1 mL-1) into 50 L containers of wastewater, 10 mL was added to T1, 10 mL to T2 with monthly replenishment, 50 mL to T3, and 50 mL to T4 with monthly replenishment. The CT was kept without inoculum. Initially, L. plantarum LP5r showed values ​​above 6 log10 CFU g-1. In T1 and T3 decreased to undetectable values, but in T2 and T4 remained above 4 log10 CFU g-1. Enterobacteriaceae were initially 5.46 log10 CFU g-1 and decreased to 4.88 and 4.73 log10 CFU g-1 for T2 and T4 and increased to 7.31 log10 CFU g-1 in CT. Coliforms were reduced from 7.38 log10 CFU g-1 to 2.95 and 2.11 log10 CFU g-1 in T2 and T4. Initial suspended solids were 19 997 mg L-1, which decreased to 6058.3 mg L-1 and 4118.9 mg L-1 for CT and T4. The pH did not differ between samples. An initial BOD5 of 7680 mg L-1 was detected in all samples, which decreased to 2385 mg L-1 for CT and 820 mg L-1 for T4, and the COD decreased from 17 827 mg L-1 to 4839 mg L-1 and 1649 mg L-1 for the CT and T4 samples. Lactiplantibacillus plantarum LP5 positively influences the microbiological quality and COD and BOD5 of the dairy's wastewater.

This study investigates the impact of Lactiplantibacillus plantarum postbiotics (LPP) on microbiological and chemical alterations in raw rainbow trout fillets stored at 4°C. LPP, containing chemicals such as methyl ester, oleic acid, and eucalyptol, demonstrated considerable radical scavenging action and improved cellular safety, enhancing cell survival by 118.70% to 170.60% and elevating SOD (20.10-33.14 mU mg-1) and GSH-Px (99.80-120.30 mU mg-1) activity. The use of LPP (1.5%, 0.8%, 0.5%) and potassium sorbate (PS) in raw fish fillets resulted in a significant decrease in microbial proliferation, with the 1.5% LPP treatment achieving a reduction in Listeria monocytogenes count by 5.6 ± 0.07 log CFU g-1 by day 2. Additionally, chemical parameters showed marked stability; the pH value increased from 6.22 ± 0.08 to 6.4 ± 0.03 in the 1.5% LPP-treated fillets by day 12. Total volatile basic nitrogen levels for the same treatment remained below the acceptable threshold of 25 mg 100 g-1 until day 8 (21.23 ± 0.19 mg 100 g-1), while TBA levels peaked at 1.1 ± 0.02 mg kg-1 on day 12. This approach prolonged shelf life by up to 12 days, maintaining fillet quality with no adverse sensory consequences.

This study aimed to investigate the presence of antimicrobial resistant Escherichia coli (E. coli) among healthy day-old broiler and layer chicks in the absence of in ovo or day-of-hatch antibiotic administration. A total of 100 pooled samples from 14 hatcheries across western Algeria were collected for analyses. Antimicrobial susceptibility testing was performed using the disc-diffusion method. Genes encoding antibiotic resistance, integrons, and phylogenetic groups were screened using Polymerase Chain Reaction (PCR), with the genetic relatedness of extended spectrum beta-lactamase (ESBL)-producing isolates determined via multilocus sequence typing. Sixty-eight samples contained E. coli, with high levels of resistance to multiple antibiotics found among broiler (92.10%) and layer chicks (100%) (no significant statistical association, P < 0.05). Multidrug-resistant (MDR)/ESBL-producing isolates were detected in samples from both broiler (n = 11) and layer (n = 2) hatcheries, from which three and five harbored blaCTX-M-1 and blaCTX-M-14, respectively. Additionally, tetA (n = 7), sul1 (n = 5), aac(6´)-Ib-cr (n = 2), and int1 (n = 7) genes were detected. Isolates belonged to the clones ST10 (n = 1), ST617 (n = 1), ST405 (n = 3), ST69 (n = 4), ST224 (n = 3), and ST4494 (n = 1). Study findings indicate that even in the absence of any prior antibiotic administration, day-old chicks in western Algerian hatcheries carry MDR isolates capable of spreading across the national poultry sector, representing a significant public health concern.

Resuscitation-promoting factors (Rpfs) are proteins essential for reactivating microorganisms from the viable but non-culturable (VBNC) state and exhibit considerable diversity across bacterial species. Rhodococcus erythropolis KB1 is an efficient petroleum-degrading actinomycete with strong environmental adaptability. Its genome encodes a variety of Rpf proteins. In this study, we characterized these Rpfs through multiple sequence alignments, domain analysis, tertiary structure modeling, and biological activity assays. Each protein harbors a conserved Rpf domain of ∼70 amino acids and auxiliary domains such as DUF348, G5, and LysM. Reverse Transcription Quantitative Polymerase Chain (RT-qPCR) analysis revealed that rpf1 was highly expressed during the logarithmic phase in R. erythropolis KB1, while rpf4 and rpf5 exhibited lower expression levels. All recombinant proteins, expressed and purified from Escherichia coli, demonstrated muralytic activity. Notably, the muralytic activity was independent of auxiliary domain complexity, with Rpf5 showing the highest activity (18.24 ± 1.06 U nmol-1). Furthermore, all Rpfs promoted the growth and resuscitation of VBNC R. erythropolis KB1 cells, with Rpf5 providing the greatest effect. The efficiencies of the recombinant proteins in promoting bacterial growth and VBNC cell resuscitation varied significantly, and these variations were strongly correlated with their muralytic activities.

Gastrointestinal tract of humans provides a niche to thousands of microbes, referred as gut microbiota (GM). GM establishes an intricate relationship with other organs via gut-organ axis, and modulates host health. The structure and functioning of these gut microbes can be influenced by the type of external exposome an individual experiences. Depending upon GM perturbations and host genotype, this can result in variable health implications. On the other hand, the huge arsenal of enzymes possessed by GM can chemically alter the xenobiotic structure. Its consequences can be numerous, including formation of harmful metabolites that cause organ damage, reversal of host detoxification pathways, or favourable health effects. Additionally, GM-mediated bio-transformation of pharmaceuticals can alter their pharmacokinetics and pharmacodynamics, potentially yielding variable drug responses, resulting into prolonged or ineffective treatments. To address this bi-facial relationship and the pivotal role of GM, this review incorporates recent in vitro, in vivo, and multiomics studies. It also suggests the need of machine learning approaches to decode the complex host-microbiota-xenobiotics interactions. These knowledge will aid in comprehending recent rise in chronic lifestyle-diseases which poses a huge burden on the health sector, and can also be a learning curve in making formulations and therapies for personalized treatment.

The overuse of antibiotics has accelerated the emergence of antibiotic-resistant bacteria, necessitating alternative treatment options. Micromonospora spp., known for producing bioactive metabolites, is a promising source of novel antimicrobials. This study evaluated the antimicrobial potential of metabolic ethyl-acetate extracts from three Micromonospora strains against multidrug-resistant (MDR) Gram-negative clinical isolates of enteric origin. Using the Kirby-Bauer modified disc diffusion method, following Clinical and Laboratory Standards Institute guidelines, the extract from Micromonospora strain 65SH exhibited the most potent activity, with minimum inhibitory concentrations of 25 µg/ml against Enterobacter aerogenes and 12.5 µg/ml against Escherichia coli. 16S rRNA gene sequencing identified the strain as closely related to Micromonospora fluminis (99.6% similarity). Further analysis using LC-QTOF-MS/MS non-targeted metabolomics identified six bioactive compounds-melibiose, oligomycin A, queuine, heptelidic acid, diethyl phthalate, and 2'-deoxyguanosine-linked to the inhibition of bacterial enzymes essential for proliferation. Molecular modeling suggested that these compounds disrupt E. coli ATP synthase and inhibit ATP-dependent bacterial topoisomerases. This study integrates metabolomics, molecular docking, and genomics, offering robust mechanistic insights into ATP synthase inhibition. Future research will include fecal isolate testing, detailed structural elucidation using nuclear magnetic resonance (NMR) spectroscopy, and experimental validation to explore the therapeutic potential of Micromonospora-derived compounds.