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31 records · Page 2Linked to original sources
PubMed2025

Reduction in ARGs and Mobile Genetic Elements Using 2-Bromoethane Sulfonate in an MFC-Powered Fenton System.

The integration of an MFC-powered Fenton (MFC-Fenton) system into the traditional anaerobic composting process can promote excess dewatered sludge (ES) decomposition. However, the antibiotic resistance gene (ARG) profiles in ES treated by MFC-Fenton systems remain poorly understood; in addition, the effect of adding 2-bromoethane sulfonate (BES, a methane inhibitor) during ES treatment using an MFC-Fenton system on ARG levels is largely unexplored. The present work focused on investigating the effects of BES and bioelectrochemical processes on ARG and MGE abundances and unraveling the ARG attenuation mechanism. According to our findings, adding BES promoted ARG reduction in ES in an MFC-Fenton system. The average ARG levels in the MFC-Fenton samples containing high BES contents (0.4 or 0.5 g BES/g VSS) markedly declined relative to those in samples containing lower BES levels. Moreover, macrolide transporter ATP-binding protein, macrolide-efflux protein, and macB levels markedly decreased as BES levels increased. BES supplementation and bioelectrochemical assistance were crucial for altering the ARG composition in the MFC-Fenton system. Changes in the microbial community composition had the greatest effect on the variation in ARG composition. Furthermore, the Actinobacteria and Firmicutes levels accounted for 52.8% of the overall ARG variation. Among MGEs, plasmids, insertion sequences, and integrons showed lower levels within the sludge metagenomes. Typically, sulI, sulII, tetG, and bla TEM levels were positively correlated with metal resistance genes (MRGs), and their levels markedly declined following the MFC-Fenton process. Thus, the collective evidence indicates that BES synergizes with bioelectrogenesis to reduce ARG abundance.

Sewage↗
PubMed2026

The Rhizosphere Microbiome: A Key Mediator of Crop Responses to Fertilization Strategies.

The rhizosphere microbiome, the plant's "second genome" is pivotal for crop nutrient acquisition, health, and stress responses. While fertilization ensures high agricultural yields, a key challenge is reshaping this microbiome to boost crop performance. This review synthesizes how mineral, organic, and bio-organic/microbial inoculant fertilizers affect rhizosphere microbial structure, diversity, and function. Long-term excessive mineral fertilizers (especially nitrogen) reduce microbial diversity, diminish beneficial groups (e.g., diazotrophs, PGPR), and disrupt microbial networks via soil acidification and altered root exudates, causing continuous cropping obstacles. In contrast, organic fertilizers improve soil microenvironments, maintaining high microbial diversity, enriching beneficial taxa (e.g., Proteobacteria, Actinobacteria), and enhancing community complexity. Bio-organic fertilizers/microbial inoculants "engineer" the microbiome by introducing exogenous beneficial microbes (e.g., Bacillus, Pseudomonas, AMF), directly promoting growth, suppressing diseases, and "reconditioning" indigenous beneficial communities. We also clarify how fertilization regulates plant-microbe dialog via root exudates and rhizosphere chemistry (e.g., pH, ion balance), discuss current challenges (causality, lab-to-field translation, genotype-microbiome-fertilization interactions), and outline future directions. Integrating rhizosphere microbiome management into fertilization is crucial for reducing chemical fertilizer reliance and advancing agricultural green transformation.

fertilization strategies microbial community assem↗
PubMed2026

Two-sample Mendelian randomization study of gut microbiota and inflammatory proteins: Predictive, preventive, and personalized treatment for migraine.

The human gut microbiota is increasingly recognized as a significant factor in the pathogenesis of migraine, potentially via inflammatory pathways. Identifying specific human gut microbiota components associated with migraines, along with the investigation of particular inflammatory proteins, is essential for advancing primary prediction, targeted prevention, and personalized treatment strategies for migraines. We conducted a two-sample Mendelian randomization study using publicly available summary statistics from genome-wide association studies. Data for 473 human gut microbiota taxa were obtained from the Finnish national health survey conducted by the National Institute for Health and Welfare study (FINRISK, n = 5959 European participants). Genome-wide association study data (https://www.ebi.ac.uk/gwas/) for 91 circulating inflammatory proteins were obtained from 14,824 participants across 11 cohorts using the Olink Target 96 Inflammation panel. Migraine outcome data were obtained from the FinnGen R12 release, with cases defined using ICD-10 code G43. All genome-wide association study analyses were adjusted for sex, age, genotyping batch, and 10 genetic principal components to control population stratification (genomic inflation factors: 1.00–1.05). Inverse variance-weighted Mendelian randomization was the primary analysis method, with Mendelian randomization-Egger, weighted median, and mode-based methods as sensitivity analyses. Two-step Mendelian randomization mediation analysis quantified the proportion of the effects of human gut microbiota on migraine that are mediated through inflammatory proteins. Thirty-seven bacterial genera were found to be associated with migraine using the inverse variance-weighted method. Of these, 18 genera exhibited a negative association, while 19 genera demonstrated a positive association with migraine risk. Additionally, eight inflammatory proteins were found to increase the risk of migraine. Among human gut microbiota, four were observed to reduce inflammatory protein levels, whereas another four were associated with increased inflammatory protein levels. Additionally, five gut microbiota were identified to influence migraine through inflammatory proteins in both Mendelian randomization analyses. Specifically, Actinobacteria, Brachyspiraceae, CAG-269 sp001915995, and Paraglaciecola were found to affect migraine outcomes via inflammatory proteins, with mediation proportions of 12%, 19%, 15.5%, and 6.7%, respectively. Lawsonibacter sp002161175 was identified to influence migraine risk through Oncostatin-M and SLAM, with mediation proportions of 15.6% and 11.3%, respectively. Our study elucidated the role of specific human gut microbiota alterations in the pathogenesis of migraine and highlighted the mediating effects of inflammatory proteins. Targeting these particular human gut microbiota alterations offers a promising strategy for predictive, preventive, and personalized medicine in migraine management, resulting in substantial clinical advancements.

causality↗
PubMed2026

Microbial and functional shifts between flare and remission in a single-center cohort of children with inflammatory bowel disease.

BACKGROUND: Gut microbial dysbiosis is central to the pathogenesis of inflammatory bowel disease (IBD). While gut microbiome differences between patients with and without IBD are well established, microbiome changes associated with disease activity and remission remain limited, particularly in paediatric populations. AIM: To examine intra-individual taxonomic and functional gut microbiome changes during transition from active flare to remission under maintenance immunosuppression in a pilot single-center Singapore cohort of children with IBD. METHODS: Paired stool samples and clinical data were collected from seven patients with paediatric IBD [5 Crohn's disease (CD), 2 ulcerative colitis; &#x2264; 18 years] during active disease/flare (visit 1; Pediatric CD Activity Index/Pediatric Ulcerative Colitis Activity Index &#x2265; 10) and subsequent clinical remission (visit 2; Pediatric CD Activity Index/Pediatric Ulcerative Colitis Activity Index < 10). Samples underwent shotgun metagenomic sequencing for high-resolution taxonomic profiling and functional annotation of Kyoto Encyclopaedia of Genes and Genomes pathways. RESULTS: Gut microbial diversity was reduced during flare compared to remission, with Actinobacteria abundance significantly higher in remission. Two distinct microbial clusters differentiated flare and remission states: The remission cluster was enriched with Bifidobacterium adolescentis, Bifidobacterium dentium, Lactobacillus gasseri, Faecalibacterium prausnitzii, while the flare state showed increased Klebsiella pneumoniae. Remission was further characterized by a downregulation of pathogenic microbes and an upregulation of beneficial microbes including a higher abundance of the butyrate producer Anaerostipes hadrus (P = 0.046). Microbial functional genes enriched in remission were predominantly associated with metabolic pathways including vitamin and cofactor biosynthesis, as well as carbohydrate, amino acid, and lipid metabolism. CONCLUSION: The transition from flare to remission in Singaporean children with IBD is characterized by functional remodeling of the gut microbiome, which may contribute to recovery processes related to intestinal barrier integrity, cellular maintenance, and tissue repair. Targeted modulation of the gut microbiome may help sustain remission in paediatric IBD.

Functional shift↗
PubMed2025

Gene amir_2071 of Actinosynnema mirum DSM 43827 encodes a dimethylallyltryptophan synthase superfamily protein responsible for the production of prenylated tyrosine.

Actinosynnema mirum DSM 43827 is a bacterium from the small genus Actinosynnema within the rapidly growing actinomycete family Pseudonocardiaceae (Land M et al.&#xa0;Stand Genomic Sci 1:46-53&#xa0;2009). Despite its diverse repertoire of specialized metabolite biosynthetic gene clusters (BGCs), the potential of A. mirum for production of bioactive molecules is not fully explored. Here, we used a heterologous expression approach to gain deeper insight into this issue. In this work we report that expression of in silico predicted BGC#4 from A. mirum in S. albus Del14 and S. lividans &#x394;YA9 led to production of several prenylated derivatives of tyrosine. Their most likely structures, according to MS and MS/MS data, agreed with 4-O-prenyl-(L)-tyrosine and its N-acetyl derivative, previously described in lichen-forming fungi (Iacovelli R et al.&#xa0;J Nat Prod 87:2243-2254&#xa0;2024). Further experiments confirm the production of the aforementioned compounds is governed by a single structural gene, amir_2071 for prenyltransferase of dimethylallyltryptophan synthase (DMATS) superfamily, whose homologs are abundant in bacterial genomes.

Tyrosine↗
PubMed2026

Draft genome sequence data of Streptomyces antibioticus SCBA4 isolated from the Soils of Surigao del Sur, Philippines.

The draft genome of Streptomyces antibioticus SCBA4 isolated from the soils of Surigao del Sur, Philippines is reported here. S. antibioticus is a member of the phylum Actinomycetota, a diverse group of Gram positive, high G+C content bacteria well known for their production of a variety of bioactive compounds. Sequencing using the Illumina NovaSeq 6000 platform yielded a 8,616,999 bp genome across 36 contigs with 7621 coding sequences, 87 tRNA, and 1 tmRNA. Consistent with the members of the same phylum, the GC content was 71.83% and was found to contain putative gene clusters of secondary metabolites such as NRPs, terpenes and polyketides. The genome sequence has been deposited at NCBI under the accession number JBSWZT020000000.

Actinobacteria↗
PubMed2026

Genomic and transcriptomic characterization of genes expressed at 20&#xa0;MPa by the marine actinobacterium Kocuria flava.

A marine hydrocarbonoclastic actinobacterium Kocuria flava IOS11 was isolated from 3500&#xa0;m deep-sea water of the Indian Ocean. The isolate efficiently degraded phenanthrene (250&#xa0;mg/L) achieving 82 and 98% of degradation at 0.1&#xa0;MPa and 20&#xa0;MPa, respectively within a period of 5&#xa0;days. Whole genome, transcriptomee and metabolomic analysis elucidated its phenanthrene biodegradation efficiency under in situ deep-sea conditions. The genome sequence comprises 3.47&#xa0;Mb distributed across 88 scaffolds with a high GC content of 74.30%. The genome analysis encoded 3126 genes including 3052 protein coding sequences with functional annotation identifying a broad array of genes associated with PAHs degradation, environmental stress adaptation, biosurfactant and siderophore synthesis. Transcriptome profiling under 0.1 and 20&#xa0;MPa conditions with phenanthrene as a sole carbon source revealed enhanced expression of hydrocarbon degrading genes, transporters, biosurfactant associated enzymes and stress responsive genes including integrases, DNA repair protein Rad, alanine ligase, heat and cold shock proteins under high pressure conditions underscoring the deep-sea adaptation capabilities of the strain. The degradation pathway of phenanthrene was proposed through integrated genome, transcriptome and metabolomic analysis. These studies provided K. flava IOS11 as a metabolically versatile and pressure adapted bacterium with promising potential for bioremediation application in extreme marine environment.

Transcriptome↗
PubMed2024

Natural product discovery in soil actinomycetes: unlocking their potential within an ecological context.

Natural products (NPs) produced by bacteria, particularly soil actinomycetes, often possess diverse bioactivities and play a crucial role in human health, agriculture, and biotechnology. Soil actinomycete genomes contain a vast number of predicted biosynthetic gene clusters (BGCs) yet to be exploited. Understanding the factors governing NP production in an ecological context and activating cryptic and silent BGCs in soil actinomycetes will provide researchers with a wealth of molecules with potential novel applications. Here, we highlight recent advances in NP discovery strategies employing ecology-inspired approaches and discuss the importance of understanding the environmental signals responsible for activation of NP production, particularly in a soil microbial community context, as well as the challenges that remain.

Soil Microbiology↗
PubMed2026

Discovery of Glycosylated &#x3b2;-Amino Acid-Containing Macrolactams from Nonomuraea sp. 0L2P via Genome Mining.

&#x3b2;-Amino acid-containing macrolactams (&#x3b2;-AACMs) are a class of bioactive natural products characterized by nitrogen-containing starter units within polyketide-derived macrocycles. Here, we report four previously undescribed macrolactams, gruelactams A-D (1-4), from Nonomuraea sp. 0L2P, discovered through an integrated approach combining genome mining, 15N-labeling, and antibacterial screening. Their planar structures were elucidated by comprehensive spectroscopic analyses, including 1D and 2D NMR and HRESI-MS, and their configurations were partially assigned based on ROESY data and bioinformatic analysis. Genome sequencing and antiSMASH analysis identified a putative type I polyketide synthase (PKS) biosynthetic gene cluster, enabling the proposal of a biosynthetic pathway. Bioactivity assays showed that gruelactam D (4) exhibits antibacterial activity against Bacillus cereus and Staphylococcus aureus, with MIC values of 8 and 16 &#x3bc;g/mL, respectively. These findings expand the chemical diversity of &#x3b2;-AACMs and demonstrate the utility of genome-guided approaches for discovering bioactive natural products from rare actinomycetes.

Anti-Bacterial Agents↗
PubMed2025

Genomes of 211 Actinomycete Strains from Diverse Environments.

Actinomycetes are a highly diverse group of microorganisms that have long been recognized as a valuable source of antibiotics and other bioactive metabolites. Recent advances in genome mining have revealed a wealth of previously unexplored silent secondary metabolite biosynthetic gene clusters (smBGCs) in actinomycete genomes, underscoring their untapped bioactivity potential. Here, we present the genome sequences of 211 actinomycete strains isolated from various environmental sources, generated through high-throughput sequencing. The resulting genome assemblies exhibit high completeness and accuracy, offering high-quality data for downstream analyses and biological resource exploration.

Actinobacteria↗
PubMed2025

Streptomyces huangiella sp. nov., an endophytic actinomycete isolated from Pheretima aspergillum, a promising candidate for biological pathogen control.

UNLABELLED: Pheretima aspergillum (E. Perrier) is an annelid of the genus Pheretima in the family Megascolecidae, a species of earthworm, whose dried body (Guang Dilong) is a traditional Chinese animal medicine. A new actinobacterium strain, named HD1123-B1T, was isolated from the gut contents of Pheretima aspergillum caught in the wild in Guangzhou, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain was primarily identified as a member of the genus Streptomyces, sharing more than 98% sequence identity to Streptomyces endocoffeicus CA3R110T (98.80%), Streptomyces coffeae CA1R205T (98.47%), and Streptomyces iranensis HM35T (97.93%). The whole genome size of strain HD1123-B1T was approximately 8.9 Mbp, with 7,464 predicted genes and 71.42 mol% DNA C+G content. Comparative genomic analyses based on digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values revealed that strain HD1123-B1T represents a novel species within the genus Streptomyces. Additionally, 38 biosynthetic gene clusters for secondary metabolites were also predicted in the genome of strain HD1123-B1T. Based on LC-MS/MS analysis, the nigericin biosynthesis gene cluster has been completely characterized. The ethyl acetate crude extract of strain HD1123-B1T exhibited remarkable antibacterial activity against gram-positive bacteria (methicillin-resistant Staphylococcus aureus ATCC 25213, etc) and gram-negative bacteria Ralstonia solanacearum GIM 1.70. Based on these results, HD1123-B1T could be confirmed as an isolate that represents a novel species of the genus Streptomyces, for which the name Streptomyces huangiella sp. nov. is proposed. IMPORTANCE: As the largest genus of the phylum Actinomycetes, Streptomyces is a kind of microbial resources with great practical and economic value. Due to their unique physiological properties and metabolic capacity, Streptomyces have become an important source of bioactive compounds in the world and play an indispensable role in medical and industrial fields. With the advancement of molecular biology and genomics, researchers can more deeply explore the metabolic potential of Actinomycetes, discovering and developing new biologically active compounds. These new compounds may possess various biological activities, such as antibacterial, antiviral, antifungal, and antiparasitic properties, further promoting the development of medicine and related industries. Based on genomic analysis and antibacterial activity, the strain HD1123-B1T was indicated to be a promising candidate for biological pathogen control.

Streptomyces↗