Indian Journal of Microbiology最新文献

Salmonella, a foodborne pathogen, poses a significant threat to public health. This concern is exacerbated by emerging antibiotic resistance. Bacteriophages and their endolysins are promising alternatives to antibiotics. Endolysins play a crucial role in bacterial lysis in the phage life cycle. Leveraging these proteins as antimicrobial agents may offer a potential solution for controlling pathogenic contamination in food. Structural and functional analysis of LysSM5 endolysin derived from vB_SenA_SM5, a Salmonella phage, was studied using computational tools. Functional annotation, physicochemical characteristics, and 3D structure of the LysSM5 were predicted. Validation and quality assessment were performed using various computational tools like Conserved Domain Search, ProtParam, SWISS-Model server, PROCHECK, Verify3D, and ERRAT server. The molecular weight of LysSM5 was 28.8 kDa, 264 amino acids, and an isoelectric point of 8.9. The sequence of LysSM5 comprised of an N-terminal peptidoglycan-binding domain (residues 9-64) and a C-terminal N-acetyl-β-D-muramidase domain (residues 90-263), interconnected by a linker sequence. Phylogenetic analysis using MEGA X revealed that LysSM5 shared similarities with endolysins from phages active against E. coli and various Salmonella serovars. This indicates that LysSM5 may have a broad spectrum of activity, making it a versatile candidate for combating a range of bacterial pathogens. The structure was predicted by using the SWISS-Model server, validated by Ramachandran plot analysis (91.8% residues in favored regions) and quality assessments (ERRAT score: 98.016, Verify3D: 95.44% residues with ≥ 0.1 score). These high-quality scores confirm that LysSM5's predicted structure is accurate and reliable for further analysis. Molecular docking showed a robust binding affinity of LysSM5 to peptidoglycan (- 13.9 kcal/mol), indicating its potential effectiveness in targeting and interacting with bacterial cell walls for antimicrobial applications. Molecular dynamics simulations were performed using the iMODS web server, indicating high stability of the LysSM5-peptidoglycan complex, with an eigenvalue of 8.873650e-05, suggesting that LysSM5 can effectively bind to and disrupt bacterial cell walls, making it a promising candidate for further development in antimicrobial applications.

Beginning with the centralization of young tea (Yt) to encourage low branch growth, subsequent light pruning (LP) and deep skiffing (DS) techniques are employed to promote branch spread, ensuring an ideal leaf area index and manageable plucking height. This study investigates the effects of LP and DS compared to Yt on soil biota, a previously unexplored topic. Soil samples from Yt, LP, and DS sites within the Rajgarh Tea Estate in Assam, India, were analyzed for standard parameters and metagenomic DNA using Illumina sequencing. While all samples exhibited a clay loam texture with minimal parameter variation, significant variations in soil phyla abundance were observed. Acidobacteria dominated across all samples, but linear discriminant analysis revealed distinct phyla compositions. At the genus level, Geobacter, Verticiella, and Glaciihabitans were most abundant in S11, S7, and S9 samples, respectively. However, the relative abundance of phyla in the soil samples from Yt, LP, and DS sites varies significantly. But the difference in bacterial community at genus level resolution was not significant at p value 0.05 level. These findings indicate that pruning and skiffing primarily impact on the relative abundance of soil phyla, not microbial diversity. Understanding the soil microbiota in relation to tea cultivation practices through metagenomics can pave the way for developing new microbial consortia for an integrated crop management system in tea cultivation.

Zinc oxide nanoparticles (ZnO-NPs) are recognized as highly promising materials with applications in diverse fields, from therapeutics to agriculture. Hence, the present study aimed to biosynthesize ZnO-NPs employing the endophytic Streptomyces sp. 4VPT5-9 isolated from the halophytic plant Salicornia brachiata and evaluate the biological activity against plant pathogen Fusarium oxysporum NCIM 1008 and human breast (MDA-MB-231) and colorectal cancer (HCT-116) cell lines. The cell-free supernatant of the strain 4VPT5-9 was used as a greener attempt for the biosynthesis of ZnO-NPs. Biosynthesized ZnO-NPs exhibited an absorption peak at 287 nm. The hexagonal crystalline structure of the biosynthesized ZnO-NPs was validated through X-ray diffraction studies. These biosynthesized ZnO-NPs exhibited an irregular shape and varied in size, ranging between 120 and 150 nm with d-spacing value 0.26 nm. Moreover, FI-IR analysis showed different absorption peaks confirming the presence of different functional groups and formation of biosynthesized ZnO-NPs. XPS analysis confirmed the presence of Zn(II)O at different varied bending energies. The antifungal assay revealed that biosynthesized ZnO-NPs showed a pronounced inhibitory zone (12 mm) and the least MIC value of 60 µg/mL against plant pathogen F. oxysporum NCIM 1008. Moreover, the biosynthesized ZnO-NPs showed significant anticancer activity against MDA-MB-231 human breast cancer and HCT-116 human colorectal cell lines in a dose- and time-dependent manner. From this study, it is evident that an eco-conscious approach could pave a novel path for biosynthesis of ZnO-NPs through a halophytic plant-associated actinomycetes.

Natural interaction among the endosymbiont microorganisms specifically fungi with plants have been noticed with a great utility. It has been observed that there is presence of fungal endophytes in most of the plant tested for isolation of endophytic association. Such fungi have received attention recently due to their capacity to produce several unique bioactive chemicals that were previously unknown to biological systems. These endophytes could be an important source of secondary metabolites that can be explored for discovery of novel compounds which can be used as medicine or growth enhancers of plants or animals. The secondary metabolites from endophytic fungi have been reported for their antimicrobial, antioxidant, anticancer, and antidiabetic activity and offer protection against pathogens and pests and improve plant survival during the stress. The current review article highlights the significance of biologically active substances obtained from fungal diverse endophytes associated with plants.

Unsaturated fatty acids serve a crucial role, enhancing the fluidity of microorganism membranes during fermentation which improves their nutrient assimilation besides contributing to the mouthfeel by influencing sensory aspects such as body, texture, and smoothness of wine. In the present study, three fermentation parameters i.e. °Brix, inoculum (Saccharomyces cerevisiae strain MK680910) concentration and oleic acid concentration were optimized by response surface methodology (RSM) to obtain maximum ethanol concentration. The fermentation of black grapes (hybrid H27) was carried out using S. cerevisiae MK680910 under the runs suggested by RSM to optimize the above mentioned three fermentation parameters. The solutions revealed that 17.6°Brix, 5.9% (v/v) inoculum (S. cerevisiae strain MK680910) concentration and 8.08 mg/L oleic acid concentration produces 9.413% (v/v) ethanol concentration with fermentation efficiency of 73.492% and 1.295 g/100 mL residual sugars. Validation of ethanolic fermentation led to 9.478% (v/v) ethanol concentration with fermentation efficiency of 73.540%; which shows that the model is well fitted. Microoxygenation (MOX) involves controlled exposing wine to limited amounts of oxygen during aging for the development of favorable attributes thus enhancing the overall quality of the wine in terms of stabilizing colour, enriching aroma profiles, and adding layers of complexity to the finished product. In the present study, total phenols were increased from 217.5 mg/100 mL of control to 297.5 mg/100 ml of 0.025 LPM incremental dose over three months of MOX treatment. The highest sensory score of 8.05 ± 0.14 was obtained for 0.025 LPM incremental treatment. Volatile profiling of wines through Gas chromatography mass spectrometry reported the presence of 5 more volatile sensory components with the use of 0.025 LPM incremental dose of red wine microoxygenation treatment besides glycerine, alcohols and organic acids found in control.

Supplementary information: The online version supplementary material available at 10.1007/s12088-024-01357-9.

[This corrects the article DOI: 10.1007/s12088-024-01306-6.].

Bacterial infections have become a global public health problem in recent decades, mainly due to infections caused by Gram-negative bacteria with antibiotic resistance profiles, which were responsible for over 3 million deaths in 2019. Polymyxin B (PMB) and polymyxin E (PME or colistin) are cyclic cationic polypeptide antimicrobials that have re-emerged in clinical practice due to the high rates of morbidity and mortality in infections caused by Gram-negative multidrug-resistant or extensively drug-resistant. Although polymyxins have antibacterial potential, they still have low stability and adverse effects, thus limiting their administration. To overcome these limitations, the use of controlled release systems such as liposomes, nanoparticles, and nanotubes is a viable strategy. Therefore, the objective of this review article is to present recent studies that address the antibacterial activity of PMB and PME encapsulated in nanocarriers against Gram-negative bacteria and to highlight the advantages of these nanocarriers and how they can overcome polymyxin limitations and bacterial resistance to polymyxin, as well as increasing drugs efficacy and safety. The preparation of this narrative review was based on the following steps: identification of the theme, establishment of inclusion and exclusion criteria, analysis and selection of articles, interpretation of data and results, and the writing of this article. Nanoparticles, electrostatic nanocomplexes, nanostructured lipid carriers, liposomes, and halloysite nanotubes can enhance bacterial activity from both PMB and PME, reducing minimum inhibitory concentration, inhibiting and eradicating biofilm, as well as prolonging polymyxins activity, reducing toxicity, and improving bioavailability. The strategy of encapsulation of polymyxin in nanocarriers has demonstrated a significant enhancement in polymyxin activity and pharmacokinetics, resulting in elevated therapeutic efficacy. Therefore, nanocarriers containing polymyxin emerge as a promising and innovative strategy to address this global challenge in public health.

In this study, high-throughput sequencing (HTS) was used to demonstrate the microbial community diversity and succession of the casing soil during Oudemansiella raphanipes cultivation. The abundance and diversity of bacteria and fungi were the highest in the original sample of vegetable soil, and then decreased in casing soil, but they increased at the end of the mushroom formation. As the mushroom formation progressed, the abundance of some bacteria such as Massilia, Sphingomonas, and Cupriavidus increased, and they are often found in heavy metal contaminated soils. In terms of fungi, the dominant fungi in the vegetable soil and at the end of the mushroom formation stage were Thermoascus, and the abundance of some plant and animal pathogens increased in the first and second mushroom formation stages, such as Candida, Aspergillus, Trichoderma, and Chaetomium. The above results showed a decrease in the number of microbial species and an increase of harmful microorganisms, which might inhibit the growth of mushroom. Furthermore, we disinfected and sterilized the casing soil to investigate the effect of different treatments of casing soil on the growth and quality of Oudemansiella raphanipes. Results showed that the casing soil was beneficial for the cultivation of Oudemansiella raphanipes, but microorganisms in the casing soil might not be necessary for the growth of mushroom. Sterilization treatment of the casing soil could improve yield and quality more than conventional disinfection treatment. In future studies, different matrix materials can be explored to replace soil cover to achieve soilless cultivation which is more efficient and hygienic.

Preterm mother-neonate dyads are often exposed to broad-spectrum antibiotics. We studied preterm dyads for multidrug-resistant potentially pathogenic bacteria (MDR-PPB).To determine colonisation rates of MDR-PPB in mother's milk and neonatal oral and rectal swabs and identify genetically identical strains across the 3 samples. We enrolled lactating mother-neonate dyads, and cultured milk and neonatal oral, rectal swabs under aseptic conditions. We identified bacteria using MALDI-TOF, focusing on a panel of 13 neonatal pathogens of interest. Sensitivity was tested using Vitek2. If the milk, oral, and rectal swab samples from a mother-neonate dyad showed the same species and antibiogram, multi-locus sequence type (MLST) was performed. Of 130 dyads screened, we enrolled 100. 14 milk samples (from 14 mothers) had pathogens of interest, including 9 (64%) MDR bacteria. 82 isolates were grown from the oral swabs (77 neonates), of which 58 (70.7%) were MDR. 130 isolates were grown from the rectal swabs (96 neonates), of which 104 (80%) were MDR. Two mother-neonate dyads had MDR Escherichia coli and Klebsiella pneumoniae species cultured from all three samples with identical antibiograms. On MLST, DNA sequencing analysis of the PCR products showed no variation at all 7 loci of E. coli (Sequence Type-405), whereas, with K. pneumoniae, variations were observed in 4 loci (infB, mdh, phoE,rpoB). An alarming proportion of preterm mother's milk, oral swab and rectal swabs have MDR-PPB. MLST suggested that a pathogenic strain of E. coli was transmitted from mother's milk to the neonate's gut.

Polycyclic aromatic hydrocarbons (PAHs) are biodegraded primarily by bacterial activities from polluted environments. From an oily sludge disposals site an Achromobacter xylosoxidans bacterium (designated as strain IITR150) was isolated with capability to grow and degrade multiple PAHs. Strain IITR150 was found to utilize naphthalene, phenanthrene, anthracene, benz(a)pyrene, benz(a)anthracene, and fluoranthene as the carbon source for its growth. Initially, the bacterium was screened based on its ability to turn indole into indigo and formed metabolites of the indole pathway such as indoxyl, isatin and indirubin. A 1014 bp gene encoding for a naphthalene 1,2-dioxygenase was found to initiate the biodegradation of naphthalene to have 42.85% homology to reported genes. Whole genome sequencing of A. xylosoxidans IITR150 had showed 5.9 Mb genome size containing 5625 predicted CDS. Among 5625 predicted CDS, cytochrome P450, catechol 2,3-dioxygenase (catE), naphthalene 1,2-dioxygenase system ferredoxin-NAD(P) ( +) reductase component (nahA), naphthalene 1,2-dioxygenase system, and ferredoxin components (nahB) genes were identified that indicated the metabolic potential of the bacterium for utilization of different aromatic compounds. Besides identification of PAHs degrading genes along with genomic insights suggests the robustness of the bacteria. Also, a cytochrome P450 (cytP450) enzymes that play a pivotal role in the detoxification of xenobiotics was found in IITR150, when aligned with three other cytP450 showed over 99.0% similarity at amino acid level. In conclusion, experimental and whole genome analysis provide capabilities of strain IITR150 involved in PAHs metabolism which could be useful in biodegradation of mixed PAHs contaminated soils.

Supplementary information: The online version contains supplementary material available at 10.1007/s12088-024-01407-2.