JournalTOCs

Archives of Microbiology
Journal Prestige (SJR): 0.644

Citation Impact (citeScore): 2
Number of Followers: 9

Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1432-072X - ISSN (Online) 0302-8933
Published by Springer-Verlag

[2468 journals]

Folate from probiotic bacteria and its therapeutic applications
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  Abstract: Folate, an essential water soluble vitamin B9 that cannot be synthesized naturally by the bodily function. Dietary sources or probiotic-folates are the two biological modes for acquiring the target vitamin which aids DNA synthesis and repair. Probiotics are known for their divergent health benefits and have garnered significant interest. Particularly in microbial strains that produce folate offers a promising way to enhance the level of folate. Notably, folate-producing probiotic strain includes Lactiplantibacillus, Lactococcus, Bifidobacterium, and Streptococcus. As an emerging source of health benefits, folate producing probiotics helps in improving the gut microbiota for overall well-being of human body. On the other side, chemically synthesized folic acid were not highly advantageous as they lacks absorption, conversion and excretion. Hence, usage of microbial-folate are safer as it can easily undergo absorption and reduces severe side effects. The present review mainly focus on folate one-carbon metabolism, its significance in human health, folate deficiency and malabsorption, adverse effects and folate synthesis from probiotic bacterial strains, and also toxicological impacts. In particular, the beneficiary role of these probiotic strains were found to be associated with therapeutic applications in several diseases such as autoimmune disorder, metabolic disorders, and cardiovascular diseases (CVDs), wound healing, drug delivery and cancer.
  PubDate: 2025-04-18
hsa-miR-330-5p regulates serine palmitoyltransferase long chain base
subunit 1 and augments host protective immune response against Leishmania
donovani infection
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  Abstract: Leishmaniasis, caused by the protozoan parasites of the genus Leishmania, poses a significant global health challenge, particularly in the resource-limited regions where it causes high mortality. Regardless in the progress of treatment strategies, the emergence of drug resistance and limited efficacy requires the search of novel therapy and therapeutic targets. MicroRNAs, the crucial post-transcriptional regulators of gene expression, play critical roles in host–pathogen interactions. Here, we screened the miRNAs dysregulated during Leishmania donovani infection through literature search. hsa-miR-330-5p, one of the miRNAs which through human KEGG 2021 and Human Cyc 2016 analysis was found to be involved in multiple pathways including sphingolipid signaling pathway. Sphingolipids are important class of lipids involved in different cellular processes and therefore are the targets of many pathogens including Leishmania. hsa-miR-330-5p was found downregulated after 24 h of Leishmania donovani infection in THP-1 derived human macrophages. Target prediction of sphingolipid biosynthetic genes through in silico prediction tools showed 3/ UTR of serine palmitoyltransferase long chain base subunit 1 to be a target of hsa-miR-330-5p. The in silico target prediction of hsa-miR-330-5p was validated by cloning the 3/ UTR target sequence of gene, transfecting and performing luciferase assay in HEK 293 T cell line. Transfection of mimic of hsa-miR-330-5p reduced the luciferase activity which validated the in silico target prediction. Further, mimic of hsa-miR-330-5p inhibited the expression of the target gene, serine palmitoyltransferase long chain base subunit 1 and augmented the expression of pro-inflammatory cytokines in L. donovani infected THP-1 derived macrophages. Mimic of hsa-miR-330-5p also led to a significant reduction in the intracellular parasite burden in both THP-1 derived as well as primary human macrophages. This study has not only identified the sphingolipid biosynthesis regulatory miRNA but will also help in the development of novel and effective treatment strategy against leishmaniasis in future.
  PubDate: 2025-04-16
Statistical factorial design for optimum reduction of tellurite and
production of tellurium nanostructure by a novel strain Phytobacter
diazotrophicus Te1
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  Abstract: A tellurite-reducing isolate (Te1) was recovered from a soil sample receiving industrial effluents from Ismailia Canal, Egypt. The isolate exhibited dark black colonies when grown on solid medium containing potassium tellurite, which indicated the reduction of tellurite to black tellurium. The isolate was identified using 16S rRNA gene sequencing and was submitted to GenBank as Phytobacter diazotrophicus strain Te1 (PP724698). The tellurite reduction percentage was 96.5% ± 0.354%. Moreover, energy-dispersive X-ray (EDX) analysis confirmed the presence of tellurium nanostructure, with a 3.7 keV absorption peak along with phosphorus, sulfur, and oxygen, revealing a complex biogenic nature. Fourier-transform infrared (FTIR) spectroscopy identified distinct absorption peaks within the 400–4000 cm−1 range, corresponding to various vibrational modes of chemical bonds, including those of lipids, proteins, polysaccharides, and free radicals. X-ray diffraction (XRD) analysis highlighted the nanoscale crystalline structure of the material, with broad peaks confirming limited crystallite size and structural disorder, and revealed tellurium peaks on a hexagonal phase at 2-theta values of 27.36°, 38.19° and 40.20°. According to the results of the response optimizer and the subsequent validation experiments, complete reduction of tellurium was achieved at a medium pH of 6.8, incubation temperature of 33.5 °C, tellurite concentration of 1375 μM, and agitation speed of 110 rpm for 96 h. Black Te nanostructure was visible intracellularly and extracellularly upon examination using the transmission electron microscope. To the best of the authors’ knowledge, this is the first report of tellurite reduction by Phytobacter diazotrophicus.
  PubDate: 2025-04-15
Genome-wide identification and expression analysis of epigenetic regulator
gene families in the medicinal mushroom Ganoderma lucidum
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  Abstract: Epigenetic regulator (ER) genes, crucial for fungal growth and development, remain largely unexplored in Ganoderma lucidum, a medicinal mushroom valued for its bioactive compounds. This study identified 81 ER genes in G. lucidum, distributed across 12 chromosomes and classified into six families: 3 chromatin remodelers, 4 DNA methyltransferases, 7 histone acetyltransferases, 22 histone deacetylases, 23 histone methyltransferases, and 22 histone demethyltransferases. Comparative and phylogenetic analyses with other species revealed conserved orthologs and species-specific clusters. Gene duplication analysis suggested whole-genome duplication expanded ER gene families, primarily histone demethyltransferases under purifying selection. Additionally, gene structure, motif, and domain analyses revealed family-specific intron/exon organization and conserved domains. Transcriptome profiling across four developmental stages (mycelium, primordia, young and mature fruiting body) revealed dynamic stage-specific expression patterns, suggesting their developmental significance. The result of qRT-PCR validated the expression patterns for 18 ER genes, laying foundation for future research exploring epigenetic regulation in fungal development and bioactive compound production.
  PubDate: 2025-04-15
Environmental fate of antibiotic resistance genes in livestock farming
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  Abstract: As emerging environmental pollutants, antibiotic resistance genes (ARGs) are prevalent in livestock farms and their surrounding environments. Although existing studies have focused on ARGs in specific environmental media, comprehensive research on ARGs within farming environments and their adjacent areas remains scarce. This review explores the sources, pollution status, and transmission pathways of ARGs from farms to the surrounding environment. Drawing on the “One Health” concept, it also discusses the potential risks of ARGs transmission from animals to human pathogens and the resulting impact on human health. Our findings suggest that the emergence of ARGs in livestock farming environments primarily results from intrinsic resistance and genetic mutations, while their spread is largely driven by horizontal gene transfer. The distribution of ARGs varies according to the type of resistance genes, seasonal changes, and the medium in which they are present. ARGs are disseminated into the surrounding environment via pathways such as manure application, wastewater discharge, and aerosol diffusion. They may be absorbed by humans, accumulating in the intestinal microbiota and subsequently affecting human health. The spread of ARGs is influenced by the interplay of microbial communities, antibiotics, heavy metals, emerging pollutants, and environmental factors. Additionally, we have outlined three control strategies: reducing the emergence of ARGs at the source, controlling their spread, and minimizing human exposure. This article provides a theoretical framework and scientific guidance for understanding the cross-media migration of microbial resistance in livestock farming environments.
  PubDate: 2025-04-11
Staphylococcus hominis as a source of antimicrobial peptides:
identification of a new peptide with potential antimicrobial properties
using in silico approach
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  Abstract: The rapid progression of antimicrobial resistance, fueled by the excessive use of antibiotics, has become a major public health concern. Among the pathogens contributing to this crisis, Staphylococcus aureus stands out as a significant therapeutic challenge, especially with the rise of resistant strains like Methicillin-Resistant S. aureus (MRSA). In this context, antimicrobial peptides (AMPs) emerge as a promising alternative, thanks to their unique mechanisms of action. Exploring the genomes of species such as Staphylococcus hominis, known for producing AMPs effective against S. aureus, offers promising opportunities for discovering novel therapeutic agents. In this study, Average Nucleotide Identity (ANI) combined with phylogenetic analysis identified a potential emerging subspecies of Staphylococcus hominis. The core genome analysis led to the identification of a potential antimicrobial peptide. The peptide model simulated with the S. aureus membrane model in molecular dynamics revealed that it interacts primarily with the lipids head groups, leading to an overall rigidification of the bacterial membrane.
  PubDate: 2025-04-11
Exploring the potential of bacterial-derived EVs for targeted enzyme
replacement therapy: mechanisms, applications, and future directions
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  Abstract: Extracellular vesicles (EVs) are membrane-bound vesicles produced by cells which promote intercellular communication by delivering different contents such as DNA, RNA, and proteins. These vesicles, nano-sized and released into the extracellular space, are present everywhere under both normal and pathological conditions. Probiotic-derived EVs can serve as nanocarriers for therapeutic cargo, particularly in enzyme replacement therapy (ERT). Traditional ERT for lysosomal storage diseases (LSDs) faces significant challenges, including the inability of enzymes to cross the blood–brain barrier (BBB) and their susceptibility to degradation. Studies show EVs can transport enzyme cargoes across the BBB, accurately delivering them to tissues affected by LSDs. Probiotic EVs also possess immunomodulatory properties, providing therapeutic benefits in inflammatory conditions. However, their potential for delivering deficient enzymes in LSDs remains unclear. This review discusses using probiotic EVs in ERT for targeted enzyme delivery to treat LSDs more efficiently than other exosomes. This novel strategy minimizes off-target delivery and enhances immunomodulatory effects, making it more advantageous than live probiotic bacteria. Probiotic EVs show promise for therapeutic approaches, especially in treating LSDs and inflammatory diseases, by modulating immune responses and delivering enzymes across biological barriers like the BBB. Future research should optimize production, engineer targeted therapies, and confirm safety and efficacy through clinical trials. Expanding studies to include diverse probiotic strains could uncover new therapeutic applications, enhancing their versatility and effectiveness.
  PubDate: 2025-04-10
Applications of endophytic fungi in plant disease control
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  Abstract: Diseases caused by pathogenic microorganisms (bacteria, fungi, and viruses) have resulted in the quality and yield of crops, which has seriously affected the development of the agricultural economy. The prolonged use of chemical fungicides for prevention and control can lead to environmental pollution, hindering the sustainable development of safe and eco-friendly agriculture while also promoting the resistance of pathogenic microorganisms. Nevertheless, non–pathogenic endophytic fungi that form symbiotic relationships with plants still exhibit significant antagonistic effects on pathogenic microorganisms, even in small concentrations. These fungi pose no threat to human health and are highly beneficial to the ecological environment, making them an ideal alternative to chemical fungicides. They are increasingly being recognized and have been subjected to comprehensive research. Based on this, this article summarizes the types of endophytic fungi with biocontrol effects in recent years. It focuses on elucidating the mechanisms of their biocontrol from physiological and molecular perspectives. In addition, the application and development challenges of biocontrol agents (BCAs) derived from these fungi are also discussed, including difficulties in elucidating their mechanisms of action during research and development, challenges in strain selection and improvement, difficulties in controlling environmental adaptability, and stringent storage conditions. The aim is to develop more effective endophytic fungi as emerging biocontrol resources for agricultural production.
  PubDate: 2025-04-09
Harnessing killer yeast system: from molecular insight to real world
biocontrol solution
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  Abstract: The biocontrol mechanisms of yeasts are gaining global attention as a vital response to the rising threat of antimicrobial resistance in emerging pathogens. With their diverse genetic traits, yeasts present potent antagonistic capabilities that have extensive applications across various sectors. This review examines the fundamental mechanisms and molecular bases of yeast antagonism, emphasizing innovative screening techniques for identifying effective strains. Key molecular methods, including gene identification, sequence analysis, and expression studies, reveal insights into their modes of action, such as nutrient competition, mycocin production, and volatile organic compound release. While the potential of antagonistic yeasts spans crop protection, food safety, and disease prevention, their commercial availability remains limited. To foster adoption, there is an urgent need for advanced screening methods and deeper molecular understanding. Future research should prioritize the optimization and commercialization of yeast-based biocontrol products, effectively bridging the gap between scientific discovery and practical application in combating harmful pathogens. Graphical abstract
  PubDate: 2025-04-08
Computational prediction of Homo sapiens–Candida albicans
protein–protein interactions reveal key virulence factors using dual
RNA-Seq data analysis
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  Abstract: A prevalent pathobiont, Candida albicans, accounts for approximately 70% of fungal infections worldwide owing to its virulence traits that culminate in devastating fatalities within healthcare facilities. Protein–protein interactions (PPIs) between Homo sapiens and C. albicans play a pivotal role in infection and disease progression. Additionally, scarcity of information on H. sapiens–C. albicans protein–protein interactions makes it difficult to understand the molecular mechanisms underlying infection and host immune responses. Investigating these PPIs can provide crucial insights into host–pathogen relationships and facilitate the development of novel therapeutic interventions. To address this challenge, we utilized computational techniques based on homology and domain to project 56,515 human-fungal pathogen protein–protein interactions (HF-PPIs) involving 6830 human and 486 C. albicans proteins. We have identified 16 key virulence factors of C. albicans, including SOD1, ERG10, GFA1, and VPS4, as potential therapeutic targets. As evidenced by dual RNA-Seq data acquired at various stages of infection such as 15, 30, 60, 120, and 240 min, these fungal genes interact with down-regulated human immunomodulatory genes specifically, ADRM1, DAXX, RYBP, SGTA, and SRGN. In addition to their intrinsically disordered regions, these human genes are particularly susceptible to fungal manipulation. Through the identification of experimentally validated virulence factors and their interaction partners, this investigation constructs HF-PPI between H. sapiens and C. albicans. Our knowledge of human-fungal pathogen protein–protein interactions will be improved by integrating computational and experimental data in order to facilitate the development of efficient fungal infection prevention and treatment protocols.
  PubDate: 2025-04-06
Deciphering antibiotic resistance, quorum sensing, and biofilm forming
genes of Micrococcus luteus from hemodialysis tunneled cuffed catheter
tips of renal failure patients
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  Abstract: Catheter-related bloodstream infections create a significant challenge in healthcare system, often complicated by antibiotic resistance and biofilm formation of multi-drug resistance and virulent bacterial pathogens. This study focused on biofilm-forming efficiency, and underlying genetic mechanisms in Micrococcus luteus HL_Chru_C3, isolated from a hemodialysis catheter tip. The isolate exhibited resistance to multiple antibiotic classes, including beta-lactams and glycopeptides. Biofilm assays revealed that M. luteus HL_Chru_C3 formed optimum biofilms at high concentration of carbohydrates (500 mM), and pH 5 but there was no significant role of mineral salts. Whole-genome sequencing and bioinformatic analysis using CARD, KAAS, and KEGG databases identified genes associated with antibiotic resistance (ftsI, pbp1a/2, vanY, alr, ddl, murF, mraY, and murG), quorum sensing (genes from the opp family, sec, cylA, ccfA, phnA, phnB, phzC, rpfB, clp, and toxE), and biofilm formation (phnA, phnB, cyaB, vfr, vps, glgC, wecB, wecC, and cysE). The predicted mechanisms of action for these genes, based on homology to other organisms, suggest complex interactions contributing to the observed phenotypes. This study provides an insight into the genetic basis of antibiotic resistance and biofilm formation in M. luteus HL_Chru_C3 isolated from a hemodialysis catheter, highlighting the need for effective infection control strategies to combat CRBSIs.
  PubDate: 2025-04-05
Development and application of an interbacterial DNA delivery system based
on M13 bacteriophage
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  Abstract: With the rapid development in synthetic biology, bacterial therapy has been widely applied in disease diagnosis and treatment. A key step in regulating the execution of specific instructions by engineered bacteria in vivo involves the transfer of information between bacteria. Currently, small molecule compounds and proteins are commonly used as carriers for inter-bacterial information transfer. However, DNA, as an information carrier, boasts higher information capacity and ease of editing. Based on this, we have developed an engineered bacterial DNA delivery system using M13 bacteriophage to study the cooperative response mechanisms between bacteria. Firstly, we leveraged the ability of engineered bacteria to secrete phagemid DNA into the extracellular environment via bacteriophages and to acquire phagemid DNA through infection by extracellular phagemids, thereby developing a dynamic phagemid replenishment system. This system can maintain the stability of phagemid DNA in environments lacking antibiotic selection pressure, constructing a stable DNA delivery platform for phagemid output. Subsequently, using this engineered bacterial DNA delivery system, we modularized gene circuits and placed them in two different engineered bacteria. Through DNA transfer, we achieved a cooperative response to signals between the two bacteria, laying the groundwork for multi-bacterial joint regulation. Our research not only provides an effective tool for information transfer in engineered bacteria but also offers a novel approach for multi-bacterial therapy.
  PubDate: 2025-04-05
Determining the effect of a new truncated CecropinA-Magenin2 (CE-MA)
hybrid peptide on the expression of multidrug-resistant (MDR)
Mycobacterium tuberculosis efflux genes
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  Abstract: A significant issue in treating bacterial infections is multidrug resistance (MDR) microbes. Drug efflux pumps that reduce cellular drug accumulation are frequently linked to drug resistance. In this study, we set out to determine the effects of CE-MA truncated peptide derivatives against MDR Mycobacterium tuberculosis. Following the assessment of the minimum inhibitory concentrations (MICs) of these peptides against MDR Mycobacterium tuberculosis, a Real-Time PCR was used to examine the expression of six drug efflux pump genes. Next, an MTT assay was performed to test the cytotoxicity of peptides against the A549 cell line. The outcomes demonstrated that CE-MA significantly upregulated gene expression of mmr, and Rv0876c (⩾ 4-fold) than untreated bacteria. Also, under CMt2 stress, significant overexpression of Rv0876c and drrA was seen. However, the results show that upregulation in CMt2-treated bacteria in comparison CE-MA treated bacteria is significantly less for genes tap (P
  PubDate: 2025-04-03
S alinicoccus bachuensis sp. nov., a novel halophilic bacterium, isolated
from rhizosphere soil surrounding Tamarix chinensis Lour. plants in Bachu
County, Xinjiang, China
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  Abstract: The strain Bachu38T was isolated from the rhizosphere soil of Tamarix chinensis Lour. plants in Bachu County, Xinjiang, China. This strain exhibited growth under a wide range of conditions, with temperature tolerance from 8 to 45°C (optimal at 28°C), pH adaptability between 7.0 and 10.0 (optimal range 8.0–9.0), and NaCl concentration tolerance spanning 2–20% (w/v), with optimal growth observed at 8% NaCl concentration. The cells displayed a spherical morphology and were Gram-positive, non-motile, and devoid of flagella. Biochemical characterization demonstrated positive reactions for both oxidase and catalase activities. Phylogenetic analysis of the 16S rRNA gene sequences revealed that strain Bachu38T forms an independent branch within the genus Salinicoccus, sharing the highest sequence similarity with S. roseus DSM 5351 T (98.43%) and S. amylolyticus JC304T (98.29%). The whole genome comprised 2.62 Mb, with a G + C content of 49.5%. When compared with the related strains, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were 71.34–90.99% and 17.20–42.40%, respectively, which were below the suggested species identification threshold (ANI:
  PubDate: 2025-04-03
SirA, CsrBC and HilD form in vivo a regulatory cascade that controls the
SP1-1 and SPI-2 gene expression when Salmonella Typhimurium is in the
intestinal lumen and are required for cecal colonization and liver
dissemination in the avian model
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  Abstract: When Salmonella Typhimurium grows in LB in vitro, BarA/SirA system induces the expression of CsrB/C, that sequester the regulator CsrA, thus derepressing HilD regulator. HilD activated induces HilA and SsrB expression, central regulators of SPI-1 and SPI-2, respectively. We analyze the in vivo contribution of these genes in 1-day- and 1-week-old chickens infected with a Wild Type strain of S. Typhimurium and the ΔsirA, ΔcsrB/C and ΔhilD mutants. CFUs determination in liver and cecum showed that the mutants colonized both organs in lower amounts compared with WT strain in both chicken models and they were affected in the ability to produce histological injuries in these organs. We analyzed whether these genes operate in cascade in vivo and prior to intestinal invasion, by analyzing hilA, ssrAB, hilD, csrB and sirA expression in the cecal contents of chickens inoculated with Wild Type and mutants 120 min after inoculation. Expression of hilA and ssrB, but not csrB and sirA, was decreased in ΔhilD strain. Expression of hilD, hilA and ssrB, but not sirA, was decreased in samples of ΔcsrB/C. In SirA absence, expression of all genes was decreased. Our findings demonstrate that SirA, CsrB/C and HilD conform a regulatory cascade in vivo, when Salmonella is in intestinal lumen and this cascade controls the expression of HilA and SsrB prior to intestinal invasion. We also demonstrate that these genes are necessary for the production of lesions during S. Typhimurium infection in chickens.
  PubDate: 2025-04-02
Unveiling multiple copies of MlaC highlights its multifaceted nature
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  Abstract: The maintenance of the lipid asymmetry (Mla) system plays a critical role in facilitating the transport of phospholipids between the inner and outer membranes of the Gram-negative bacteria. In E. coli, the system consists of six proteins: MlaA-OmpF/C complex (outer membrane), MlaC (periplasm), and MlaFEDB complex (inner membrane). Despite extensive research on the core proteins (MlaFED) of the Mla system, the occurrence of Mla components like MlaA, MlaB, and MlaC in diderm remains uncertain. Therefore, this gap presents a significant opportunity for further investigation, particularly regarding MlaC, which serves as the sole mobile component of the Mla system. This has led to the identification of multiple copies of MlaC in 63 distinct genera of Proteobacteria and related phyla. Interestingly, amongst these genera, the genetic arrangements of the mla operon were observed to be varying and, thus, were further categorized into four distinct groups. The variations among the genetic organization of the mla operons suggest their evolution through various processes, such as duplications, losses, rearrangements, and fusions. Further, the results of this study highlight the MlaC’s substrate promiscuity, illuminating new avenues for the Mla system.
  PubDate: 2025-04-02
Newly developed antibiotics against multidrug-resistant and
carbapenem-resistant Gram-negative bacteria: action and resistance
mechanisms
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  Abstract: Antimicrobial resistance stands as one of the most urgent global health concerns in the twenty-first century, with projections suggesting that deaths related to drug-resistant infections could escalate to 10 million by 2050 if proactive measures are not implemented. In intensive care settings, managing infections caused by multidrug-resistant (MDR) Gram-negative bacteria is particularly challenging, posing a significant threat to public health and contributing substantially to both morbidity and mortality. There are numerous studies on the antibiotics responsible for resistance in Gram-negative bacteria, but comprehensive research on resistance mechanisms against new antibiotics is rare. Considering the possibility that antibiotics may no longer be effective in combating diseases, it is crucial to comprehend the problem of emerging resistance to newly developed antibiotics and to implement preventive measures to curb the spread of resistance. Mutations in porins and efflux pumps play a crucial role in antibiotic resistance by altering drug permeability and active efflux. Porin modifications reduce the influx of antibiotics, whereas overexpression of efflux pumps, particularly those in the resistance-nodulation-cell division (RND) family, actively expels antibiotics from bacterial cells, significantly lowering intracellular drug concentrations and leading to treatment failure.This review examines the mechanisms of action, resistance profiles, and pharmacokinetic/pharmacodynamic characteristics of newly developed antibiotics designed to combat infections caused by MDR and carbapenem-resistant Gram-negative pathogens. The antibiotics discussed include ceftazidime-avibactam, imipenem-relebactam, ceftolozane-tazobactam, meropenem-vaborbactam, aztreonam-avibactam, delafloxacin, temocillin, plazomicin, cefiderocol, and eravacycline.
  PubDate: 2025-04-02
Genome mining reveals the biosynthetic potential of a novel Lysinibacillus
zambalensis sp. nov., isolated from a hyperalkaline spring
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  Abstract: A novel bacterium, designated as strain M3T, was isolated from a hyperalkaline spring in the Philippines and identified as a new species within the genus Lysinibacillus through 16 S rRNA gene sequence and genomic analyses. Although strain M3T shared a high 16 S rRNA gene sequence similarity (> 98.7%) with many Lysinibacillus species, the digital DNA-DNA hybridization and orthologous average nucleotide identity values between strain M3T and its closet relative, Lysinibacillus xylanilyticus DSM 23,493T, were 41.2% and 90.6%, respectively—both below the established threshold for prokaryotic species delineation. Genome mining of the 5.3 Mbp-draft genome of strain M3T revealed eight biosynthetic gene clusters, which shared little sequence similarity with characterized clusters, suggesting the potential for encoding novel specialized metabolites. The cells of strain M3T were Gram-stain-positive, aerobic, rod-shaped, non-motile, and capable of endospore formation. Optimum growth was observed at 30 °C, pH 8.0, and 0.5% (w/v) NaCl. The major respiratory quinone was menaquinone-7, and the predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and two unknown phospholipids. Its fatty acid profile showed an elevated level of iso-C15:0, and the peptidoglycan type was determined to be A4α (L-Lys–D-Asp). This study contributes to the growing database and understanding of the genus and aims to help drive future research on the bioactive potential of the genus. Lysinibacillus zambalensis sp. nov. is proposed with strain M3T as the type strain (= TISTR 10640T = BIOTECH 10973T).
  PubDate: 2025-04-02
Microbial enhanced oil recovery: process perspectives, challenges, and
advanced technologies for its efficient applications and feasibility
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  Abstract: The depletion of crude oil resources, coupled with increasing energy demands, underscores the urgency for innovative recovery strategies. Despite traditional oil recovery operations, a substantial portion of residual oil (~70%) persists within the intricate capillary networks of oil reservoirs’ pore spaces. Microbial Enhanced Oil Recovery (MEOR) is an ecofriendly and cost-effective tertiary oil recovery method that offers a sustainable approach by utilizing microorganisms and their metabolites to extract this residual oil from mature or depleted reservoirs. MEOR is an emerging process gaining global attention, with numerous research studies and field trials underway worldwide. This review explores microbial strategies for modifying reservoir rheological properties, underscores the significance of microbial physiology and diversity, and examines omics technologies for deciphering microbial mechanisms to enhance the efficiency of MEOR. Cutting-edge advancements, including genetically modified microbes, enzyme-based techniques, and nanotechnology, have been discussed as potential enhancers of MEOR efficiency. The economic feasibility and integration of MEOR with Carbon Capture and Utilization (CCUS) are also assessed, emphasizing its role amid declining conventional oil production. Further, the economic and application feasibility along with patents related to MEOR technologies is presented which underscores its commercial viability. By addressing challenges and proposing solutions, this review provides a comprehensive outlook on MEOR’s future, aiming to guide research and development for its successful application in sustainable oil recovery.
  PubDate: 2025-04-01
Cra-controlled antisense RNA-downregulation of isocitrate dehydrogenase in
Escherichia coli
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  Abstract: Catabolite repressor activator (Cra) protein (formerly called FruR) found in E. coli is known to regulate the expression of many genes positively and negatively in response to the intracellular levels of fructose-1-phosphate (F-1-P) and fructose-1,6-bisphopahate (F-1,6-bisP). In this paper, we report synthesis and characterization of a conditionally expressed antisense RNA corresponding to 101 bp of isocitrate dehydrogenase (icd) gene (as-icd) under Cra (FruR) responsive promoter fruB (PfruB as-icd construct denoted as pVS2K3) in E. coli K-12 derivative (DH5α) and E. coli B derivative (BL21) strains. Previous studies have shown that ICD mutants accumulated citrate intracellularly but failed to grow on glucose in absence of glutamate. Hence, a conditional downregulation of icd gene could be helpful in overcoming this lethality and also aid in understanding the flux towards citrate accumulation. Effect of pVS2K3 construct was monitored in E. coli DH5α and E. coli BL21 during growth on carbon sources wherein the fruB promoter is active (glucose) or repressed (glycerol). A 3-to 4-fold decrease in ICDH activity was observed in E. coli DH5α expressing pVS2K3 on glucose but no change in ICDH activity was observed in E. coli BL21 expressing pVS2K3 on glucose. This alteration could be attributed to the anomalous Cra regulation seen in E. coli B strain which could be a crucial factor while choosing PfruB promoter for expression studies.
  PubDate: 2025-04-01

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