Progress In Microbes & Molecular Biology

Phylogenomics, antimicrobial resistance, and mobile genetic elements in clinical Clostridioides difficile isolates from Hong Kong, China

2026-08-07T16:58:19+08:00

Whole-genome sequencing enables high-resolution characterisation of the evolutionary and accessory-genome diversity of Clostridioides difficile beyond conventional sequence typing. We analysed 118 clinical C. difficile genomes from Hong Kong using recombination-filtered phylogenomics, pangenome analysis, antimicrobial-resistance and virulence screening, mobile-element context analysis and functional annotation. The population comprised 24 sequence types and formed distinct phylogenetic clusters that were broadly consistent with multilocus sequence typing assignments. Pangenome analysis identified 9,140 gene clusters and supported an open pangenome structure, indicating ongoing gene acquisition and loss within the population. Accessory-genome divergence increased with core-genome SNP distance (Spearman's ρ = 0.437, p < 1 × 10^-5), although some closely related isolates retained substantial differences in gene content, suggesting recent accessory-genome turnover. Antimicrobial resistance determinants showed stronger associations with mobile genetic elements (MGE) than with virulence-associated loci. In particular, erm(B), AAC/APH-family genes and tet(M) were frequently detected and commonly linked to insertion-sequence- or transposon-associated contexts, whereas major toxin loci showed limited evidence of local mobility. Functional annotation revealed broadly conserved functional profiles dominated by transcription-, metabolism-, and signal transduction-related categories, alongside significant sequence type-associated variation in KEGG pathway composition (PERMANOVA R² = 0.434, p = 0.001), with ST54 forming a distinct functional cluster. Collectively, these findings demonstrate that this Hong Kong C. difficile population is structured by stable evolutionary lineages while maintaining extensive accessory-genome diversity, and highlight the prominent role of MGE in shaping antimicrobial-resistance architecture relative to the largely conserved virulence repertoire.

Influence of Extraction Methods on Phytochemical Composition, Antioxidant, and Antibacterial Activities of Monolluma quadrangula from Yemen: A GC-MS Analysis

2026-11-05T15:17:02+08:00

Monolluma quadrangula (Forssk.) Plowes [syn. Caralluma quadrangula (Forssk.) N.E.Br.] is a medicinal plant widely distributed throughout the Arabian Peninsula, particularly in Yemen, Saudi Arabia, and Oman, where it has traditionally been used to treat various ailments, including diabetes and gastric ulcers. This study aimed to evaluate the effects of three extraction methods Soxhlet extraction, ultrasound-assisted extraction, and maceration on the phytochemical composition, antioxidant potential, and antibacterial activity of methanolic extracts of M. quadrangula. To the best of our knowledge, this is the first study to comprehensively compare these three extraction methods for M. quadrangula collected from Yemen, providing baseline data on its phytochemical profile and biological activities. Phytochemical screening was performed to detect major secondary metabolites, while bioactive compounds were identified using gas chromatography mass spectrometry (GC–MS). Total phenolic and flavonoid contents were determined spectrophotometrically. Antioxidant activity was evaluated using DPPH, ABTS, and ferric reducing power assays, and antibacterial activity was assessed using the broth microdilution method. Phytochemical screening confirmed the presence of terpenoids, alkaloids, and saponins in all extracts, whereas tannins and carotenoids were not detected. GC–MS analysis identified numerous constituents, including phenolic compounds, terpenoids, alcohols, and organic acids. The Soxhlet extract exhibited the highest extraction yield (18.3%) and total phenolic content (51.6 ± 0.05 mg GAE/g extract), whereas the ultrasound-assisted extract showed the highest flavonoid content (43.8 ± 0.02 mg RE/g extract). All extracts demonstrated antioxidant activity, with the ultrasound-assisted extract showing the strongest activity according to the DPPH, ABTS, and FRAP assays, with values of 169.27 ± 1.19 μg/mL, 1404.69 ± 2.16 μg/mL, and 47.46 ± 0.02 mg TE/g extract, respectively. In the antibacterial assays, the Soxhlet extract showed notable inhibitory activity against Escherichia coli CIP 53126 and Pseudomonas aeruginosa CIP 82118, whereas the ultrasound-assisted extract showed the greatest activity against Bacillus subtilis CIP 5262, with a minimum inhibitory concentration (MIC) of 15.6 mg/mL. Overall, the extraction method significantly influenced the phytochemical composition and biological activities of the extracts. Soxhlet and ultrasound-assisted extraction produced the most promising results for different measured parameters, particularly extraction yield, phenolic content, flavonoid content, antioxidant activity, and antibacterial activity. These findings provide baseline evidence supporting further investigation of this species as a potential source of natural antioxidant and antibacterial agents. Future studies should focus on isolating and characterizing the principal bioactive constituents, elucidating their mechanisms of action, and evaluating their safety and efficacy in relevant biological models before potential pharmaceutical or nutraceutical applications are considered.

Integrated Methylation–Expression Profiling of Solute Carrier Genes Prioritizes Four Candidates for Further Evaluation in Early-Stage Colorectal Cancer

2026-10-21T17:09:33+08:00

Colorectal cancer (CRC) is frequently diagnosed beyond the earliest stages, underscoring the need for molecular changes detectable during early disease. Previous studies identified widespread differential methylation of solute carrier (SLC) genes in CRC; however, whether these alterations are accompanied by concordant expression changes at Stage I, and which SLC genes warrant further prioritization, remain unclear. We integrated a previously generated CRC methylome dataset comprising 2,277 differentially methylated probes mapped to 336 SLC genes with stage-stratified TCGA colon adenocarcinoma (COAD) and rectal adenocarcinoma (READ) gene-expression and promoter-methylation data through UALCAN. Twenty-eight genes showed significant changes in both molecular layers, and 15 retained canonical inverse methylation–expression relationships in Stage I CRC. Four genes were prioritized based on concordance across COAD and READ and supporting CRC evidence. SLC5A7 was downregulated and promoter-hypermethylated, with expression p = 1.88 × 10⁻⁵ (COAD) and 2.10 × 10⁻² (READ), and methylation p < 1 × 10⁻¹² and 3.12 × 10⁻³, respectively. In contrast, SLC7A5 was upregulated and hypomethylated (expression: 3.67 × 10⁻¹² and 4.02 × 10⁻⁷; methylation: 1.11 × 10⁻¹⁶ and 3.79 × 10⁻⁴), as were SLC39A10 (expression: 2.83 × 10⁻¹¹ and 1.97 × 10⁻⁸; methylation: 3.73 × 10⁻⁶ and 1.76 × 10⁻³) and SLC7A11 (expression: 2.92 × 10⁻⁸ and 3.06 × 10⁻²; methylation: <1 × 10⁻¹² and 3.00 × 10⁻⁴), with values reported for COAD and READ, respectively. By integrating promoter methylation with expression at Stage I, this study narrows previously reported SLC methylation alterations to four candidate genes showing concordant early-stage molecular dysregulation across colon and rectal cancer datasets. Together, these results prioritize four SLC genes for further functional and clinical validation in early-stage CRC. Their diagnostic utility remains to be established in independent cohorts.

Pangenomics and Comparative Biosynthetic Diversity of Malaysian Mangrove-Derived Streptomyces albidoflavus MUM256 among S. albidoflavus-Assigned Genomes

2026-10-07T19:20:21+08:00

Streptomyces sp. MUM256, isolated from Malaysian mangrove soil, has previously shown antioxidant and selective anticancer activities, including induction of cell-cycle arrest and apoptosis in colon cancer cells. However, its precise taxonomic position and biosynthetic potential remained unresolved at the whole-genome and population levels. Here, we sequenced a high-quality long-read genome of MUM256 and integrated genome-based taxonomy, pangenomics and comparative biosynthetic gene cluster (BGC) analysis. The final assembly comprised a single 6.89-Mb contig with 73.4% G+C content, 98.5% BUSCO completeness and 5,897 predicted protein-coding sequences. Genome-based analyses consistently assigned MUM256 to Streptomyces albidoflavus, with NRRL B-1271 identified as its closest GTDB-Tk placement reference. A quality-filtered cohort of 151 genomes revealed an open pangenome comprising 21,082 gene clusters, including 2,684 strict-core clusters, with continued gene-family accumulation supported by Heaps' law modelling (γ = 0.307). Population-scale genome mining of 119 quality-filtered genomes identified 2,651 BGC records grouped into 178 gene cluster families (GCFs), of which 84.3% were rare or singleton. MUM256 contained 18 predicted BGCs representing 18 GCFs, all shared with other members of the analysed S. albidoflavus-assigned genomes. Comparative analysis of fredericamycin A-like and SF2768-like loci further revealed population-level variation in BGC prevalence and architecture. Together, these findings establish MUM256 as S. albidoflavus and provide a population-genomic framework for prioritising biosynthetic loci for future metabolomic and functional validation.

Early colonization by Enterobacteriaceae in the developing gut microbiota of preterm infants: A culture-based insight

2026-05-15T15:49:24+08:00

The gut microbiome plays a significant role in human health and disease pathogenesis. In preterm infants, gut dysbiosis often results in early dominance of opportunistic pathogens, particularly members of the Enterobacteriaceae family. Enterobacteriaceae can serve as potential reservoirs of opportunistic pathogens, antibiotic-resistance determinants and may contribute to major neonatal morbidities, including necrotizing enterocolitis (NEC) and late-onset sepsis (LOS). This study aims to isolate and identify Enterobacteriaceae, as well as to explore the diversity of isolated Klebsiella pneumoniae from meconium/early stool samples of preterm infants collected from a neonatal intensive care unit (NICU) in Johor Bahru, Malaysia. A combination of culture-based isolation technique, phenotypic and genotypic identification methods was used to identify the culturable Enterobacteriaceae in the gut of preterm infants. Three main bacterial families were successfully isolated and identified from the stool samples of preterm infants, which include Enterobacteriaceae, 46% (76/166 isolates), Staphylococcaceae, 22% (37/166), Enterococcaceae, 22% (37/166) and others, 10% (16/166). It was clear that Enterobacteriaceae was one of the predominant bacterial groups during the early gut colonization in preterm infants, making up to 46% of all isolates. Within the Enterobacteriaceae family, K. pneumoniae, 74% (56/76 isolates) dominates, followed by Escherichia coli, 15% (11/76), Klebsiella aerogenes, 9% (7/76), Citrobacter europaeus, 1% (1/76), and Citrobacter freundii, 1% (1/76). The high number of Enterobacteriaceae isolates, particularly K. pneumoniae, followed by E. coli are concerning as these bacterial species are often associated with hospital-acquired infections in the NICU. Our findings provide insight into the early gut colonization patterns of culturable gut bacteria in preterm infants. It highlights the importance of continuous microbiological monitoring and infection control measures within the NICU to mitigate potential Enterobacteriaceae-associated infections.

Glycerol extract of Water hyacinth (Eichhornia crassipes (Mart.) Solms) attenuates hydrogen peroxide (H2O2)-induced cell death in HT22 hippocampal neurons

2026-09-30T16:38:49+08:00

Neurological disorders continue to represent a significant global health burden, ranking among the leading causes of mortality and long-term disability. The persistent lack of effective therapeutic interventions reflects an incomplete understanding of the complex molecular mechanisms underlying neuronal cell death in the diseased brain. Among these, oxidative stress has been identified as a critical secondary injury mechanism that exacerbates neuronal damage. Recently, Eichhornia crassipes (Mart.), commonly known as water hyacinth, has emerged as a promising source of bioactive compounds with notable anti-inflammatory and antioxidant properties, making it a potential candidate for the development of neuroprotective therapies. This study aimed to assess the neuroprotective potential of E. crassipes extracts (ultrasound-assisted maceration), with glycerol extract (GE) emerging as the most effective extract, using a cell-based model of oxidative stress-induced by hydrogen peroxide (H₂O₂) in hippocampal HT22 cells. Cell viability of HT22 cells were measured through MTT assay, in order to determine cytotoxicity of extracts (0.5 mg/ml – 5 mg/ml) and protective effects of the extracts against H₂O₂ (via co-treatment assay). Our study revealed that H₂O₂ was able to induce cell viability loss in HT22 cells in a dose-dependent manner, and the IC₅₀ value of H₂O₂was determined as approximately 655.3 µM. Following the co-treatment assay, GE at 0.8 mg/ml displayed a significant protective effect by alleviating H₂O₂(700 µM)-induced cell death as compared to the H₂O₂alone group (67.4 ± 4.4% viability vs. 52.4 ± 1.4%, p < 0.05), while aqueous and mixed extracts did not display significant protective trend. These preliminary findings suggest that glycerol-based E. crassipes extract possesses underexplored neuroprotective potential against H₂O₂-induced oxidative stress in neuronal cells, though further mechanistic and in vivo investigation are required to validate these effects and establish translation relevance.

Microbial Siderophores in Sustainable Agriculture: Molecular Insights, Smart Delivery Systems, and Biotechnological Applications

2026-05-04T17:54:53+08:00

Microbial siderophores are low-molecular-weight compounds with a strong affinity for ferric (FSe³⁺) ions. They play a pivotal role in plant-microbial interactions by enhancing iron bioavailability to plants, primarily through the chelation and mobilization of iron under iron-limited conditions. Their versatile and multifunctional nature has positioned them as promising agents for sustainable and eco-friendly agriculture. However, the practical application of siderophore-based systems is constrained by challenges related to stability, bioavailability, environmental degradation, and large-scale production. This review examines recent advancements in siderophore-mediated agricultural practices and applications, with a focus on formulation strategies and delivery systems, including seed coatings, foliar sprays, and nanoparticle-based encapsulation approaches. The review further highlights key technological innovations integrating nanotechnology, microbiology, and artificial intelligence (AI) for precision agriculture. Particular emphasis is placed on controlled-release systems, production scalability, and field-level applicability. Existing knowledge gaps, particularly in large-scale production and commercialization, are discussed alongside future prospects involving synthetic biology and engineered microbial systems. Siderophore-based technologies represent a transformative approach toward enhancing soil health, crop productivity, and sustainable bioeconomy development.

Molecular Mechanisms of Melanogenesis in Hyperpigmentation: From Signaling Pathways to Nanocarrier-Based Therapeutic Strategies

2026-09-07T11:51:57+08:00

Hyperpigmentation remains a complex dermatological challenge, often resistant to conventional topical therapies due to the skin’s inherent barrier function and the chemical instability of active depigmenting agents. Traditional formulations of depigmentation agents frequently suffer from poor dermal penetration and dose-dependent toxicity, leading to localized irritation and high relapse rates. This review highlights the transformative role of cosmeceutical nanotechnology in overcoming these limitations through advanced delivery systems, including lipid-based nanocarriers, polymeric nanoparticles, and microbiota-derived metabolite platforms. These nanosystems enhance the stability, controlled release, and targeted delivery of active compounds to melanocytes within the basal epidermis while modulating key molecular pathways involved in melanogenesis. Their mechanisms include inhibition of tyrosinase activity through active-site copper chelation, suppression of microphthalmia-associated transcription factor (MITF) signaling, and disruption of melanosome transport and transfer to keratinocytes. Emerging microbiota-based approaches further contribute by regulating oxidative stress, inflammation, and pigmentation while helping maintain skin homeostasis. Experimental and clinical evidence demonstrates that nanocosmeceutical formulations significantly improve depigmenting efficacy. Despite these advantages, challenges remain regarding nanotoxicity, long-term safety, large-scale manufacturing, and the lack of harmonized regulatory frameworks governing nanocosmeceuticals. As demand for effective and minimally invasive skincare continues to grow, nanotechnology provides a promising strategy for developing safer, more stable, and highly bioavailable therapies for hyperpigmentation. Continued research, standardized safety evaluation, and clearer regulatory guidelines are essential to facilitate the successful clinical translation and commercialization of nanotechnology-based depigmenting formulations.

Microbial and Molecular Drivers of early-Onset Colorectal Cancer

2026-10-15T15:54:26+08:00

Global incidence of early-onset colorectal cancer (EO-CRC) has increased by approximately 2% annually over the past three decades, representing a fundamental shift in the epidemiology of colorectal cancer (CRC). EO-CRC, defined as a diagnosis before the age of 50, now accounts for approximately 10-12% of all new CRC cases, while incidence rates in older populations have stabilized or declined. This narrative review compares the molecular, genetic, epigenetic, and microbial landscapes of EO-CRC and late onset colorectal cancer (LO-CRC) through synthesis of the available evidence. We highlight growing evidence that EO-CRC may not be just an early manifestation of sporadic disease but rather a heterogeneous malignancy with distinct molecular signatures by combining data from recent multi-omics studies and large-scale genomic consortia such as TCGA and GECCO. Notably, emerging multi-omics evidence highlights a distinct microbiome signature in EO-CRC, with enrichment of Flavonifractor plautii and genotoxic pks+ (polyketide synthase-positive) Escherichia coli, which may contribute to early carcinogenesis through flavonoid depletion, immune modulation, and colibactin-mediated DNA damage. These molecular and microbial features correlate clinically with a left-sided anatomical predominance, advanced stage at diagnosis, and aggressive histopathological characteristics, including mucinous and signet ring cell differentiation, particularly in patients under 35 years. These findings have important clinical implications for age-stratified screening, biomarker-guided risk assessment, and the development of targeted therapeutic strategies tailored to younger CRC patients. This review highlights critical gaps related to missing heritability and proposes a precision oncology framework for age-stratified screening and biomarker directed therapy. Addressing the unmet clinical need for earlier detection strategies tailored to younger populations remains a central priority for reducing the growing public health burden of this disease. Although hereditary syndromes such as Lynch syndrome are enriched among younger patients (16-25%), the majority of EO-CRC cases are sporadic and exhibit a predominantly microsatellite stable (MSS), low tumour mutational burden (TMB) phenotype, suggesting distinct non-hereditary molecular and environmental drivers. Transcriptomic analyses demonstrate a marked enrichment of the CMS2 subtype in EO-CRC (~75%) compared to LO-CRC (~40%), reflecting dominant activation of canonical Wnt/MYC signalling pathways. Somatically, the mutational landscape of EO-CRC may exhibit a distinct hierarchy of driver mutations, with an increased frequency of TP53 and CTNNB1 mutations and a reduced frequency of BRAF V600E and APC mutations compared with older patients. Epigenetically, young tumours have been reported to present with more extensive global hypomethylation, especially of LINE-1 elements, and more pronounced methylation canyon erosion, compared with the CpG Island Methylator Phenotype (CIMP-High) commonly observed in right-sided tumours of older patients.

Probiotic Modulation of the Skin Microbiome: Emerging Therapeutic Strategies in Dermatology

2026-10-12T17:15:15+08:00

The skin microbiome is a dynamic microbial ecosystem that plays a fundamental role in maintaining epidermal barrier integrity, regulating immune homeostasis, and protecting against pathogenic colonisation. Dysbiosis of the skin microbiota has been implicated in numerous dermatological disorders, including acne vulgaris, atopic dermatitis, psoriasis, rosacea, and premature skin ageing, highlighting the microbiome as an emerging therapeutic target. In this context, probiotics have attracted increasing attention as microbiome-based interventions owing to their ability to restore microbial equilibrium and modulate host-microbe interactions. This review critically evaluates the current understanding of probiotics in dermatology, with particular emphasis on the molecular mechanisms underlying their therapeutic effects. Recent studies demonstrate that probiotics exert strain-specific activities through competitive exclusion of pathogens, production of antimicrobial peptides and bioactive metabolites, modulation of Toll-like receptor (TLR)-mediated signalling, regulation of nuclear factor kappa B (NFκB) and mitogen-activated protein kinase (MAPK) pathways, enhancement of tight junction proteins and ceramide synthesis, and modulation of cytokine networks involved in cutaneous immunity. Representative probiotic strains, including Lacticaseibacillus rhamnosus GG, Lactobacillus acidophilus, Lactobacillus plantarum, Bifidobacterium species, Bacillus coagulans, Saccharomyces boulardii, and Enterococcus faecium, are discussed with respect to their strain-specific molecular effectors and dermatological applications. Clinical evidence supporting oral and topical probiotic interventions is critically appraised, highlighting both therapeutic potential and the heterogeneity of existing studies. Emerging advances in postbiotics, engineered probiotics, synthetic biology, CRISPR-based microbiome editing, multi-omics technologies, and artificial intelligence-driven precision microbiome medicine are also discussed as future directions. Despite encouraging findings, important challenges remain, including strain standardisation, formulation stability, regulatory harmonisation, and the need for robust multicentre clinical trials. Collectively, current evidence suggests that probiotics represent promising adjunctive strategies for microbiome-targeted dermatological therapy; however, further molecular and translational investigations are required to facilitate their integration into scientifically validated precision dermatology.

Molecular Mechanisms Linking E‑cigarette Exposure to Cancer Metastatic Behaviour: Focus on Epithelial-to-Mesenchymal Transition and Inflammation: A Systematic Review

2026-10-15T15:30:36+08:00

Electronic cigarette use has been mushrooming globally in recent years, with an estimated 82 million vapers worldwide, including 14.3 million in Southeast Asia. Although e-cigarettes are generally considered a safer alternative to traditional cigarettes, their long-term health effects, particularly on cancer progression and metastasis, remain uncertain. This systematic review evaluated the existing literature to determine whether e-cigarette exposure influences cancer cell metastatic behaviour. A systematic search was conducted using predefined terms in MEDLINE, PubMed, and Web of Science from database inception to 1^st May 2025. The studies must be primary research and investigate the effects of e-cigarette exposure on cancer cell metastasis. Seven eligible studies were selected, assessed for reliability using the SciRAP tool, and synthesised manually. The literature evaluated several aspects of cancer metastasis, including cell invasion, migration and motility, morphological changes, tumour area, growth, proliferation, colonisation or localisation, cell viability, and immunological changes. Evidence synthesis suggests that e-cigarette exposure may promote cancer cell migration; however, these findings are constrained by the small number of studies, methodological limitations, and lack of long-term investigations. Reported effects varied depending on cancer cell type, nicotine presence, and e-liquid flavouring. Current preclinical data indicate e-cigarette exposure may promote cancer metastatic behaviour through epithelial-to-mesenchymal transition (EMT) induction (E-cadherin loss, vimentin upregulation), RAGE-mediated inflammatory signalling, and CCL5/CCR5-dependent monocyte recruitment. However, all seven included studies were rated “not reliable” by SciRAP (methodological quality scores 47–70%), rendering evidence preliminary. Future studies require physiologically relevant direct aerosol exposure systems, cigarette smoke comparators for relative risk assessment, diverse cancer models, and longitudinal clinical investigations to establish the true impact of vaping on cancer metastasis.

Whole-genome sequencing of Streptomyces sp. MUM 161J from mangrove soil in East Malaysia

2026-11-04T17:58:49+08:00

Whole-genome sequencing provides an essential foundation for investigating the genetic diversity and biosynthetic potential of Streptomyces, a genus widely recognised for its production of structurally diverse secondary metabolites. Here, we report the genome sequence of Streptomyces sp. MUM 161J using PacBio Revio high-fidelity whole-genome sequencing. A total of 117,499 reads comprising 1,656,239,452 bases, with a read N50 of 14,515 bp, were assembled using Hifiasm version 0.25.0-r726. The resulting assembly comprised two contigs totaling 11,071,069 bp, with a contig N50 of 10,651,607 bp and a G+C content of 71.03%. The length-weighted mean mapped depth was 149.2×, and 99.99% of primary reads mapped to the assembly. BUSCO recovered 98.9% complete lineage markers, while CheckM2 estimated 100.0% completeness and 0.56% contamination. Genome annotation using Bakta identified 8,894 standard coding-sequence predictions, including 24 pseudogene calls, plus three separately reported short open reading frames. The annotation also included 70 tRNA features, 18 rRNA genes and two transfer-messenger RNA features. Genome-based comparisons revealed close relatedness to Streptomyces malaysiensis JCM 10672^T, with an average nucleotide identity of 98.84% and digital DNA–DNA hybridisation of 87.5%. AntiSMASH analysis predicted 46 biosynthetic regions, highlighting the potential for diverse specialised metabolite biosynthesis. The genome sequence provides a valuable resource for subsequent taxonomic, comparative and functional investigations, while further analysis of the contig relationships and chromosomal termini will be needed to resolve its physical genome organisation.